diff --git a/.gitignore b/.gitignore index 825841a0..96fc94a6 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,3 @@ -configure config.log config.status Makefile @@ -7,6 +6,8 @@ easel *.o *.dSYM *.stamp +*.exe +!binaries/*.exe src/*_example src/*_example? src/*_utest @@ -47,3 +48,4 @@ src/makehmmerdb src/nhmmer src/nhmmscan src/phmmer +mman-win32/ diff --git a/README.md b/README.md index d62e1079..0b245bda 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,129 @@ +# Port of HMMER to Windows using MinGW + +This project is a port of HMMER source code to the [MInGW](https://www.mingw-w64.org) compiler. + +With the exception of `hmmpgmd` and `hmmpgmd_shard` the Windows native executables pass all tests. + +If prefer not to do your own build the resulting executables are in the [binaries](/binaries) directory. + +The source code in this project was created from [hmmer](https://github.com/jones-gareth/hmmer/tree/mingw-build) +and [easel](https://github.com/jones-gareth/easel/tree/mingw-build) forks of the develop branches +of [HMMER](https://github.com/EddyRivasLab/hmmer/tree/develop). + +## Build Recipe + +The following recipe describes how to build native executables for windows using +[MSYS2](https://www.msys2.org/) and [MInGW](https://www.mingw-w64.org/). At the time + of writing the compiler was `gcc version 11.2.0 (Rev1, Built by MSYS2 project)` + +**Prerequisites** + +Prior to building install MSYS2, For example use [chocolately](https://chocolatey.org/) +(`choco.exe install msys2`), or an +[installer](https://repo.msys2.org/distrib/x86_64/) + +In the MSYS2 shell install these packages (picking all groups) + +```console +pacman -S base-devel gcc vim cmake +pacman -S mingw-w64-x86_64-toolchain +pacman -S diffutils +``` + +There is no mman library for windows, but a wrapper is available for MinGW. +Download it from [github](https://github.com/alitrack/mman-win32) and build +in MSYS2 (here installing it to c:\local). + +```console +./configure --prefix=c:/local +mingw32-make.exe +mingw32-make.exe install +``` + +**Download code** + +```console +git clone https://github.com/jones-gareth/hmmer +cd hmmer +git clone https://github.com/jones-gareth/easel +``` + +**Configure HMMER** + +If `configure` is not present it will need to be generated on a LINUX system using `autoconf`. + +Run configure (here installing to c:\local and looking for mman header files and library in c:\local): + +```console +CPPFLAGS="-Ic:/local/include" LDFLAGS=" -static -Lc:/local/lib" CFLAGS="-g -O0" ./configure --prefix=c:/local +``` +Check that configure has picked up the mman library. + +```console +HMMER configuration: + compiler: gcc -g -O0 -pthread + host: x86_64-w64-mingw32 + linker: -static -Lc:/local/lib + libraries: -lmman -lpthread + DP implementation: sse +``` + +**Make, test and install** + +```console +mingw32-make.exe clean +mingw32-make.exe dev # build everything- there should be no warnings +rm -rf src/impl +cp -r src/impl_sse src/impl # No symlinks on windows, so this needs to be copied +mingw32-make.exe check # Run the tests. 2 will fail +mingw32-make.exe install # install if you're happy with test results +``` + +### Porting notes + +The presence of carriage returns (`\r`) in `config.sub` or `config.guess` will cause `autoconf` to fail. +Git operations may result in the insertion of `\r` depending on the `core.autocrlf` setting. + +Windows (and MinGW) do not support POSIX signals or sockets. Lack of socket support +mean that the client server daemon +commands `hmmpgmd` and `hmmpgmd_shard` do not function (the executables are compiled, but they +won't work.) + +Use of shell commands in C system calls is not properly supported. For example, code like + +```C +popen("cat esltmpfile 2>/dev/null"); +system("gzip -c eslfile 2>/dev/null > eslfile.gz"); +``` + +Will compile but not generally run (at least not in any portable fashion). +I disabled unit tests that use this type of code. + +1. Case 5 in esl_buffer_utest::main +2. esl_buffer_utest::utestOpenPipe +3. The gzip output case in esl_buffer_utest::utestSetOffset +4. esl_buffer_utest::utest_halfnewline (requires signals) + +The temporary files created by `esl_tmpfile` will persist on the filesystem in TEMP. +In Windows it is not possible to delete a file that is in use. + +### Failed tests + +All tests except `hmmpgmd_ga` and `hmmpgmd_shard_ga` should pass. +Since the `hmmpgmd` and `hmmpgmd_shard` commands are broken that is expected. + +```console + exercise 297 [ hmmpgmd_ga] ... FAILED [command failed] + exercise 299 [ hmmpgmd_shard_ga] ... FAILED [command failed] + +2 of 307 exercises at level <= 2 FAILED. +``` + +The tests use the perl and python executables installed in the MSYS2 shell. + +Test code at a level > 2 has not been ported and may not run correctly (because of windows text mode, +the test scripts frequently need changes even when the commands function correctly). + ## HMMER - biological sequence analysis using profile HMMs [![](https://travis-ci.org/EddyRivasLab/hmmer.svg?branch=develop)](https://travis-ci.org/EddyRivasLab/hmmer) diff --git a/binaries/hmmalign.exe b/binaries/hmmalign.exe new file mode 100644 index 00000000..35606760 Binary files /dev/null and b/binaries/hmmalign.exe differ diff --git a/binaries/hmmbuild.exe b/binaries/hmmbuild.exe new file mode 100644 index 00000000..ae9de2b2 Binary files /dev/null and b/binaries/hmmbuild.exe differ diff --git a/binaries/hmmconvert.exe b/binaries/hmmconvert.exe new file mode 100644 index 00000000..2de77177 Binary files /dev/null and b/binaries/hmmconvert.exe differ diff --git a/binaries/hmmemit.exe b/binaries/hmmemit.exe new file mode 100644 index 00000000..b004bf54 Binary files /dev/null and b/binaries/hmmemit.exe differ diff --git a/binaries/hmmfetch.exe b/binaries/hmmfetch.exe new file mode 100644 index 00000000..c488b5ed Binary files /dev/null and b/binaries/hmmfetch.exe differ diff --git a/binaries/hmmlogo.exe b/binaries/hmmlogo.exe new file mode 100644 index 00000000..c736d0d7 Binary files /dev/null and b/binaries/hmmlogo.exe differ diff --git a/binaries/hmmpress.exe b/binaries/hmmpress.exe new file mode 100644 index 00000000..786df673 Binary files /dev/null and b/binaries/hmmpress.exe differ diff --git a/binaries/hmmscan.exe b/binaries/hmmscan.exe new file mode 100644 index 00000000..de3c4f8e Binary files /dev/null and b/binaries/hmmscan.exe differ diff --git a/binaries/hmmsearch.exe b/binaries/hmmsearch.exe new file mode 100644 index 00000000..62a63f7a Binary files /dev/null and b/binaries/hmmsearch.exe differ diff --git a/binaries/hmmsim.exe b/binaries/hmmsim.exe new file mode 100644 index 00000000..7ff8fa74 Binary files /dev/null and b/binaries/hmmsim.exe differ diff --git a/binaries/hmmstat.exe b/binaries/hmmstat.exe new file mode 100644 index 00000000..3683728b Binary files /dev/null and b/binaries/hmmstat.exe differ diff --git a/configure b/configure new file mode 100644 index 00000000..61d24cd4 --- /dev/null +++ b/configure @@ -0,0 +1,9259 @@ +#! /bin/sh +# Guess values for system-dependent variables and create Makefiles. +# Generated by GNU Autoconf 2.69 for HMMER 3.3.2. +# +# Report bugs to . +# +# +# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc. +# +# +# This configure script is free software; the Free Software Foundation +# gives unlimited permission to copy, distribute and modify it. +## -------------------- ## +## M4sh Initialization. ## +## -------------------- ## + +# Be more Bourne compatible +DUALCASE=1; export DUALCASE # for MKS sh +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : + emulate sh + NULLCMD=: + # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which + # is contrary to our usage. Disable this feature. + alias -g '${1+"$@"}'='"$@"' + setopt NO_GLOB_SUBST +else + case `(set -o) 2>/dev/null` in #( + *posix*) : + set -o posix ;; #( + *) : + ;; +esac +fi + + +as_nl=' +' +export as_nl +# Printing a long string crashes Solaris 7 /usr/bin/printf. +as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\' +as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo +as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo +# Prefer a ksh shell builtin over an external printf program on Solaris, +# but without wasting forks for bash or zsh. +if test -z "$BASH_VERSION$ZSH_VERSION" \ + && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then + as_echo='print -r --' + as_echo_n='print -rn --' +elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then + as_echo='printf %s\n' + as_echo_n='printf %s' +else + if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then + as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"' + as_echo_n='/usr/ucb/echo -n' + else + as_echo_body='eval expr "X$1" : "X\\(.*\\)"' + as_echo_n_body='eval + arg=$1; + case $arg in #( + *"$as_nl"*) + expr "X$arg" : "X\\(.*\\)$as_nl"; + arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;; + esac; + expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl" + ' + export as_echo_n_body + as_echo_n='sh -c $as_echo_n_body as_echo' + fi + export as_echo_body + as_echo='sh -c $as_echo_body as_echo' +fi + +# The user is always right. +if test "${PATH_SEPARATOR+set}" != set; then + PATH_SEPARATOR=: + (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && { + (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 || + PATH_SEPARATOR=';' + } +fi + + +# IFS +# We need space, tab and new line, in precisely that order. Quoting is +# there to prevent editors from complaining about space-tab. +# (If _AS_PATH_WALK were called with IFS unset, it would disable word +# splitting by setting IFS to empty value.) +IFS=" "" $as_nl" + +# Find who we are. Look in the path if we contain no directory separator. +as_myself= +case $0 in #(( + *[\\/]* ) as_myself=$0 ;; + *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break + done +IFS=$as_save_IFS + + ;; +esac +# We did not find ourselves, most probably we were run as `sh COMMAND' +# in which case we are not to be found in the path. +if test "x$as_myself" = x; then + as_myself=$0 +fi +if test ! -f "$as_myself"; then + $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2 + exit 1 +fi + +# Unset variables that we do not need and which cause bugs (e.g. in +# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1" +# suppresses any "Segmentation fault" message there. '((' could +# trigger a bug in pdksh 5.2.14. +for as_var in BASH_ENV ENV MAIL MAILPATH +do eval test x\${$as_var+set} = xset \ + && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || : +done +PS1='$ ' +PS2='> ' +PS4='+ ' + +# NLS nuisances. +LC_ALL=C +export LC_ALL +LANGUAGE=C +export LANGUAGE + +# CDPATH. +(unset CDPATH) >/dev/null 2>&1 && unset CDPATH + +# Use a proper internal environment variable to ensure we don't fall + # into an infinite loop, continuously re-executing ourselves. + if test x"${_as_can_reexec}" != xno && test "x$CONFIG_SHELL" != x; then + _as_can_reexec=no; export _as_can_reexec; + # We cannot yet assume a decent shell, so we have to provide a +# neutralization value for shells without unset; and this also +# works around shells that cannot unset nonexistent variables. +# Preserve -v and -x to the replacement shell. +BASH_ENV=/dev/null +ENV=/dev/null +(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV +case $- in # (((( + *v*x* | *x*v* ) as_opts=-vx ;; + *v* ) as_opts=-v ;; + *x* ) as_opts=-x ;; + * ) as_opts= ;; +esac +exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"} +# Admittedly, this is quite paranoid, since all the known shells bail +# out after a failed `exec'. +$as_echo "$0: could not re-execute with $CONFIG_SHELL" >&2 +as_fn_exit 255 + fi + # We don't want this to propagate to other subprocesses. + { _as_can_reexec=; unset _as_can_reexec;} +if test "x$CONFIG_SHELL" = x; then + as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then : + emulate sh + NULLCMD=: + # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which + # is contrary to our usage. Disable this feature. + alias -g '\${1+\"\$@\"}'='\"\$@\"' + setopt NO_GLOB_SUBST +else + case \`(set -o) 2>/dev/null\` in #( + *posix*) : + set -o posix ;; #( + *) : + ;; +esac +fi +" + as_required="as_fn_return () { (exit \$1); } +as_fn_success () { as_fn_return 0; } +as_fn_failure () { as_fn_return 1; } +as_fn_ret_success () { return 0; } +as_fn_ret_failure () { return 1; } + +exitcode=0 +as_fn_success || { exitcode=1; echo as_fn_success failed.; } +as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; } +as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; } +as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; } +if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then : + +else + exitcode=1; echo positional parameters were not saved. +fi +test x\$exitcode = x0 || exit 1 +test -x / || exit 1" + as_suggested=" as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO + as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO + eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" && + test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1 +test \$(( 1 + 1 )) = 2 || exit 1" + if (eval "$as_required") 2>/dev/null; then : + as_have_required=yes +else + as_have_required=no +fi + if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then : + +else + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +as_found=false +for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + as_found=: + case $as_dir in #( + /*) + for as_base in sh bash ksh sh5; do + # Try only shells that exist, to save several forks. + as_shell=$as_dir/$as_base + if { test -f "$as_shell" || test -f "$as_shell.exe"; } && + { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then : + CONFIG_SHELL=$as_shell as_have_required=yes + if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then : + break 2 +fi +fi + done;; + esac + as_found=false +done +$as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } && + { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then : + CONFIG_SHELL=$SHELL as_have_required=yes +fi; } +IFS=$as_save_IFS + + + if test "x$CONFIG_SHELL" != x; then : + export CONFIG_SHELL + # We cannot yet assume a decent shell, so we have to provide a +# neutralization value for shells without unset; and this also +# works around shells that cannot unset nonexistent variables. +# Preserve -v and -x to the replacement shell. +BASH_ENV=/dev/null +ENV=/dev/null +(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV +case $- in # (((( + *v*x* | *x*v* ) as_opts=-vx ;; + *v* ) as_opts=-v ;; + *x* ) as_opts=-x ;; + * ) as_opts= ;; +esac +exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"} +# Admittedly, this is quite paranoid, since all the known shells bail +# out after a failed `exec'. +$as_echo "$0: could not re-execute with $CONFIG_SHELL" >&2 +exit 255 +fi + + if test x$as_have_required = xno; then : + $as_echo "$0: This script requires a shell more modern than all" + $as_echo "$0: the shells that I found on your system." + if test x${ZSH_VERSION+set} = xset ; then + $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should" + $as_echo "$0: be upgraded to zsh 4.3.4 or later." + else + $as_echo "$0: Please tell bug-autoconf@gnu.org and sean@eddylab.org +$0: about your system, including any error possibly output +$0: before this message. Then install a modern shell, or +$0: manually run the script under such a shell if you do +$0: have one." + fi + exit 1 +fi +fi +fi +SHELL=${CONFIG_SHELL-/bin/sh} +export SHELL +# Unset more variables known to interfere with behavior of common tools. +CLICOLOR_FORCE= GREP_OPTIONS= +unset CLICOLOR_FORCE GREP_OPTIONS + +## --------------------- ## +## M4sh Shell Functions. ## +## --------------------- ## +# as_fn_unset VAR +# --------------- +# Portably unset VAR. +as_fn_unset () +{ + { eval $1=; unset $1;} +} +as_unset=as_fn_unset + +# as_fn_set_status STATUS +# ----------------------- +# Set $? to STATUS, without forking. +as_fn_set_status () +{ + return $1 +} # as_fn_set_status + +# as_fn_exit STATUS +# ----------------- +# Exit the shell with STATUS, even in a "trap 0" or "set -e" context. +as_fn_exit () +{ + set +e + as_fn_set_status $1 + exit $1 +} # as_fn_exit + +# as_fn_mkdir_p +# ------------- +# Create "$as_dir" as a directory, including parents if necessary. +as_fn_mkdir_p () +{ + + case $as_dir in #( + -*) as_dir=./$as_dir;; + esac + test -d "$as_dir" || eval $as_mkdir_p || { + as_dirs= + while :; do + case $as_dir in #( + *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( + *) as_qdir=$as_dir;; + esac + as_dirs="'$as_qdir' $as_dirs" + as_dir=`$as_dirname -- "$as_dir" || +$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$as_dir" : 'X\(//\)[^/]' \| \ + X"$as_dir" : 'X\(//\)$' \| \ + X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X"$as_dir" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ + s//\1/ + q + } + /^X\(\/\/\)[^/].*/{ + s//\1/ + q + } + /^X\(\/\/\)$/{ + s//\1/ + q + } + /^X\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` + test -d "$as_dir" && break + done + test -z "$as_dirs" || eval "mkdir $as_dirs" + } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir" + + +} # as_fn_mkdir_p + +# as_fn_executable_p FILE +# ----------------------- +# Test if FILE is an executable regular file. +as_fn_executable_p () +{ + test -f "$1" && test -x "$1" +} # as_fn_executable_p +# as_fn_append VAR VALUE +# ---------------------- +# Append the text in VALUE to the end of the definition contained in VAR. Take +# advantage of any shell optimizations that allow amortized linear growth over +# repeated appends, instead of the typical quadratic growth present in naive +# implementations. +if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then : + eval 'as_fn_append () + { + eval $1+=\$2 + }' +else + as_fn_append () + { + eval $1=\$$1\$2 + } +fi # as_fn_append + +# as_fn_arith ARG... +# ------------------ +# Perform arithmetic evaluation on the ARGs, and store the result in the +# global $as_val. Take advantage of shells that can avoid forks. The arguments +# must be portable across $(()) and expr. +if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then : + eval 'as_fn_arith () + { + as_val=$(( $* )) + }' +else + as_fn_arith () + { + as_val=`expr "$@" || test $? -eq 1` + } +fi # as_fn_arith + + +# as_fn_error STATUS ERROR [LINENO LOG_FD] +# ---------------------------------------- +# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are +# provided, also output the error to LOG_FD, referencing LINENO. Then exit the +# script with STATUS, using 1 if that was 0. +as_fn_error () +{ + as_status=$1; test $as_status -eq 0 && as_status=1 + if test "$4"; then + as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4 + fi + $as_echo "$as_me: error: $2" >&2 + as_fn_exit $as_status +} # as_fn_error + +if expr a : '\(a\)' >/dev/null 2>&1 && + test "X`expr 00001 : '.*\(...\)'`" = X001; then + as_expr=expr +else + as_expr=false +fi + +if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then + as_basename=basename +else + as_basename=false +fi + +if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then + as_dirname=dirname +else + as_dirname=false +fi + +as_me=`$as_basename -- "$0" || +$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ + X"$0" : 'X\(//\)$' \| \ + X"$0" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X/"$0" | + sed '/^.*\/\([^/][^/]*\)\/*$/{ + s//\1/ + q + } + /^X\/\(\/\/\)$/{ + s//\1/ + q + } + /^X\/\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` + +# Avoid depending upon Character Ranges. +as_cr_letters='abcdefghijklmnopqrstuvwxyz' +as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' +as_cr_Letters=$as_cr_letters$as_cr_LETTERS +as_cr_digits='0123456789' +as_cr_alnum=$as_cr_Letters$as_cr_digits + + + as_lineno_1=$LINENO as_lineno_1a=$LINENO + as_lineno_2=$LINENO as_lineno_2a=$LINENO + eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" && + test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || { + # Blame Lee E. McMahon (1931-1989) for sed's syntax. :-) + sed -n ' + p + /[$]LINENO/= + ' <$as_myself | + sed ' + s/[$]LINENO.*/&-/ + t lineno + b + :lineno + N + :loop + s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/ + t loop + s/-\n.*// + ' >$as_me.lineno && + chmod +x "$as_me.lineno" || + { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; } + + # If we had to re-execute with $CONFIG_SHELL, we're ensured to have + # already done that, so ensure we don't try to do so again and fall + # in an infinite loop. This has already happened in practice. + _as_can_reexec=no; export _as_can_reexec + # Don't try to exec as it changes $[0], causing all sort of problems + # (the dirname of $[0] is not the place where we might find the + # original and so on. Autoconf is especially sensitive to this). + . "./$as_me.lineno" + # Exit status is that of the last command. + exit +} + +ECHO_C= ECHO_N= ECHO_T= +case `echo -n x` in #((((( +-n*) + case `echo 'xy\c'` in + *c*) ECHO_T=' ';; # ECHO_T is single tab character. + xy) ECHO_C='\c';; + *) echo `echo ksh88 bug on AIX 6.1` > /dev/null + ECHO_T=' ';; + esac;; +*) + ECHO_N='-n';; +esac + +rm -f conf$$ conf$$.exe conf$$.file +if test -d conf$$.dir; then + rm -f conf$$.dir/conf$$.file +else + rm -f conf$$.dir + mkdir conf$$.dir 2>/dev/null +fi +if (echo >conf$$.file) 2>/dev/null; then + if ln -s conf$$.file conf$$ 2>/dev/null; then + as_ln_s='ln -s' + # ... but there are two gotchas: + # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail. + # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable. + # In both cases, we have to default to `cp -pR'. + ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe || + as_ln_s='cp -pR' + elif ln conf$$.file conf$$ 2>/dev/null; then + as_ln_s=ln + else + as_ln_s='cp -pR' + fi +else + as_ln_s='cp -pR' +fi +rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file +rmdir conf$$.dir 2>/dev/null + +if mkdir -p . 2>/dev/null; then + as_mkdir_p='mkdir -p "$as_dir"' +else + test -d ./-p && rmdir ./-p + as_mkdir_p=false +fi + +as_test_x='test -x' +as_executable_p=as_fn_executable_p + +# Sed expression to map a string onto a valid CPP name. +as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'" + +# Sed expression to map a string onto a valid variable name. +as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'" + + +test -n "$DJDIR" || exec 7<&0 &1 + +# Name of the host. +# hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status, +# so uname gets run too. +ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q` + +# +# Initializations. +# +ac_default_prefix=/usr/local +ac_clean_files= +ac_config_libobj_dir=. +LIBOBJS= +cross_compiling=no +subdirs= +MFLAGS= +MAKEFLAGS= + +# Identity of this package. +PACKAGE_NAME='HMMER' +PACKAGE_TARNAME='hmmer' +PACKAGE_VERSION='3.3.2' +PACKAGE_STRING='HMMER 3.3.2' +PACKAGE_BUGREPORT='sean@eddylab.org' +PACKAGE_URL='' + +# Factoring default headers for most tests. +ac_includes_default="\ +#include +#ifdef HAVE_SYS_TYPES_H +# include +#endif +#ifdef HAVE_SYS_STAT_H +# include +#endif +#ifdef STDC_HEADERS +# include +# include +#else +# ifdef HAVE_STDLIB_H +# include +# endif +#endif +#ifdef HAVE_STRING_H +# if !defined STDC_HEADERS && defined HAVE_MEMORY_H +# include +# endif +# include +#endif +#ifdef HAVE_STRINGS_H +# include +#endif +#ifdef HAVE_INTTYPES_H +# include +#endif +#ifdef HAVE_STDINT_H +# include +#endif +#ifdef HAVE_UNISTD_H +# include +#endif" + +ac_subst_vars='LTLIBOBJS +LIBOBJS +LIBGSL +HAVE_PYTHON3 +HAVE_GZIP +GROUPHMMERLIBS +NEON_CFLAGS +AVX512_CFLAGS +AVX_CFLAGS +SSE4_CFLAGS +IMPL_CHOICE +SSE_CFLAGS +VMX_CFLAGS +HMMERIMPLLIB +PTHREAD_CFLAGS +PTHREAD_LIBS +PTHREAD_CXX +PTHREAD_CC +ax_pthread_config +EGREP +GREP +SED +PIC_CFLAGS +LN_S +AR +RANLIB +STRIP +INSTALL_DATA +INSTALL_SCRIPT +INSTALL_PROGRAM +CPP +MPI_BENCHMARKS +MPI_UTESTS +OBJEXT +EXEEXT +CPPFLAGS +LDFLAGS +CFLAGS +ac_ct_CC +CC +MPICC +host_os +host_vendor +host_cpu +host +build_os +build_vendor +build_cpu +build +EASEL_URL +EASEL_VERSION +EASEL_LICENSE +EASEL_COPYRIGHT +EASEL_DATE +HMMER_SADIR +HMMER_ESLDIR +HMMER_URL +HMMER_VERSION +HMMER_LICENSE +HMMER_COPYRIGHT +HMMER_DATE +target_alias +host_alias +build_alias +LIBS +ECHO_T +ECHO_N +ECHO_C +DEFS +mandir +localedir +libdir +psdir +pdfdir +dvidir +htmldir +infodir +docdir +oldincludedir +includedir +runstatedir +localstatedir +sharedstatedir +sysconfdir +datadir +datarootdir +libexecdir +sbindir +bindir +program_transform_name +prefix +exec_prefix +PACKAGE_URL +PACKAGE_BUGREPORT +PACKAGE_STRING +PACKAGE_VERSION +PACKAGE_TARNAME +PACKAGE_NAME +PATH_SEPARATOR +SHELL' +ac_subst_files='' +ac_user_opts=' +enable_option_checking +enable_debugging +enable_gcov +enable_gprof +enable_sse +enable_vmx +enable_threads +enable_mpi +enable_pic +with_gsl +enable_largefile +' + ac_precious_vars='build_alias +host_alias +target_alias +MPICC +CC +CFLAGS +LDFLAGS +LIBS +CPPFLAGS +CPP +PIC_CFLAGS' + + +# Initialize some variables set by options. +ac_init_help= +ac_init_version=false +ac_unrecognized_opts= +ac_unrecognized_sep= +# The variables have the same names as the options, with +# dashes changed to underlines. +cache_file=/dev/null +exec_prefix=NONE +no_create= +no_recursion= +prefix=NONE +program_prefix=NONE +program_suffix=NONE +program_transform_name=s,x,x, +silent= +site= +srcdir= +verbose= +x_includes=NONE +x_libraries=NONE + +# Installation directory options. +# These are left unexpanded so users can "make install exec_prefix=/foo" +# and all the variables that are supposed to be based on exec_prefix +# by default will actually change. +# Use braces instead of parens because sh, perl, etc. also accept them. +# (The list follows the same order as the GNU Coding Standards.) +bindir='${exec_prefix}/bin' +sbindir='${exec_prefix}/sbin' +libexecdir='${exec_prefix}/libexec' +datarootdir='${prefix}/share' +datadir='${datarootdir}' +sysconfdir='${prefix}/etc' +sharedstatedir='${prefix}/com' +localstatedir='${prefix}/var' +runstatedir='${localstatedir}/run' +includedir='${prefix}/include' +oldincludedir='/usr/include' +docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' +infodir='${datarootdir}/info' +htmldir='${docdir}' +dvidir='${docdir}' +pdfdir='${docdir}' +psdir='${docdir}' +libdir='${exec_prefix}/lib' +localedir='${datarootdir}/locale' +mandir='${datarootdir}/man' + +ac_prev= +ac_dashdash= +for ac_option +do + # If the previous option needs an argument, assign it. + if test -n "$ac_prev"; then + eval $ac_prev=\$ac_option + ac_prev= + continue + fi + + case $ac_option in + *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;; + *=) ac_optarg= ;; + *) ac_optarg=yes ;; + esac + + # Accept the important Cygnus configure options, so we can diagnose typos. + + case $ac_dashdash$ac_option in + --) + ac_dashdash=yes ;; + + -bindir | --bindir | --bindi | --bind | --bin | --bi) + ac_prev=bindir ;; + -bindir=* | --bindir=* | --bindi=* | --bind=* | --bin=* | --bi=*) + bindir=$ac_optarg ;; + + -build | --build | --buil | --bui | --bu) + ac_prev=build_alias ;; + -build=* | --build=* | --buil=* | --bui=* | --bu=*) + build_alias=$ac_optarg ;; + + -cache-file | --cache-file | --cache-fil | --cache-fi \ + | --cache-f | --cache- | --cache | --cach | --cac | --ca | --c) + ac_prev=cache_file ;; + -cache-file=* | --cache-file=* | --cache-fil=* | --cache-fi=* \ + | --cache-f=* | --cache-=* | --cache=* | --cach=* | --cac=* | --ca=* | --c=*) + cache_file=$ac_optarg ;; + + --config-cache | -C) + cache_file=config.cache ;; + + -datadir | --datadir | --datadi | --datad) + ac_prev=datadir ;; + -datadir=* | --datadir=* | --datadi=* | --datad=*) + datadir=$ac_optarg ;; + + -datarootdir | --datarootdir | --datarootdi | --datarootd | --dataroot \ + | --dataroo | --dataro | --datar) + ac_prev=datarootdir ;; + -datarootdir=* | --datarootdir=* | --datarootdi=* | --datarootd=* \ + | --dataroot=* | --dataroo=* | --dataro=* | --datar=*) + datarootdir=$ac_optarg ;; + + -disable-* | --disable-*) + ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'` + # Reject names that are not valid shell variable names. + expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && + as_fn_error $? "invalid feature name: $ac_useropt" + ac_useropt_orig=$ac_useropt + ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` + case $ac_user_opts in + *" +"enable_$ac_useropt" +"*) ;; + *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--disable-$ac_useropt_orig" + ac_unrecognized_sep=', ';; + esac + eval enable_$ac_useropt=no ;; + + -docdir | --docdir | --docdi | --doc | --do) + ac_prev=docdir ;; + -docdir=* | --docdir=* | --docdi=* | --doc=* | --do=*) + docdir=$ac_optarg ;; + + -dvidir | --dvidir | --dvidi | --dvid | --dvi | --dv) + ac_prev=dvidir ;; + -dvidir=* | --dvidir=* | --dvidi=* | --dvid=* | --dvi=* | --dv=*) + dvidir=$ac_optarg ;; + + -enable-* | --enable-*) + ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'` + # Reject names that are not valid shell variable names. + expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && + as_fn_error $? "invalid feature name: $ac_useropt" + ac_useropt_orig=$ac_useropt + ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` + case $ac_user_opts in + *" +"enable_$ac_useropt" +"*) ;; + *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--enable-$ac_useropt_orig" + ac_unrecognized_sep=', ';; + esac + eval enable_$ac_useropt=\$ac_optarg ;; + + -exec-prefix | --exec_prefix | --exec-prefix | --exec-prefi \ + | --exec-pref | --exec-pre | --exec-pr | --exec-p | --exec- \ + | --exec | --exe | --ex) + ac_prev=exec_prefix ;; + -exec-prefix=* | --exec_prefix=* | --exec-prefix=* | --exec-prefi=* \ + | --exec-pref=* | --exec-pre=* | --exec-pr=* | --exec-p=* | --exec-=* \ + | --exec=* | --exe=* | --ex=*) + exec_prefix=$ac_optarg ;; + + -gas | --gas | --ga | --g) + # Obsolete; use --with-gas. + with_gas=yes ;; + + -help | --help | --hel | --he | -h) + ac_init_help=long ;; + -help=r* | --help=r* | --hel=r* | --he=r* | -hr*) + ac_init_help=recursive ;; + -help=s* | --help=s* | --hel=s* | --he=s* | -hs*) + ac_init_help=short ;; + + -host | --host | --hos | --ho) + ac_prev=host_alias ;; + -host=* | --host=* | --hos=* | --ho=*) + host_alias=$ac_optarg ;; + + -htmldir | --htmldir | --htmldi | --htmld | --html | --htm | --ht) + ac_prev=htmldir ;; + -htmldir=* | --htmldir=* | --htmldi=* | --htmld=* | --html=* | --htm=* \ + | --ht=*) + htmldir=$ac_optarg ;; + + -includedir | --includedir | --includedi | --included | --include \ + | --includ | --inclu | --incl | --inc) + ac_prev=includedir ;; + -includedir=* | --includedir=* | --includedi=* | --included=* | --include=* \ + | --includ=* | --inclu=* | --incl=* | --inc=*) + includedir=$ac_optarg ;; + + -infodir | --infodir | --infodi | --infod | --info | --inf) + ac_prev=infodir ;; + -infodir=* | --infodir=* | --infodi=* | --infod=* | --info=* | --inf=*) + infodir=$ac_optarg ;; + + -libdir | --libdir | --libdi | --libd) + ac_prev=libdir ;; + -libdir=* | --libdir=* | --libdi=* | --libd=*) + libdir=$ac_optarg ;; + + -libexecdir | --libexecdir | --libexecdi | --libexecd | --libexec \ + | --libexe | --libex | --libe) + ac_prev=libexecdir ;; + -libexecdir=* | --libexecdir=* | --libexecdi=* | --libexecd=* | --libexec=* \ + | --libexe=* | --libex=* | --libe=*) + libexecdir=$ac_optarg ;; + + -localedir | --localedir | --localedi | --localed | --locale) + ac_prev=localedir ;; + -localedir=* | --localedir=* | --localedi=* | --localed=* | --locale=*) + localedir=$ac_optarg ;; + + -localstatedir | --localstatedir | --localstatedi | --localstated \ + | --localstate | --localstat | --localsta | --localst | --locals) + ac_prev=localstatedir ;; + -localstatedir=* | --localstatedir=* | --localstatedi=* | --localstated=* \ + | --localstate=* | --localstat=* | --localsta=* | --localst=* | --locals=*) + localstatedir=$ac_optarg ;; + + -mandir | --mandir | --mandi | --mand | --man | --ma | --m) + ac_prev=mandir ;; + -mandir=* | --mandir=* | --mandi=* | --mand=* | --man=* | --ma=* | --m=*) + mandir=$ac_optarg ;; + + -nfp | --nfp | --nf) + # Obsolete; use --without-fp. + with_fp=no ;; + + -no-create | --no-create | --no-creat | --no-crea | --no-cre \ + | --no-cr | --no-c | -n) + no_create=yes ;; + + -no-recursion | --no-recursion | --no-recursio | --no-recursi \ + | --no-recurs | --no-recur | --no-recu | --no-rec | --no-re | --no-r) + no_recursion=yes ;; + + -oldincludedir | --oldincludedir | --oldincludedi | --oldincluded \ + | --oldinclude | --oldinclud | --oldinclu | --oldincl | --oldinc \ + | --oldin | --oldi | --old | --ol | --o) + ac_prev=oldincludedir ;; + -oldincludedir=* | --oldincludedir=* | --oldincludedi=* | --oldincluded=* \ + | --oldinclude=* | --oldinclud=* | --oldinclu=* | --oldincl=* | --oldinc=* \ + | --oldin=* | --oldi=* | --old=* | --ol=* | --o=*) + oldincludedir=$ac_optarg ;; + + -prefix | --prefix | --prefi | --pref | --pre | --pr | --p) + ac_prev=prefix ;; + -prefix=* | --prefix=* | --prefi=* | --pref=* | --pre=* | --pr=* | --p=*) + prefix=$ac_optarg ;; + + -program-prefix | --program-prefix | --program-prefi | --program-pref \ + | --program-pre | --program-pr | --program-p) + ac_prev=program_prefix ;; + -program-prefix=* | --program-prefix=* | --program-prefi=* \ + | --program-pref=* | --program-pre=* | --program-pr=* | --program-p=*) + program_prefix=$ac_optarg ;; + + -program-suffix | --program-suffix | --program-suffi | --program-suff \ + | --program-suf | --program-su | --program-s) + ac_prev=program_suffix ;; + -program-suffix=* | --program-suffix=* | --program-suffi=* \ + | --program-suff=* | --program-suf=* | --program-su=* | --program-s=*) + program_suffix=$ac_optarg ;; + + -program-transform-name | --program-transform-name \ + | --program-transform-nam | --program-transform-na \ + | --program-transform-n | --program-transform- \ + | --program-transform | --program-transfor \ + | --program-transfo | --program-transf \ + | --program-trans | --program-tran \ + | --progr-tra | --program-tr | --program-t) + ac_prev=program_transform_name ;; + -program-transform-name=* | --program-transform-name=* \ + | --program-transform-nam=* | --program-transform-na=* \ + | --program-transform-n=* | --program-transform-=* \ + | --program-transform=* | --program-transfor=* \ + | --program-transfo=* | --program-transf=* \ + | --program-trans=* | --program-tran=* \ + | --progr-tra=* | --program-tr=* | --program-t=*) + program_transform_name=$ac_optarg ;; + + -pdfdir | --pdfdir | --pdfdi | --pdfd | --pdf | --pd) + ac_prev=pdfdir ;; + -pdfdir=* | --pdfdir=* | --pdfdi=* | --pdfd=* | --pdf=* | --pd=*) + pdfdir=$ac_optarg ;; + + -psdir | --psdir | --psdi | --psd | --ps) + ac_prev=psdir ;; + -psdir=* | --psdir=* | --psdi=* | --psd=* | --ps=*) + psdir=$ac_optarg ;; + + -q | -quiet | --quiet | --quie | --qui | --qu | --q \ + | -silent | --silent | --silen | --sile | --sil) + silent=yes ;; + + -runstatedir | --runstatedir | --runstatedi | --runstated \ + | --runstate | --runstat | --runsta | --runst | --runs \ + | --run | --ru | --r) + ac_prev=runstatedir ;; + -runstatedir=* | --runstatedir=* | --runstatedi=* | --runstated=* \ + | --runstate=* | --runstat=* | --runsta=* | --runst=* | --runs=* \ + | --run=* | --ru=* | --r=*) + runstatedir=$ac_optarg ;; + + -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb) + ac_prev=sbindir ;; + -sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \ + | --sbi=* | --sb=*) + sbindir=$ac_optarg ;; + + -sharedstatedir | --sharedstatedir | --sharedstatedi \ + | --sharedstated | --sharedstate | --sharedstat | --sharedsta \ + | --sharedst | --shareds | --shared | --share | --shar \ + | --sha | --sh) + ac_prev=sharedstatedir ;; + -sharedstatedir=* | --sharedstatedir=* | --sharedstatedi=* \ + | --sharedstated=* | --sharedstate=* | --sharedstat=* | --sharedsta=* \ + | --sharedst=* | --shareds=* | --shared=* | --share=* | --shar=* \ + | --sha=* | --sh=*) + sharedstatedir=$ac_optarg ;; + + -site | --site | --sit) + ac_prev=site ;; + -site=* | --site=* | --sit=*) + site=$ac_optarg ;; + + -srcdir | --srcdir | --srcdi | --srcd | --src | --sr) + ac_prev=srcdir ;; + -srcdir=* | --srcdir=* | --srcdi=* | --srcd=* | --src=* | --sr=*) + srcdir=$ac_optarg ;; + + -sysconfdir | --sysconfdir | --sysconfdi | --sysconfd | --sysconf \ + | --syscon | --sysco | --sysc | --sys | --sy) + ac_prev=sysconfdir ;; + -sysconfdir=* | --sysconfdir=* | --sysconfdi=* | --sysconfd=* | --sysconf=* \ + | --syscon=* | --sysco=* | --sysc=* | --sys=* | --sy=*) + sysconfdir=$ac_optarg ;; + + -target | --target | --targe | --targ | --tar | --ta | --t) + ac_prev=target_alias ;; + -target=* | --target=* | --targe=* | --targ=* | --tar=* | --ta=* | --t=*) + target_alias=$ac_optarg ;; + + -v | -verbose | --verbose | --verbos | --verbo | --verb) + verbose=yes ;; + + -version | --version | --versio | --versi | --vers | -V) + ac_init_version=: ;; + + -with-* | --with-*) + ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'` + # Reject names that are not valid shell variable names. + expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && + as_fn_error $? "invalid package name: $ac_useropt" + ac_useropt_orig=$ac_useropt + ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` + case $ac_user_opts in + *" +"with_$ac_useropt" +"*) ;; + *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--with-$ac_useropt_orig" + ac_unrecognized_sep=', ';; + esac + eval with_$ac_useropt=\$ac_optarg ;; + + -without-* | --without-*) + ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'` + # Reject names that are not valid shell variable names. + expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && + as_fn_error $? "invalid package name: $ac_useropt" + ac_useropt_orig=$ac_useropt + ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` + case $ac_user_opts in + *" +"with_$ac_useropt" +"*) ;; + *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--without-$ac_useropt_orig" + ac_unrecognized_sep=', ';; + esac + eval with_$ac_useropt=no ;; + + --x) + # Obsolete; use --with-x. + with_x=yes ;; + + -x-includes | --x-includes | --x-include | --x-includ | --x-inclu \ + | --x-incl | --x-inc | --x-in | --x-i) + ac_prev=x_includes ;; + -x-includes=* | --x-includes=* | --x-include=* | --x-includ=* | --x-inclu=* \ + | --x-incl=* | --x-inc=* | --x-in=* | --x-i=*) + x_includes=$ac_optarg ;; + + -x-libraries | --x-libraries | --x-librarie | --x-librari \ + | --x-librar | --x-libra | --x-libr | --x-lib | --x-li | --x-l) + ac_prev=x_libraries ;; + -x-libraries=* | --x-libraries=* | --x-librarie=* | --x-librari=* \ + | --x-librar=* | --x-libra=* | --x-libr=* | --x-lib=* | --x-li=* | --x-l=*) + x_libraries=$ac_optarg ;; + + -*) as_fn_error $? "unrecognized option: \`$ac_option' +Try \`$0 --help' for more information" + ;; + + *=*) + ac_envvar=`expr "x$ac_option" : 'x\([^=]*\)='` + # Reject names that are not valid shell variable names. + case $ac_envvar in #( + '' | [0-9]* | *[!_$as_cr_alnum]* ) + as_fn_error $? "invalid variable name: \`$ac_envvar'" ;; + esac + eval $ac_envvar=\$ac_optarg + export $ac_envvar ;; + + *) + # FIXME: should be removed in autoconf 3.0. + $as_echo "$as_me: WARNING: you should use --build, --host, --target" >&2 + expr "x$ac_option" : ".*[^-._$as_cr_alnum]" >/dev/null && + $as_echo "$as_me: WARNING: invalid host type: $ac_option" >&2 + : "${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option}" + ;; + + esac +done + +if test -n "$ac_prev"; then + ac_option=--`echo $ac_prev | sed 's/_/-/g'` + as_fn_error $? "missing argument to $ac_option" +fi + +if test -n "$ac_unrecognized_opts"; then + case $enable_option_checking in + no) ;; + fatal) as_fn_error $? "unrecognized options: $ac_unrecognized_opts" ;; + *) $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2 ;; + esac +fi + +# Check all directory arguments for consistency. +for ac_var in exec_prefix prefix bindir sbindir libexecdir datarootdir \ + datadir sysconfdir sharedstatedir localstatedir includedir \ + oldincludedir docdir infodir htmldir dvidir pdfdir psdir \ + libdir localedir mandir runstatedir +do + eval ac_val=\$$ac_var + # Remove trailing slashes. + case $ac_val in + */ ) + ac_val=`expr "X$ac_val" : 'X\(.*[^/]\)' \| "X$ac_val" : 'X\(.*\)'` + eval $ac_var=\$ac_val;; + esac + # Be sure to have absolute directory names. + case $ac_val in + [\\/$]* | ?:[\\/]* ) continue;; + NONE | '' ) case $ac_var in *prefix ) continue;; esac;; + esac + as_fn_error $? "expected an absolute directory name for --$ac_var: $ac_val" +done + +# There might be people who depend on the old broken behavior: `$host' +# used to hold the argument of --host etc. +# FIXME: To remove some day. +build=$build_alias +host=$host_alias +target=$target_alias + +# FIXME: To remove some day. +if test "x$host_alias" != x; then + if test "x$build_alias" = x; then + cross_compiling=maybe + elif test "x$build_alias" != "x$host_alias"; then + cross_compiling=yes + fi +fi + +ac_tool_prefix= +test -n "$host_alias" && ac_tool_prefix=$host_alias- + +test "$silent" = yes && exec 6>/dev/null + + +ac_pwd=`pwd` && test -n "$ac_pwd" && +ac_ls_di=`ls -di .` && +ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` || + as_fn_error $? "working directory cannot be determined" +test "X$ac_ls_di" = "X$ac_pwd_ls_di" || + as_fn_error $? "pwd does not report name of working directory" + + +# Find the source files, if location was not specified. +if test -z "$srcdir"; then + ac_srcdir_defaulted=yes + # Try the directory containing this script, then the parent directory. + ac_confdir=`$as_dirname -- "$as_myself" || +$as_expr X"$as_myself" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$as_myself" : 'X\(//\)[^/]' \| \ + X"$as_myself" : 'X\(//\)$' \| \ + X"$as_myself" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X"$as_myself" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ + s//\1/ + q + } + /^X\(\/\/\)[^/].*/{ + s//\1/ + q + } + /^X\(\/\/\)$/{ + s//\1/ + q + } + /^X\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` + srcdir=$ac_confdir + if test ! -r "$srcdir/$ac_unique_file"; then + srcdir=.. + fi +else + ac_srcdir_defaulted=no +fi +if test ! -r "$srcdir/$ac_unique_file"; then + test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .." + as_fn_error $? "cannot find sources ($ac_unique_file) in $srcdir" +fi +ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work" +ac_abs_confdir=`( + cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error $? "$ac_msg" + pwd)` +# When building in place, set srcdir=. +if test "$ac_abs_confdir" = "$ac_pwd"; then + srcdir=. +fi +# Remove unnecessary trailing slashes from srcdir. +# Double slashes in file names in object file debugging info +# mess up M-x gdb in Emacs. +case $srcdir in +*/) srcdir=`expr "X$srcdir" : 'X\(.*[^/]\)' \| "X$srcdir" : 'X\(.*\)'`;; +esac +for ac_var in $ac_precious_vars; do + eval ac_env_${ac_var}_set=\${${ac_var}+set} + eval ac_env_${ac_var}_value=\$${ac_var} + eval ac_cv_env_${ac_var}_set=\${${ac_var}+set} + eval ac_cv_env_${ac_var}_value=\$${ac_var} +done + +# +# Report the --help message. +# +if test "$ac_init_help" = "long"; then + # Omit some internal or obsolete options to make the list less imposing. + # This message is too long to be a string in the A/UX 3.1 sh. + cat <<_ACEOF +\`configure' configures HMMER 3.3.2 to adapt to many kinds of systems. + +Usage: $0 [OPTION]... [VAR=VALUE]... + +To assign environment variables (e.g., CC, CFLAGS...), specify them as +VAR=VALUE. See below for descriptions of some of the useful variables. + +Defaults for the options are specified in brackets. + +Configuration: + -h, --help display this help and exit + --help=short display options specific to this package + --help=recursive display the short help of all the included packages + -V, --version display version information and exit + -q, --quiet, --silent do not print \`checking ...' messages + --cache-file=FILE cache test results in FILE [disabled] + -C, --config-cache alias for \`--cache-file=config.cache' + -n, --no-create do not create output files + --srcdir=DIR find the sources in DIR [configure dir or \`..'] + +Installation directories: + --prefix=PREFIX install architecture-independent files in PREFIX + [$ac_default_prefix] + --exec-prefix=EPREFIX install architecture-dependent files in EPREFIX + [PREFIX] + +By default, \`make install' will install all the files in +\`$ac_default_prefix/bin', \`$ac_default_prefix/lib' etc. You can specify +an installation prefix other than \`$ac_default_prefix' using \`--prefix', +for instance \`--prefix=\$HOME'. + +For better control, use the options below. + +Fine tuning of the installation directories: + --bindir=DIR user executables [EPREFIX/bin] + --sbindir=DIR system admin executables [EPREFIX/sbin] + --libexecdir=DIR program executables [EPREFIX/libexec] + --sysconfdir=DIR read-only single-machine data [PREFIX/etc] + --sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com] + --localstatedir=DIR modifiable single-machine data [PREFIX/var] + --runstatedir=DIR modifiable per-process data [LOCALSTATEDIR/run] + --libdir=DIR object code libraries [EPREFIX/lib] + --includedir=DIR C header files [PREFIX/include] + --oldincludedir=DIR C header files for non-gcc [/usr/include] + --datarootdir=DIR read-only arch.-independent data root [PREFIX/share] + --datadir=DIR read-only architecture-independent data [DATAROOTDIR] + --infodir=DIR info documentation [DATAROOTDIR/info] + --localedir=DIR locale-dependent data [DATAROOTDIR/locale] + --mandir=DIR man documentation [DATAROOTDIR/man] + --docdir=DIR documentation root [DATAROOTDIR/doc/hmmer] + --htmldir=DIR html documentation [DOCDIR] + --dvidir=DIR dvi documentation [DOCDIR] + --pdfdir=DIR pdf documentation [DOCDIR] + --psdir=DIR ps documentation [DOCDIR] +_ACEOF + + cat <<\_ACEOF + +System types: + --build=BUILD configure for building on BUILD [guessed] + --host=HOST cross-compile to build programs to run on HOST [BUILD] +_ACEOF +fi + +if test -n "$ac_init_help"; then + case $ac_init_help in + short | recursive ) echo "Configuration of HMMER 3.3.2:";; + esac + cat <<\_ACEOF + +Optional Features: + --disable-option-checking ignore unrecognized --enable/--with options + --disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no) + --enable-FEATURE[=ARG] include FEATURE [ARG=yes] + + --enable-debugging include debugging code + --enable-debugging=x also set diagnostics verbosity level to (1-3) + + --enable-gcov compile for code coverage testing + --enable-gprof compile for gcc code profiling + --enable-sse enable our SSE vector code + --enable-vmx enable our Altivec/VMX vector code + --enable-threads enable POSIX threads parallelization + --enable-mpi enable MPI parallelization + --enable-pic enable position-independent code + --disable-pic compile PIC objects [default=enabled for shared + builds on supported platforms] + --disable-largefile omit support for large files + +Optional Packages: + --with-PACKAGE[=ARG] use PACKAGE [ARG=yes] + --without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no) + --with-gsl use the GSL, GNU Scientific Library + +Some influential environment variables: + MPICC MPI C compiler command + CC C compiler command + CFLAGS C compiler flags + LDFLAGS linker flags, e.g. -L if you have libraries in a + nonstandard directory + LIBS libraries to pass to the linker, e.g. -l + CPPFLAGS (Objective) C/C++ preprocessor flags, e.g. -I if + you have headers in a nonstandard directory + CPP C preprocessor + PIC_CFLAGS compiler flags for PIC code + +Use these variables to override the choices made by `configure' or to help +it to find libraries and programs with nonstandard names/locations. + +Report bugs to . +_ACEOF +ac_status=$? +fi + +if test "$ac_init_help" = "recursive"; then + # If there are subdirs, report their specific --help. + for ac_dir in : $ac_subdirs_all; do test "x$ac_dir" = x: && continue + test -d "$ac_dir" || + { cd "$srcdir" && ac_pwd=`pwd` && srcdir=. && test -d "$ac_dir"; } || + continue + ac_builddir=. + +case "$ac_dir" in +.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;; +*) + ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'` + # A ".." for each directory in $ac_dir_suffix. + ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'` + case $ac_top_builddir_sub in + "") ac_top_builddir_sub=. ac_top_build_prefix= ;; + *) ac_top_build_prefix=$ac_top_builddir_sub/ ;; + esac ;; +esac +ac_abs_top_builddir=$ac_pwd +ac_abs_builddir=$ac_pwd$ac_dir_suffix +# for backward compatibility: +ac_top_builddir=$ac_top_build_prefix + +case $srcdir in + .) # We are building in place. + ac_srcdir=. + ac_top_srcdir=$ac_top_builddir_sub + ac_abs_top_srcdir=$ac_pwd ;; + [\\/]* | ?:[\\/]* ) # Absolute name. + ac_srcdir=$srcdir$ac_dir_suffix; + ac_top_srcdir=$srcdir + ac_abs_top_srcdir=$srcdir ;; + *) # Relative name. + ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix + ac_top_srcdir=$ac_top_build_prefix$srcdir + ac_abs_top_srcdir=$ac_pwd/$srcdir ;; +esac +ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix + + cd "$ac_dir" || { ac_status=$?; continue; } + # Check for guested configure. + if test -f "$ac_srcdir/configure.gnu"; then + echo && + $SHELL "$ac_srcdir/configure.gnu" --help=recursive + elif test -f "$ac_srcdir/configure"; then + echo && + $SHELL "$ac_srcdir/configure" --help=recursive + else + $as_echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2 + fi || ac_status=$? + cd "$ac_pwd" || { ac_status=$?; break; } + done +fi + +test -n "$ac_init_help" && exit $ac_status +if $ac_init_version; then + cat <<\_ACEOF +HMMER configure 3.3.2 +generated by GNU Autoconf 2.69 + +Copyright (C) 2012 Free Software Foundation, Inc. +This configure script is free software; the Free Software Foundation +gives unlimited permission to copy, distribute and modify it. +_ACEOF + exit +fi + +## ------------------------ ## +## Autoconf initialization. ## +## ------------------------ ## + +# ac_fn_c_try_compile LINENO +# -------------------------- +# Try to compile conftest.$ac_ext, and return whether this succeeded. +ac_fn_c_try_compile () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + rm -f conftest.$ac_objext + if { { ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compile") 2>conftest.err + ac_status=$? + if test -s conftest.err; then + grep -v '^ *+' conftest.err >conftest.er1 + cat conftest.er1 >&5 + mv -f conftest.er1 conftest.err + fi + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then : + ac_retval=0 +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_retval=1 +fi + eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno + as_fn_set_status $ac_retval + +} # ac_fn_c_try_compile + +# ac_fn_c_try_link LINENO +# ----------------------- +# Try to link conftest.$ac_ext, and return whether this succeeded. +ac_fn_c_try_link () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + rm -f conftest.$ac_objext conftest$ac_exeext + if { { ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_link") 2>conftest.err + ac_status=$? + if test -s conftest.err; then + grep -v '^ *+' conftest.err >conftest.er1 + cat conftest.er1 >&5 + mv -f conftest.er1 conftest.err + fi + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + test -x conftest$ac_exeext + }; then : + ac_retval=0 +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_retval=1 +fi + # Delete the IPA/IPO (Inter Procedural Analysis/Optimization) information + # created by the PGI compiler (conftest_ipa8_conftest.oo), as it would + # interfere with the next link command; also delete a directory that is + # left behind by Apple's compiler. We do this before executing the actions. + rm -rf conftest.dSYM conftest_ipa8_conftest.oo + eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno + as_fn_set_status $ac_retval + +} # ac_fn_c_try_link + +# ac_fn_c_try_cpp LINENO +# ---------------------- +# Try to preprocess conftest.$ac_ext, and return whether this succeeded. +ac_fn_c_try_cpp () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + if { { ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.err + ac_status=$? + if test -s conftest.err; then + grep -v '^ *+' conftest.err >conftest.er1 + cat conftest.er1 >&5 + mv -f conftest.er1 conftest.err + fi + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } > conftest.i && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then : + ac_retval=0 +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_retval=1 +fi + eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno + as_fn_set_status $ac_retval + +} # ac_fn_c_try_cpp + +# ac_fn_c_check_header_mongrel LINENO HEADER VAR INCLUDES +# ------------------------------------------------------- +# Tests whether HEADER exists, giving a warning if it cannot be compiled using +# the include files in INCLUDES and setting the cache variable VAR +# accordingly. +ac_fn_c_check_header_mongrel () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + if eval \${$3+:} false; then : + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5 +$as_echo_n "checking for $2... " >&6; } +if eval \${$3+:} false; then : + $as_echo_n "(cached) " >&6 +fi +eval ac_res=\$$3 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } +else + # Is the header compilable? +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 usability" >&5 +$as_echo_n "checking $2 usability... " >&6; } +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$4 +#include <$2> +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_header_compiler=yes +else + ac_header_compiler=no +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_compiler" >&5 +$as_echo "$ac_header_compiler" >&6; } + +# Is the header present? +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 presence" >&5 +$as_echo_n "checking $2 presence... " >&6; } +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include <$2> +_ACEOF +if ac_fn_c_try_cpp "$LINENO"; then : + ac_header_preproc=yes +else + ac_header_preproc=no +fi +rm -f conftest.err conftest.i conftest.$ac_ext +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_preproc" >&5 +$as_echo "$ac_header_preproc" >&6; } + +# So? What about this header? +case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in #(( + yes:no: ) + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&5 +$as_echo "$as_me: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5 +$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;} + ;; + no:yes:* ) + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: present but cannot be compiled" >&5 +$as_echo "$as_me: WARNING: $2: present but cannot be compiled" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: check for missing prerequisite headers?" >&5 +$as_echo "$as_me: WARNING: $2: check for missing prerequisite headers?" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: see the Autoconf documentation" >&5 +$as_echo "$as_me: WARNING: $2: see the Autoconf documentation" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&5 +$as_echo "$as_me: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5 +$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;} +( $as_echo "## ------------------------------- ## +## Report this to sean@eddylab.org ## +## ------------------------------- ##" + ) | sed "s/^/$as_me: WARNING: /" >&2 + ;; +esac + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5 +$as_echo_n "checking for $2... " >&6; } +if eval \${$3+:} false; then : + $as_echo_n "(cached) " >&6 +else + eval "$3=\$ac_header_compiler" +fi +eval ac_res=\$$3 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } +fi + eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno + +} # ac_fn_c_check_header_mongrel + +# ac_fn_c_try_run LINENO +# ---------------------- +# Try to link conftest.$ac_ext, and return whether this succeeded. Assumes +# that executables *can* be run. +ac_fn_c_try_run () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + if { { ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_link") 2>&5 + ac_status=$? + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } && { ac_try='./conftest$ac_exeext' + { { case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_try") 2>&5 + ac_status=$? + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; }; }; then : + ac_retval=0 +else + $as_echo "$as_me: program exited with status $ac_status" >&5 + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_retval=$ac_status +fi + rm -rf conftest.dSYM conftest_ipa8_conftest.oo + eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno + as_fn_set_status $ac_retval + +} # ac_fn_c_try_run + +# ac_fn_c_check_header_compile LINENO HEADER VAR INCLUDES +# ------------------------------------------------------- +# Tests whether HEADER exists and can be compiled using the include files in +# INCLUDES, setting the cache variable VAR accordingly. +ac_fn_c_check_header_compile () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5 +$as_echo_n "checking for $2... " >&6; } +if eval \${$3+:} false; then : + $as_echo_n "(cached) " >&6 +else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$4 +#include <$2> +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + eval "$3=yes" +else + eval "$3=no" +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +eval ac_res=\$$3 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } + eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno + +} # ac_fn_c_check_header_compile + +# ac_fn_c_find_uintX_t LINENO BITS VAR +# ------------------------------------ +# Finds an unsigned integer type with width BITS, setting cache variable VAR +# accordingly. +ac_fn_c_find_uintX_t () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for uint$2_t" >&5 +$as_echo_n "checking for uint$2_t... " >&6; } +if eval \${$3+:} false; then : + $as_echo_n "(cached) " >&6 +else + eval "$3=no" + # Order is important - never check a type that is potentially smaller + # than half of the expected target width. + for ac_type in uint$2_t 'unsigned int' 'unsigned long int' \ + 'unsigned long long int' 'unsigned short int' 'unsigned char'; do + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !((($ac_type) -1 >> ($2 / 2 - 1)) >> ($2 / 2 - 1) == 3)]; +test_array [0] = 0; +return test_array [0]; + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + case $ac_type in #( + uint$2_t) : + eval "$3=yes" ;; #( + *) : + eval "$3=\$ac_type" ;; +esac +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + if eval test \"x\$"$3"\" = x"no"; then : + +else + break +fi + done +fi +eval ac_res=\$$3 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } + eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno + +} # ac_fn_c_find_uintX_t + +# ac_fn_c_check_type LINENO TYPE VAR INCLUDES +# ------------------------------------------- +# Tests whether TYPE exists after having included INCLUDES, setting cache +# variable VAR accordingly. +ac_fn_c_check_type () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5 +$as_echo_n "checking for $2... " >&6; } +if eval \${$3+:} false; then : + $as_echo_n "(cached) " >&6 +else + eval "$3=no" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$4 +int +main () +{ +if (sizeof ($2)) + return 0; + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$4 +int +main () +{ +if (sizeof (($2))) + return 0; + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + +else + eval "$3=yes" +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +eval ac_res=\$$3 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } + eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno + +} # ac_fn_c_check_type + +# ac_fn_c_check_func LINENO FUNC VAR +# ---------------------------------- +# Tests whether FUNC exists, setting the cache variable VAR accordingly +ac_fn_c_check_func () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5 +$as_echo_n "checking for $2... " >&6; } +if eval \${$3+:} false; then : + $as_echo_n "(cached) " >&6 +else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +/* Define $2 to an innocuous variant, in case declares $2. + For example, HP-UX 11i declares gettimeofday. */ +#define $2 innocuous_$2 + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char $2 (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef $2 + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char $2 (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined __stub_$2 || defined __stub___$2 +choke me +#endif + +int +main () +{ +return $2 (); + ; + return 0; +} +_ACEOF +if ac_fn_c_try_link "$LINENO"; then : + eval "$3=yes" +else + eval "$3=no" +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +fi +eval ac_res=\$$3 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } + eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno + +} # ac_fn_c_check_func +cat >config.log <<_ACEOF +This file contains any messages produced by compilers while +running configure, to aid debugging if configure makes a mistake. + +It was created by HMMER $as_me 3.3.2, which was +generated by GNU Autoconf 2.69. Invocation command line was + + $ $0 $@ + +_ACEOF +exec 5>>config.log +{ +cat <<_ASUNAME +## --------- ## +## Platform. ## +## --------- ## + +hostname = `(hostname || uname -n) 2>/dev/null | sed 1q` +uname -m = `(uname -m) 2>/dev/null || echo unknown` +uname -r = `(uname -r) 2>/dev/null || echo unknown` +uname -s = `(uname -s) 2>/dev/null || echo unknown` +uname -v = `(uname -v) 2>/dev/null || echo unknown` + +/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null || echo unknown` +/bin/uname -X = `(/bin/uname -X) 2>/dev/null || echo unknown` + +/bin/arch = `(/bin/arch) 2>/dev/null || echo unknown` +/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null || echo unknown` +/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null || echo unknown` +/usr/bin/hostinfo = `(/usr/bin/hostinfo) 2>/dev/null || echo unknown` +/bin/machine = `(/bin/machine) 2>/dev/null || echo unknown` +/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null || echo unknown` +/bin/universe = `(/bin/universe) 2>/dev/null || echo unknown` + +_ASUNAME + +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + $as_echo "PATH: $as_dir" + done +IFS=$as_save_IFS + +} >&5 + +cat >&5 <<_ACEOF + + +## ----------- ## +## Core tests. ## +## ----------- ## + +_ACEOF + + +# Keep a trace of the command line. +# Strip out --no-create and --no-recursion so they do not pile up. +# Strip out --silent because we don't want to record it for future runs. +# Also quote any args containing shell meta-characters. +# Make two passes to allow for proper duplicate-argument suppression. +ac_configure_args= +ac_configure_args0= +ac_configure_args1= +ac_must_keep_next=false +for ac_pass in 1 2 +do + for ac_arg + do + case $ac_arg in + -no-create | --no-c* | -n | -no-recursion | --no-r*) continue ;; + -q | -quiet | --quiet | --quie | --qui | --qu | --q \ + | -silent | --silent | --silen | --sile | --sil) + continue ;; + *\'*) + ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;; + esac + case $ac_pass in + 1) as_fn_append ac_configure_args0 " '$ac_arg'" ;; + 2) + as_fn_append ac_configure_args1 " '$ac_arg'" + if test $ac_must_keep_next = true; then + ac_must_keep_next=false # Got value, back to normal. + else + case $ac_arg in + *=* | --config-cache | -C | -disable-* | --disable-* \ + | -enable-* | --enable-* | -gas | --g* | -nfp | --nf* \ + | -q | -quiet | --q* | -silent | --sil* | -v | -verb* \ + | -with-* | --with-* | -without-* | --without-* | --x) + case "$ac_configure_args0 " in + "$ac_configure_args1"*" '$ac_arg' "* ) continue ;; + esac + ;; + -* ) ac_must_keep_next=true ;; + esac + fi + as_fn_append ac_configure_args " '$ac_arg'" + ;; + esac + done +done +{ ac_configure_args0=; unset ac_configure_args0;} +{ ac_configure_args1=; unset ac_configure_args1;} + +# When interrupted or exit'd, cleanup temporary files, and complete +# config.log. We remove comments because anyway the quotes in there +# would cause problems or look ugly. +# WARNING: Use '\'' to represent an apostrophe within the trap. +# WARNING: Do not start the trap code with a newline, due to a FreeBSD 4.0 bug. +trap 'exit_status=$? + # Save into config.log some information that might help in debugging. + { + echo + + $as_echo "## ---------------- ## +## Cache variables. ## +## ---------------- ##" + echo + # The following way of writing the cache mishandles newlines in values, +( + for ac_var in `(set) 2>&1 | sed -n '\''s/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'\''`; do + eval ac_val=\$$ac_var + case $ac_val in #( + *${as_nl}*) + case $ac_var in #( + *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5 +$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; + esac + case $ac_var in #( + _ | IFS | as_nl) ;; #( + BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #( + *) { eval $ac_var=; unset $ac_var;} ;; + esac ;; + esac + done + (set) 2>&1 | + case $as_nl`(ac_space='\'' '\''; set) 2>&1` in #( + *${as_nl}ac_space=\ *) + sed -n \ + "s/'\''/'\''\\\\'\'''\''/g; + s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\''\\2'\''/p" + ;; #( + *) + sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p" + ;; + esac | + sort +) + echo + + $as_echo "## ----------------- ## +## Output variables. ## +## ----------------- ##" + echo + for ac_var in $ac_subst_vars + do + eval ac_val=\$$ac_var + case $ac_val in + *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;; + esac + $as_echo "$ac_var='\''$ac_val'\''" + done | sort + echo + + if test -n "$ac_subst_files"; then + $as_echo "## ------------------- ## +## File substitutions. ## +## ------------------- ##" + echo + for ac_var in $ac_subst_files + do + eval ac_val=\$$ac_var + case $ac_val in + *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;; + esac + $as_echo "$ac_var='\''$ac_val'\''" + done | sort + echo + fi + + if test -s confdefs.h; then + $as_echo "## ----------- ## +## confdefs.h. ## +## ----------- ##" + echo + cat confdefs.h + echo + fi + test "$ac_signal" != 0 && + $as_echo "$as_me: caught signal $ac_signal" + $as_echo "$as_me: exit $exit_status" + } >&5 + rm -f core *.core core.conftest.* && + rm -f -r conftest* confdefs* conf$$* $ac_clean_files && + exit $exit_status +' 0 +for ac_signal in 1 2 13 15; do + trap 'ac_signal='$ac_signal'; as_fn_exit 1' $ac_signal +done +ac_signal=0 + +# confdefs.h avoids OS command line length limits that DEFS can exceed. +rm -f -r conftest* confdefs.h + +$as_echo "/* confdefs.h */" > confdefs.h + +# Predefined preprocessor variables. + +cat >>confdefs.h <<_ACEOF +#define PACKAGE_NAME "$PACKAGE_NAME" +_ACEOF + +cat >>confdefs.h <<_ACEOF +#define PACKAGE_TARNAME "$PACKAGE_TARNAME" +_ACEOF + +cat >>confdefs.h <<_ACEOF +#define PACKAGE_VERSION "$PACKAGE_VERSION" +_ACEOF + +cat >>confdefs.h <<_ACEOF +#define PACKAGE_STRING "$PACKAGE_STRING" +_ACEOF + +cat >>confdefs.h <<_ACEOF +#define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT" +_ACEOF + +cat >>confdefs.h <<_ACEOF +#define PACKAGE_URL "$PACKAGE_URL" +_ACEOF + + +# Let the site file select an alternate cache file if it wants to. +# Prefer an explicitly selected file to automatically selected ones. +ac_site_file1=NONE +ac_site_file2=NONE +if test -n "$CONFIG_SITE"; then + # We do not want a PATH search for config.site. + case $CONFIG_SITE in #(( + -*) ac_site_file1=./$CONFIG_SITE;; + */*) ac_site_file1=$CONFIG_SITE;; + *) ac_site_file1=./$CONFIG_SITE;; + esac +elif test "x$prefix" != xNONE; then + ac_site_file1=$prefix/share/config.site + ac_site_file2=$prefix/etc/config.site +else + ac_site_file1=$ac_default_prefix/share/config.site + ac_site_file2=$ac_default_prefix/etc/config.site +fi +for ac_site_file in "$ac_site_file1" "$ac_site_file2" +do + test "x$ac_site_file" = xNONE && continue + if test /dev/null != "$ac_site_file" && test -r "$ac_site_file"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5 +$as_echo "$as_me: loading site script $ac_site_file" >&6;} + sed 's/^/| /' "$ac_site_file" >&5 + . "$ac_site_file" \ + || { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error $? "failed to load site script $ac_site_file +See \`config.log' for more details" "$LINENO" 5; } + fi +done + +if test -r "$cache_file"; then + # Some versions of bash will fail to source /dev/null (special files + # actually), so we avoid doing that. DJGPP emulates it as a regular file. + if test /dev/null != "$cache_file" && test -f "$cache_file"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: loading cache $cache_file" >&5 +$as_echo "$as_me: loading cache $cache_file" >&6;} + case $cache_file in + [\\/]* | ?:[\\/]* ) . "$cache_file";; + *) . "./$cache_file";; + esac + fi +else + { $as_echo "$as_me:${as_lineno-$LINENO}: creating cache $cache_file" >&5 +$as_echo "$as_me: creating cache $cache_file" >&6;} + >$cache_file +fi + +# Check that the precious variables saved in the cache have kept the same +# value. +ac_cache_corrupted=false +for ac_var in $ac_precious_vars; do + eval ac_old_set=\$ac_cv_env_${ac_var}_set + eval ac_new_set=\$ac_env_${ac_var}_set + eval ac_old_val=\$ac_cv_env_${ac_var}_value + eval ac_new_val=\$ac_env_${ac_var}_value + case $ac_old_set,$ac_new_set in + set,) + { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5 +$as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;} + ac_cache_corrupted=: ;; + ,set) + { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5 +$as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;} + ac_cache_corrupted=: ;; + ,);; + *) + if test "x$ac_old_val" != "x$ac_new_val"; then + # differences in whitespace do not lead to failure. + ac_old_val_w=`echo x $ac_old_val` + ac_new_val_w=`echo x $ac_new_val` + if test "$ac_old_val_w" != "$ac_new_val_w"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5 +$as_echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;} + ac_cache_corrupted=: + else + { $as_echo "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5 +$as_echo "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;} + eval $ac_var=\$ac_old_val + fi + { $as_echo "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5 +$as_echo "$as_me: former value: \`$ac_old_val'" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5 +$as_echo "$as_me: current value: \`$ac_new_val'" >&2;} + fi;; + esac + # Pass precious variables to config.status. + if test "$ac_new_set" = set; then + case $ac_new_val in + *\'*) ac_arg=$ac_var=`$as_echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;; + *) ac_arg=$ac_var=$ac_new_val ;; + esac + case " $ac_configure_args " in + *" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy. + *) as_fn_append ac_configure_args " '$ac_arg'" ;; + esac + fi +done +if $ac_cache_corrupted; then + { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5 +$as_echo "$as_me: error: changes in the environment can compromise the build" >&2;} + as_fn_error $? "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5 +fi +## -------------------- ## +## Main body of script. ## +## -------------------- ## + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + + +{ $as_echo "$as_me:${as_lineno-$LINENO}: Configuring HMMER3 for your system." >&5 +$as_echo "$as_me: Configuring HMMER3 for your system." >&6;} + +################################################################ +# 3. Info on the package +################################################################ +# +# AC_INIT args set these output variables and preprocessor symbols: +# PACKAGE_NAME e.g. "HMMER" +# PACKAGE_VERSION e.g. "3.2" +# PACKAGE_BUGREPORT e.g. "sean@eddylab.org" +# PACKAGE_TARNAME e.g. "hmmer" +# From them, AC_INIT automatically derives one more: +# PACKAGE_STRING , e.g. "HMMER 3.2" +# and we define additional output variables of our own: +# HMMER_DATE release date: e.g. "August 2017" +# HMMER_COPYRIGHT one-line copyright string +# HMMER_LICENSE one-line license string +# HMMER_VERSION copy of version code, e.g. "3.2" +# HMMER_URL URL home for HMMER. +# And we have to define the relevant package variables for Easel as well. +# +# We avoid using AC_INIT's PACKAGE_ variables anywhere, because we want to be able +# to use HMMER as a library inside other packages, with no name clashes. +################################################################ + +HMMER_DATE="Nov 2020" +HMMER_COPYRIGHT="Copyright (C) 2020 Howard Hughes Medical Institute." +HMMER_LICENSE="Freely distributed under the BSD open source license." +HMMER_VERSION=$PACKAGE_VERSION +HMMER_URL="http://hmmer.org/" + +HMMER_ESLDIR="easel" +HMMER_SADIR="libdivsufsort" + +EASEL_DATE="Nov 2020" +EASEL_COPYRIGHT="Copyright (C) 2020 Howard Hughes Medical Institute." +EASEL_LICENSE="Freely distributed under the BSD open source license." +EASEL_VERSION="0.48" +EASEL_URL="http://bioeasel.org/" + + + + + + + + + + + + + + + + + +cat >>confdefs.h <<_ACEOF +#define HMMER_DATE "$HMMER_DATE" +_ACEOF + + +cat >>confdefs.h <<_ACEOF +#define HMMER_COPYRIGHT "$HMMER_COPYRIGHT" +_ACEOF + + +cat >>confdefs.h <<_ACEOF +#define HMMER_LICENSE "$HMMER_LICENSE" +_ACEOF + + +cat >>confdefs.h <<_ACEOF +#define HMMER_VERSION "$HMMER_VERSION" +_ACEOF + + +cat >>confdefs.h <<_ACEOF +#define HMMER_URL "$HMMER_URL" +_ACEOF + + + +cat >>confdefs.h <<_ACEOF +#define EASEL_DATE "$EASEL_DATE" +_ACEOF + + +cat >>confdefs.h <<_ACEOF +#define EASEL_COPYRIGHT "$EASEL_COPYRIGHT" +_ACEOF + + +cat >>confdefs.h <<_ACEOF +#define EASEL_LICENSE "$EASEL_LICENSE" +_ACEOF + + +cat >>confdefs.h <<_ACEOF +#define EASEL_VERSION "$EASEL_VERSION" +_ACEOF + + +cat >>confdefs.h <<_ACEOF +#define EASEL_URL "$EASEL_URL" +_ACEOF + + + +# Figure out what host we're compiling on. +# Three GNU scripts must be included in the distro: +# install.sh, config.guess, config.sub +# This sets four shell variables: +# host example: i686-pc-linux-gnu +# host_cpu example: i686 +# host_vendor example: pc +# host_os example: linux-gnu +ac_aux_dir= +for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do + if test -f "$ac_dir/install-sh"; then + ac_aux_dir=$ac_dir + ac_install_sh="$ac_aux_dir/install-sh -c" + break + elif test -f "$ac_dir/install.sh"; then + ac_aux_dir=$ac_dir + ac_install_sh="$ac_aux_dir/install.sh -c" + break + elif test -f "$ac_dir/shtool"; then + ac_aux_dir=$ac_dir + ac_install_sh="$ac_aux_dir/shtool install -c" + break + fi +done +if test -z "$ac_aux_dir"; then + as_fn_error $? "cannot find install-sh, install.sh, or shtool in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" "$LINENO" 5 +fi + +# These three variables are undocumented and unsupported, +# and are intended to be withdrawn in a future Autoconf release. +# They can cause serious problems if a builder's source tree is in a directory +# whose full name contains unusual characters. +ac_config_guess="$SHELL $ac_aux_dir/config.guess" # Please don't use this var. +ac_config_sub="$SHELL $ac_aux_dir/config.sub" # Please don't use this var. +ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var. + + +# Make sure we can run config.sub. +$SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 || + as_fn_error $? "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5 + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking build system type" >&5 +$as_echo_n "checking build system type... " >&6; } +if ${ac_cv_build+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_build_alias=$build_alias +test "x$ac_build_alias" = x && + ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"` +test "x$ac_build_alias" = x && + as_fn_error $? "cannot guess build type; you must specify one" "$LINENO" 5 +ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` || + as_fn_error $? "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5 + +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_build" >&5 +$as_echo "$ac_cv_build" >&6; } +case $ac_cv_build in +*-*-*) ;; +*) as_fn_error $? "invalid value of canonical build" "$LINENO" 5;; +esac +build=$ac_cv_build +ac_save_IFS=$IFS; IFS='-' +set x $ac_cv_build +shift +build_cpu=$1 +build_vendor=$2 +shift; shift +# Remember, the first character of IFS is used to create $*, +# except with old shells: +build_os=$* +IFS=$ac_save_IFS +case $build_os in *\ *) build_os=`echo "$build_os" | sed 's/ /-/g'`;; esac + + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking host system type" >&5 +$as_echo_n "checking host system type... " >&6; } +if ${ac_cv_host+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test "x$host_alias" = x; then + ac_cv_host=$ac_cv_build +else + ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` || + as_fn_error $? "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5 +fi + +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_host" >&5 +$as_echo "$ac_cv_host" >&6; } +case $ac_cv_host in +*-*-*) ;; +*) as_fn_error $? "invalid value of canonical host" "$LINENO" 5;; +esac +host=$ac_cv_host +ac_save_IFS=$IFS; IFS='-' +set x $ac_cv_host +shift +host_cpu=$1 +host_vendor=$2 +shift; shift +# Remember, the first character of IFS is used to create $*, +# except with old shells: +host_os=$* +IFS=$ac_save_IFS +case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac + + + + + + +################################################################ +# 4. Process the ./configure command line +################################################################ + +# --enable-debugging - set basic debugging (level 0) +# --enable-debugging=x - set debugging level to (1-3) +# +# At all levels, including 0, replaces CFLAGS w/ "-g -Wall" (so it assumes gcc). +# Sets eslDEBUGLEVEL preprocessor symbol, which compiles in debugging support, to 0..3. +# +# Check whether --enable-debugging was given. +if test "${enable_debugging+set}" = set; then : + enableval=$enable_debugging; enable_debugging=$enableval +else + enable_debugging=no +fi + + +case $enable_debugging in + yes) +$as_echo "#define eslDEBUGLEVEL 1" >>confdefs.h +;; + 1) +$as_echo "#define eslDEBUGLEVEL 1" >>confdefs.h +;; + 2) +$as_echo "#define eslDEBUGLEVEL 2" >>confdefs.h +;; + 3) +$as_echo "#define eslDEBUGLEVEL 3" >>confdefs.h +;; + no) +$as_echo "#define eslDEBUGLEVEL 0" >>confdefs.h +;; + *) as_fn_error $? "Unknown argument to --enable-debugging: $enable_debugging" "$LINENO" 5;; +esac + + +# Check whether --enable-gcov was given. +if test "${enable_gcov+set}" = set; then : + enableval=$enable_gcov; enable_gcov=$enableval +else + enable_gcov=no +fi + +# Check whether --enable-gprof was given. +if test "${enable_gprof+set}" = set; then : + enableval=$enable_gprof; enable_gprof=$enableval +else + enable_gprof=no +fi + + +# Check whether --enable-sse was given. +if test "${enable_sse+set}" = set; then : + enableval=$enable_sse; enable_sse=$enableval +else + enable_sse=check +fi + +# Check whether --enable-vmx was given. +if test "${enable_vmx+set}" = set; then : + enableval=$enable_vmx; enable_vmx=$enableval +else + enable_vmx=check +fi + + +# Check whether --enable-threads was given. +if test "${enable_threads+set}" = set; then : + enableval=$enable_threads; enable_threads=$enableval +else + enable_threads=check +fi + +# Check whether --enable-mpi was given. +if test "${enable_mpi+set}" = set; then : + enableval=$enable_mpi; enable_mpi=$enableval +else + enable_mpi=no +fi + + +# Check whether --enable-pic was given. +if test "${enable_pic+set}" = set; then : + enableval=$enable_pic; enable_pic=$enableval +else + enable_pic=no +fi + + + +# Check whether --with-gsl was given. +if test "${with_gsl+set}" = set; then : + withval=$with_gsl; with_gsl=$withval +else + with_gsl=no +fi + + + + + +# If a vector implementation is force-selected, make sure only one is, +# and turn off checking for the others. +vecsel=0 +if test "$enable_sse" = "yes"; then vecsel=$((vecsel+1)); fi +if test "$enable_vmx" = "yes"; then vecsel=$((vecsel+1)); fi +if [ $vecsel -gt 1 ]; then + as_fn_error $? "Select only one implementation: sse or vmx" "$LINENO" 5 +elif [ $vecsel -eq 1 ]; then + if test "$enable_sse" = "check"; then enable_sse="no"; fi + if test "$enable_vmx" = "check"; then enable_vmx="no"; fi +fi + + +################################################################ +# 5. Checks for programs, including ${CC} and ${CFLAGS}. +################################################################ + +# Choose our compiler - which might be mpicc, if enable_mpi is "yes". +# AX_PROG_CC_MPI will call AC_PROG_CC if enable_mpi is "no". +# +# If CFLAGS hasn't been set by the user, set it to an empty string +# in the environment. This prevents AC_PROG_CC from setting it to +# "-g -O2" or "-g". Some of our --enable-* options will add to CFLAGS. +# +# The `: ${CFLAGS=""}` shell syntax uses the null operator `:` to +# discard the output of `${CFLAGS=""}`, which returns the value of +# CFLAGS if already set. +# +: ${CFLAGS=""} + + + + { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether to compile using MPI" >&5 +$as_echo_n "checking whether to compile using MPI... " >&6; } + if test x"$enable_mpi" = xyes; then + _ax_prog_cc_mpi_mpi_wanted=yes + else + _ax_prog_cc_mpi_mpi_wanted=no + fi + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $_ax_prog_cc_mpi_mpi_wanted" >&5 +$as_echo "$_ax_prog_cc_mpi_mpi_wanted" >&6; } + + if test x"$_ax_prog_cc_mpi_mpi_wanted" = xyes; then + if test -z "$CC" && test -n "$MPICC"; then + CC="$MPICC" + else + if test -n "$ac_tool_prefix"; then + for ac_prog in mpicc mpixlc_r mpixlc hcc mpxlc_r mpxlc sxmpicc mpifcc mpgcc mpcc cmpicc cc gcc + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. +set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_CC+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CC="$ac_tool_prefix$ac_prog" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 +$as_echo "$CC" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + + test -n "$CC" && break + done +fi +if test -z "$CC"; then + ac_ct_CC=$CC + for ac_prog in mpicc mpixlc_r mpixlc hcc mpxlc_r mpxlc sxmpicc mpifcc mpgcc mpcc cmpicc cc gcc +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_ac_ct_CC+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CC="$ac_prog" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5 +$as_echo "$ac_ct_CC" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + + test -n "$ac_ct_CC" && break +done + + if test "x$ac_ct_CC" = x; then + CC="" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + CC=$ac_ct_CC + fi +fi + + fi + fi + ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu +if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args. +set dummy ${ac_tool_prefix}gcc; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_CC+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CC="${ac_tool_prefix}gcc" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 +$as_echo "$CC" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + +fi +if test -z "$ac_cv_prog_CC"; then + ac_ct_CC=$CC + # Extract the first word of "gcc", so it can be a program name with args. +set dummy gcc; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_ac_ct_CC+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CC="gcc" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5 +$as_echo "$ac_ct_CC" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + if test "x$ac_ct_CC" = x; then + CC="" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + CC=$ac_ct_CC + fi +else + CC="$ac_cv_prog_CC" +fi + +if test -z "$CC"; then + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args. +set dummy ${ac_tool_prefix}cc; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_CC+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CC="${ac_tool_prefix}cc" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 +$as_echo "$CC" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + + fi +fi +if test -z "$CC"; then + # Extract the first word of "cc", so it can be a program name with args. +set dummy cc; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_CC+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else + ac_prog_rejected=no +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then + ac_prog_rejected=yes + continue + fi + ac_cv_prog_CC="cc" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +if test $ac_prog_rejected = yes; then + # We found a bogon in the path, so make sure we never use it. + set dummy $ac_cv_prog_CC + shift + if test $# != 0; then + # We chose a different compiler from the bogus one. + # However, it has the same basename, so the bogon will be chosen + # first if we set CC to just the basename; use the full file name. + shift + ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@" + fi +fi +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 +$as_echo "$CC" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + +fi +if test -z "$CC"; then + if test -n "$ac_tool_prefix"; then + for ac_prog in cl.exe + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. +set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_CC+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CC="$ac_tool_prefix$ac_prog" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 +$as_echo "$CC" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + + test -n "$CC" && break + done +fi +if test -z "$CC"; then + ac_ct_CC=$CC + for ac_prog in cl.exe +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_ac_ct_CC+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CC="$ac_prog" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5 +$as_echo "$ac_ct_CC" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + + test -n "$ac_ct_CC" && break +done + + if test "x$ac_ct_CC" = x; then + CC="" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + CC=$ac_ct_CC + fi +fi + +fi + + +test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error $? "no acceptable C compiler found in \$PATH +See \`config.log' for more details" "$LINENO" 5; } + +# Provide some information about the compiler. +$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5 +set X $ac_compile +ac_compiler=$2 +for ac_option in --version -v -V -qversion; do + { { ac_try="$ac_compiler $ac_option >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compiler $ac_option >&5") 2>conftest.err + ac_status=$? + if test -s conftest.err; then + sed '10a\ +... rest of stderr output deleted ... + 10q' conftest.err >conftest.er1 + cat conftest.er1 >&5 + fi + rm -f conftest.er1 conftest.err + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } +done + +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +ac_clean_files_save=$ac_clean_files +ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out" +# Try to create an executable without -o first, disregard a.out. +# It will help us diagnose broken compilers, and finding out an intuition +# of exeext. +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler works" >&5 +$as_echo_n "checking whether the C compiler works... " >&6; } +ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'` + +# The possible output files: +ac_files="a.out conftest.exe conftest a.exe a_out.exe b.out conftest.*" + +ac_rmfiles= +for ac_file in $ac_files +do + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;; + * ) ac_rmfiles="$ac_rmfiles $ac_file";; + esac +done +rm -f $ac_rmfiles + +if { { ac_try="$ac_link_default" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_link_default") 2>&5 + ac_status=$? + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; }; then : + # Autoconf-2.13 could set the ac_cv_exeext variable to `no'. +# So ignore a value of `no', otherwise this would lead to `EXEEXT = no' +# in a Makefile. We should not override ac_cv_exeext if it was cached, +# so that the user can short-circuit this test for compilers unknown to +# Autoconf. +for ac_file in $ac_files '' +do + test -f "$ac_file" || continue + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) + ;; + [ab].out ) + # We found the default executable, but exeext='' is most + # certainly right. + break;; + *.* ) + if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no; + then :; else + ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` + fi + # We set ac_cv_exeext here because the later test for it is not + # safe: cross compilers may not add the suffix if given an `-o' + # argument, so we may need to know it at that point already. + # Even if this section looks crufty: it has the advantage of + # actually working. + break;; + * ) + break;; + esac +done +test "$ac_cv_exeext" = no && ac_cv_exeext= + +else + ac_file='' +fi +if test -z "$ac_file"; then : + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +$as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error 77 "C compiler cannot create executables +See \`config.log' for more details" "$LINENO" 5; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +$as_echo "yes" >&6; } +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler default output file name" >&5 +$as_echo_n "checking for C compiler default output file name... " >&6; } +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_file" >&5 +$as_echo "$ac_file" >&6; } +ac_exeext=$ac_cv_exeext + +rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out +ac_clean_files=$ac_clean_files_save +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of executables" >&5 +$as_echo_n "checking for suffix of executables... " >&6; } +if { { ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_link") 2>&5 + ac_status=$? + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; }; then : + # If both `conftest.exe' and `conftest' are `present' (well, observable) +# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will +# work properly (i.e., refer to `conftest.exe'), while it won't with +# `rm'. +for ac_file in conftest.exe conftest conftest.*; do + test -f "$ac_file" || continue + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;; + *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` + break;; + * ) break;; + esac +done +else + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error $? "cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details" "$LINENO" 5; } +fi +rm -f conftest conftest$ac_cv_exeext +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5 +$as_echo "$ac_cv_exeext" >&6; } + +rm -f conftest.$ac_ext +EXEEXT=$ac_cv_exeext +ac_exeext=$EXEEXT +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include +int +main () +{ +FILE *f = fopen ("conftest.out", "w"); + return ferror (f) || fclose (f) != 0; + + ; + return 0; +} +_ACEOF +ac_clean_files="$ac_clean_files conftest.out" +# Check that the compiler produces executables we can run. If not, either +# the compiler is broken, or we cross compile. +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5 +$as_echo_n "checking whether we are cross compiling... " >&6; } +if test "$cross_compiling" != yes; then + { { ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_link") 2>&5 + ac_status=$? + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } + if { ac_try='./conftest$ac_cv_exeext' + { { case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_try") 2>&5 + ac_status=$? + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; }; }; then + cross_compiling=no + else + if test "$cross_compiling" = maybe; then + cross_compiling=yes + else + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error $? "cannot run C compiled programs. +If you meant to cross compile, use \`--host'. +See \`config.log' for more details" "$LINENO" 5; } + fi + fi +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5 +$as_echo "$cross_compiling" >&6; } + +rm -f conftest.$ac_ext conftest$ac_cv_exeext conftest.out +ac_clean_files=$ac_clean_files_save +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5 +$as_echo_n "checking for suffix of object files... " >&6; } +if ${ac_cv_objext+:} false; then : + $as_echo_n "(cached) " >&6 +else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.o conftest.obj +if { { ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compile") 2>&5 + ac_status=$? + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; }; then : + for ac_file in conftest.o conftest.obj conftest.*; do + test -f "$ac_file" || continue; + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM ) ;; + *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'` + break;; + esac +done +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error $? "cannot compute suffix of object files: cannot compile +See \`config.log' for more details" "$LINENO" 5; } +fi +rm -f conftest.$ac_cv_objext conftest.$ac_ext +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_objext" >&5 +$as_echo "$ac_cv_objext" >&6; } +OBJEXT=$ac_cv_objext +ac_objext=$OBJEXT +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5 +$as_echo_n "checking whether we are using the GNU C compiler... " >&6; } +if ${ac_cv_c_compiler_gnu+:} false; then : + $as_echo_n "(cached) " >&6 +else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ +#ifndef __GNUC__ + choke me +#endif + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_compiler_gnu=yes +else + ac_compiler_gnu=no +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +ac_cv_c_compiler_gnu=$ac_compiler_gnu + +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5 +$as_echo "$ac_cv_c_compiler_gnu" >&6; } +if test $ac_compiler_gnu = yes; then + GCC=yes +else + GCC= +fi +ac_test_CFLAGS=${CFLAGS+set} +ac_save_CFLAGS=$CFLAGS +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5 +$as_echo_n "checking whether $CC accepts -g... " >&6; } +if ${ac_cv_prog_cc_g+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_save_c_werror_flag=$ac_c_werror_flag + ac_c_werror_flag=yes + ac_cv_prog_cc_g=no + CFLAGS="-g" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_prog_cc_g=yes +else + CFLAGS="" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + +else + ac_c_werror_flag=$ac_save_c_werror_flag + CFLAGS="-g" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_prog_cc_g=yes +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + ac_c_werror_flag=$ac_save_c_werror_flag +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5 +$as_echo "$ac_cv_prog_cc_g" >&6; } +if test "$ac_test_CFLAGS" = set; then + CFLAGS=$ac_save_CFLAGS +elif test $ac_cv_prog_cc_g = yes; then + if test "$GCC" = yes; then + CFLAGS="-g -O2" + else + CFLAGS="-g" + fi +else + if test "$GCC" = yes; then + CFLAGS="-O2" + else + CFLAGS= + fi +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5 +$as_echo_n "checking for $CC option to accept ISO C89... " >&6; } +if ${ac_cv_prog_cc_c89+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_cv_prog_cc_c89=no +ac_save_CC=$CC +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include +#include +struct stat; +/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */ +struct buf { int x; }; +FILE * (*rcsopen) (struct buf *, struct stat *, int); +static char *e (p, i) + char **p; + int i; +{ + return p[i]; +} +static char *f (char * (*g) (char **, int), char **p, ...) +{ + char *s; + va_list v; + va_start (v,p); + s = g (p, va_arg (v,int)); + va_end (v); + return s; +} + +/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has + function prototypes and stuff, but not '\xHH' hex character constants. + These don't provoke an error unfortunately, instead are silently treated + as 'x'. The following induces an error, until -std is added to get + proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an + array size at least. It's necessary to write '\x00'==0 to get something + that's true only with -std. */ +int osf4_cc_array ['\x00' == 0 ? 1 : -1]; + +/* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters + inside strings and character constants. */ +#define FOO(x) 'x' +int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1]; + +int test (int i, double x); +struct s1 {int (*f) (int a);}; +struct s2 {int (*f) (double a);}; +int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int); +int argc; +char **argv; +int +main () +{ +return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1]; + ; + return 0; +} +_ACEOF +for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \ + -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" +do + CC="$ac_save_CC $ac_arg" + if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_prog_cc_c89=$ac_arg +fi +rm -f core conftest.err conftest.$ac_objext + test "x$ac_cv_prog_cc_c89" != "xno" && break +done +rm -f conftest.$ac_ext +CC=$ac_save_CC + +fi +# AC_CACHE_VAL +case "x$ac_cv_prog_cc_c89" in + x) + { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5 +$as_echo "none needed" >&6; } ;; + xno) + { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5 +$as_echo "unsupported" >&6; } ;; + *) + CC="$CC $ac_cv_prog_cc_c89" + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5 +$as_echo "$ac_cv_prog_cc_c89" >&6; } ;; +esac +if test "x$ac_cv_prog_cc_c89" != xno; then : + +fi + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + + + + + + +# Check for compiler +# Needs to be split off into an extra macro to ensure right expansion +# order. + + +if test x"$_ax_prog_cc_mpi_mpi_wanted" = xno; then : + _ax_prog_cc_mpi_mpi_found=no +else + + ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + + # test whether MPI_Init is available + # We do not use AC_SEARCH_LIBS here, as it caches its outcome and + # thus disallows corresponding calls in the other AX_PROG_*_MPI + # macros. + for lib in NONE mpi mpich; do + save_LIBS=$LIBS + if test x"$lib" = xNONE; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for function MPI_Init" >&5 +$as_echo_n "checking for function MPI_Init... " >&6; } + else + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for function MPI_Init in -l$lib" >&5 +$as_echo_n "checking for function MPI_Init in -l$lib... " >&6; } + LIBS="-l$lib $LIBS" + fi + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char MPI_Init (); +int +main () +{ +return MPI_Init (); + ; + return 0; +} +_ACEOF +if ac_fn_c_try_link "$LINENO"; then : + _ax_prog_cc_mpi_mpi_found=yes +else + _ax_prog_cc_mpi_mpi_found=no +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $_ax_prog_cc_mpi_mpi_found" >&5 +$as_echo "$_ax_prog_cc_mpi_mpi_found" >&6; } + if test "x$_ax_prog_cc_mpi_mpi_found" = "xyes"; then + break; + fi + LIBS=$save_LIBS + done + + # Check for header + if test x"$_ax_prog_cc_mpi_mpi_found" = xyes; then : + + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for mpi.h" >&5 +$as_echo_n "checking for mpi.h... " >&6; } + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +$as_echo "yes" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } + _ax_prog_cc_mpi_mpi_found=no + +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + +fi + ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + + +fi + +# Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND: +if test x"$_ax_prog_cc_mpi_mpi_found" = xyes; then : + + + +$as_echo "#define HAVE_MPI 1" >>confdefs.h + + +$as_echo "#define HMMER_MPI 1" >>confdefs.h + + MPI_UTESTS="mpi_utest" + + MPI_BENCHMARKS="mpi_benchmark" + + + : + +else + + + if test x"$enable_mpi" = xyes; then + as_fn_error $? "MPI library not found for --enable-mpi" "$LINENO" 5; + fi + + : + +fi + + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu +if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args. +set dummy ${ac_tool_prefix}gcc; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_CC+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CC="${ac_tool_prefix}gcc" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 +$as_echo "$CC" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + +fi +if test -z "$ac_cv_prog_CC"; then + ac_ct_CC=$CC + # Extract the first word of "gcc", so it can be a program name with args. +set dummy gcc; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_ac_ct_CC+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CC="gcc" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5 +$as_echo "$ac_ct_CC" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + if test "x$ac_ct_CC" = x; then + CC="" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + CC=$ac_ct_CC + fi +else + CC="$ac_cv_prog_CC" +fi + +if test -z "$CC"; then + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args. +set dummy ${ac_tool_prefix}cc; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_CC+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CC="${ac_tool_prefix}cc" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 +$as_echo "$CC" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + + fi +fi +if test -z "$CC"; then + # Extract the first word of "cc", so it can be a program name with args. +set dummy cc; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_CC+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else + ac_prog_rejected=no +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then + ac_prog_rejected=yes + continue + fi + ac_cv_prog_CC="cc" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +if test $ac_prog_rejected = yes; then + # We found a bogon in the path, so make sure we never use it. + set dummy $ac_cv_prog_CC + shift + if test $# != 0; then + # We chose a different compiler from the bogus one. + # However, it has the same basename, so the bogon will be chosen + # first if we set CC to just the basename; use the full file name. + shift + ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@" + fi +fi +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 +$as_echo "$CC" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + +fi +if test -z "$CC"; then + if test -n "$ac_tool_prefix"; then + for ac_prog in cl.exe + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. +set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_CC+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_CC="$ac_tool_prefix$ac_prog" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 +$as_echo "$CC" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + + test -n "$CC" && break + done +fi +if test -z "$CC"; then + ac_ct_CC=$CC + for ac_prog in cl.exe +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_ac_ct_CC+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_CC="$ac_prog" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5 +$as_echo "$ac_ct_CC" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + + test -n "$ac_ct_CC" && break +done + + if test "x$ac_ct_CC" = x; then + CC="" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + CC=$ac_ct_CC + fi +fi + +fi + + +test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error $? "no acceptable C compiler found in \$PATH +See \`config.log' for more details" "$LINENO" 5; } + +# Provide some information about the compiler. +$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5 +set X $ac_compile +ac_compiler=$2 +for ac_option in --version -v -V -qversion; do + { { ac_try="$ac_compiler $ac_option >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compiler $ac_option >&5") 2>conftest.err + ac_status=$? + if test -s conftest.err; then + sed '10a\ +... rest of stderr output deleted ... + 10q' conftest.err >conftest.er1 + cat conftest.er1 >&5 + fi + rm -f conftest.er1 conftest.err + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } +done + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5 +$as_echo_n "checking whether we are using the GNU C compiler... " >&6; } +if ${ac_cv_c_compiler_gnu+:} false; then : + $as_echo_n "(cached) " >&6 +else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ +#ifndef __GNUC__ + choke me +#endif + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_compiler_gnu=yes +else + ac_compiler_gnu=no +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +ac_cv_c_compiler_gnu=$ac_compiler_gnu + +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5 +$as_echo "$ac_cv_c_compiler_gnu" >&6; } +if test $ac_compiler_gnu = yes; then + GCC=yes +else + GCC= +fi +ac_test_CFLAGS=${CFLAGS+set} +ac_save_CFLAGS=$CFLAGS +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5 +$as_echo_n "checking whether $CC accepts -g... " >&6; } +if ${ac_cv_prog_cc_g+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_save_c_werror_flag=$ac_c_werror_flag + ac_c_werror_flag=yes + ac_cv_prog_cc_g=no + CFLAGS="-g" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_prog_cc_g=yes +else + CFLAGS="" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + +else + ac_c_werror_flag=$ac_save_c_werror_flag + CFLAGS="-g" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_prog_cc_g=yes +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + ac_c_werror_flag=$ac_save_c_werror_flag +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5 +$as_echo "$ac_cv_prog_cc_g" >&6; } +if test "$ac_test_CFLAGS" = set; then + CFLAGS=$ac_save_CFLAGS +elif test $ac_cv_prog_cc_g = yes; then + if test "$GCC" = yes; then + CFLAGS="-g -O2" + else + CFLAGS="-g" + fi +else + if test "$GCC" = yes; then + CFLAGS="-O2" + else + CFLAGS= + fi +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5 +$as_echo_n "checking for $CC option to accept ISO C89... " >&6; } +if ${ac_cv_prog_cc_c89+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_cv_prog_cc_c89=no +ac_save_CC=$CC +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include +#include +struct stat; +/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */ +struct buf { int x; }; +FILE * (*rcsopen) (struct buf *, struct stat *, int); +static char *e (p, i) + char **p; + int i; +{ + return p[i]; +} +static char *f (char * (*g) (char **, int), char **p, ...) +{ + char *s; + va_list v; + va_start (v,p); + s = g (p, va_arg (v,int)); + va_end (v); + return s; +} + +/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has + function prototypes and stuff, but not '\xHH' hex character constants. + These don't provoke an error unfortunately, instead are silently treated + as 'x'. The following induces an error, until -std is added to get + proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an + array size at least. It's necessary to write '\x00'==0 to get something + that's true only with -std. */ +int osf4_cc_array ['\x00' == 0 ? 1 : -1]; + +/* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters + inside strings and character constants. */ +#define FOO(x) 'x' +int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1]; + +int test (int i, double x); +struct s1 {int (*f) (int a);}; +struct s2 {int (*f) (double a);}; +int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int); +int argc; +char **argv; +int +main () +{ +return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1]; + ; + return 0; +} +_ACEOF +for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \ + -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" +do + CC="$ac_save_CC $ac_arg" + if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_prog_cc_c89=$ac_arg +fi +rm -f core conftest.err conftest.$ac_objext + test "x$ac_cv_prog_cc_c89" != "xno" && break +done +rm -f conftest.$ac_ext +CC=$ac_save_CC + +fi +# AC_CACHE_VAL +case "x$ac_cv_prog_cc_c89" in + x) + { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5 +$as_echo "none needed" >&6; } ;; + xno) + { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5 +$as_echo "unsupported" >&6; } ;; + *) + CC="$CC $ac_cv_prog_cc_c89" + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5 +$as_echo "$ac_cv_prog_cc_c89" >&6; } ;; +esac +if test "x$ac_cv_prog_cc_c89" != xno; then : + +fi + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C preprocessor" >&5 +$as_echo_n "checking how to run the C preprocessor... " >&6; } +# On Suns, sometimes $CPP names a directory. +if test -n "$CPP" && test -d "$CPP"; then + CPP= +fi +if test -z "$CPP"; then + if ${ac_cv_prog_CPP+:} false; then : + $as_echo_n "(cached) " >&6 +else + # Double quotes because CPP needs to be expanded + for CPP in "$CC -E" "$CC -E -traditional-cpp" "/lib/cpp" + do + ac_preproc_ok=false +for ac_c_preproc_warn_flag in '' yes +do + # Use a header file that comes with gcc, so configuring glibc + # with a fresh cross-compiler works. + # Prefer to if __STDC__ is defined, since + # exists even on freestanding compilers. + # On the NeXT, cc -E runs the code through the compiler's parser, + # not just through cpp. "Syntax error" is here to catch this case. + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#ifdef __STDC__ +# include +#else +# include +#endif + Syntax error +_ACEOF +if ac_fn_c_try_cpp "$LINENO"; then : + +else + # Broken: fails on valid input. +continue +fi +rm -f conftest.err conftest.i conftest.$ac_ext + + # OK, works on sane cases. Now check whether nonexistent headers + # can be detected and how. + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include +_ACEOF +if ac_fn_c_try_cpp "$LINENO"; then : + # Broken: success on invalid input. +continue +else + # Passes both tests. +ac_preproc_ok=: +break +fi +rm -f conftest.err conftest.i conftest.$ac_ext + +done +# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. +rm -f conftest.i conftest.err conftest.$ac_ext +if $ac_preproc_ok; then : + break +fi + + done + ac_cv_prog_CPP=$CPP + +fi + CPP=$ac_cv_prog_CPP +else + ac_cv_prog_CPP=$CPP +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $CPP" >&5 +$as_echo "$CPP" >&6; } +ac_preproc_ok=false +for ac_c_preproc_warn_flag in '' yes +do + # Use a header file that comes with gcc, so configuring glibc + # with a fresh cross-compiler works. + # Prefer to if __STDC__ is defined, since + # exists even on freestanding compilers. + # On the NeXT, cc -E runs the code through the compiler's parser, + # not just through cpp. "Syntax error" is here to catch this case. + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#ifdef __STDC__ +# include +#else +# include +#endif + Syntax error +_ACEOF +if ac_fn_c_try_cpp "$LINENO"; then : + +else + # Broken: fails on valid input. +continue +fi +rm -f conftest.err conftest.i conftest.$ac_ext + + # OK, works on sane cases. Now check whether nonexistent headers + # can be detected and how. + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include +_ACEOF +if ac_fn_c_try_cpp "$LINENO"; then : + # Broken: success on invalid input. +continue +else + # Passes both tests. +ac_preproc_ok=: +break +fi +rm -f conftest.err conftest.i conftest.$ac_ext + +done +# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. +rm -f conftest.i conftest.err conftest.$ac_ext +if $ac_preproc_ok; then : + +else + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error $? "C preprocessor \"$CPP\" fails sanity check +See \`config.log' for more details" "$LINENO" 5; } +fi + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + +# Find a good install program. We prefer a C program (faster), +# so one script is as good as another. But avoid the broken or +# incompatible versions: +# SysV /etc/install, /usr/sbin/install +# SunOS /usr/etc/install +# IRIX /sbin/install +# AIX /bin/install +# AmigaOS /C/install, which installs bootblocks on floppy discs +# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag +# AFS /usr/afsws/bin/install, which mishandles nonexistent args +# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff" +# OS/2's system install, which has a completely different semantic +# ./install, which can be erroneously created by make from ./install.sh. +# Reject install programs that cannot install multiple files. +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a BSD-compatible install" >&5 +$as_echo_n "checking for a BSD-compatible install... " >&6; } +if test -z "$INSTALL"; then +if ${ac_cv_path_install+:} false; then : + $as_echo_n "(cached) " >&6 +else + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + # Account for people who put trailing slashes in PATH elements. +case $as_dir/ in #(( + ./ | .// | /[cC]/* | \ + /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \ + ?:[\\/]os2[\\/]install[\\/]* | ?:[\\/]OS2[\\/]INSTALL[\\/]* | \ + /usr/ucb/* ) ;; + *) + # OSF1 and SCO ODT 3.0 have their own names for install. + # Don't use installbsd from OSF since it installs stuff as root + # by default. + for ac_prog in ginstall scoinst install; do + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_prog$ac_exec_ext"; then + if test $ac_prog = install && + grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then + # AIX install. It has an incompatible calling convention. + : + elif test $ac_prog = install && + grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then + # program-specific install script used by HP pwplus--don't use. + : + else + rm -rf conftest.one conftest.two conftest.dir + echo one > conftest.one + echo two > conftest.two + mkdir conftest.dir + if "$as_dir/$ac_prog$ac_exec_ext" -c conftest.one conftest.two "`pwd`/conftest.dir" && + test -s conftest.one && test -s conftest.two && + test -s conftest.dir/conftest.one && + test -s conftest.dir/conftest.two + then + ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c" + break 3 + fi + fi + fi + done + done + ;; +esac + + done +IFS=$as_save_IFS + +rm -rf conftest.one conftest.two conftest.dir + +fi + if test "${ac_cv_path_install+set}" = set; then + INSTALL=$ac_cv_path_install + else + # As a last resort, use the slow shell script. Don't cache a + # value for INSTALL within a source directory, because that will + # break other packages using the cache if that directory is + # removed, or if the value is a relative name. + INSTALL=$ac_install_sh + fi +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $INSTALL" >&5 +$as_echo "$INSTALL" >&6; } + +# Use test -z because SunOS4 sh mishandles braces in ${var-val}. +# It thinks the first close brace ends the variable substitution. +test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}' + +test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}' + +test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644' + +if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args. +set dummy ${ac_tool_prefix}strip; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_STRIP+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$STRIP"; then + ac_cv_prog_STRIP="$STRIP" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_STRIP="${ac_tool_prefix}strip" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +fi +fi +STRIP=$ac_cv_prog_STRIP +if test -n "$STRIP"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5 +$as_echo "$STRIP" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + +fi +if test -z "$ac_cv_prog_STRIP"; then + ac_ct_STRIP=$STRIP + # Extract the first word of "strip", so it can be a program name with args. +set dummy strip; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_ac_ct_STRIP+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_STRIP"; then + ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_STRIP="strip" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +fi +fi +ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP +if test -n "$ac_ct_STRIP"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5 +$as_echo "$ac_ct_STRIP" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + if test "x$ac_ct_STRIP" = x; then + STRIP="" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + STRIP=$ac_ct_STRIP + fi +else + STRIP="$ac_cv_prog_STRIP" +fi + +if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args. +set dummy ${ac_tool_prefix}ranlib; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_RANLIB+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$RANLIB"; then + ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +fi +fi +RANLIB=$ac_cv_prog_RANLIB +if test -n "$RANLIB"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $RANLIB" >&5 +$as_echo "$RANLIB" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + +fi +if test -z "$ac_cv_prog_RANLIB"; then + ac_ct_RANLIB=$RANLIB + # Extract the first word of "ranlib", so it can be a program name with args. +set dummy ranlib; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_ac_ct_RANLIB+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_RANLIB"; then + ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ac_ct_RANLIB="ranlib" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +fi +fi +ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB +if test -n "$ac_ct_RANLIB"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_RANLIB" >&5 +$as_echo "$ac_ct_RANLIB" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + if test "x$ac_ct_RANLIB" = x; then + RANLIB=":" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + RANLIB=$ac_ct_RANLIB + fi +else + RANLIB="$ac_cv_prog_RANLIB" +fi + +# Extract the first word of "ar", so it can be a program name with args. +set dummy ar; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_path_AR+:} false; then : + $as_echo_n "(cached) " >&6 +else + case $AR in + [\\/]* | ?:[\\/]*) + ac_cv_path_AR="$AR" # Let the user override the test with a path. + ;; + *) + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +as_dummy="$PATH:/usr/ccs/bin:/usr/xpg4/bin" +for as_dir in $as_dummy +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_path_AR="$as_dir/$ac_word$ac_exec_ext" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + + test -z "$ac_cv_path_AR" && ac_cv_path_AR=":" + ;; +esac +fi +AR=$ac_cv_path_AR +if test -n "$AR"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AR" >&5 +$as_echo "$AR" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ln -s works" >&5 +$as_echo_n "checking whether ln -s works... " >&6; } +LN_S=$as_ln_s +if test "$LN_S" = "ln -s"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +$as_echo "yes" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no, using $LN_S" >&5 +$as_echo "no, using $LN_S" >&6; } +fi + + +# Select our default optimization flags in CFLAGS. +# --enable-gcov, --enable-gprof, and --enable-debugging are mutually exclusive. +# +if test "$enable_gcov" = "yes"; then + CFLAGS="${CFLAGS} -g -Wall -fprofile-arcs -ftest-coverage" +elif test "$enable_gprof" = "yes"; then + CFLAGS="${CFLAGS} -O -g -pg" +elif test "$enable_debugging" != "no"; then + if test "$GCC" = "yes"; then + CFLAGS="${CFLAGS} -g -Wall" + else + as_fn_error $? "--enable-debugging only works for a gcc-like compiler" "$LINENO" 5 + fi +elif test x"${CFLAGS}" = x; then + CFLAGS="-O3" +fi + + +# PIC (position-independent code) for shared library support +# +if test "$enable_pic" = "yes"; then + +# Check whether --enable-pic was given. +if test "${enable_pic+set}" = set; then : + enableval=$enable_pic; enable_pic="$enableval" + test "x$enable_pic" = x && enable_pic=auto +else + enable_pic=auto +fi + +# disable PIC by default for static builds +if test "$enable_pic" = auto && test "$enable_static" = yes; then + enable_pic=no +fi +# if PIC hasn't been explicitly disabled, try to figure out the flags +if test "$enable_pic" != no; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to produce PIC" >&5 +$as_echo_n "checking for $CC option to produce PIC... " >&6; } + # allow the user's flags to override + if test "x$PIC_CFLAGS" = x; then + # see if we're using GCC + if test "x$GCC" = xyes; then + case "$host_os" in + aix*|beos*|cygwin*|irix5*|irix6*|osf3*|osf4*|osf5*) + # PIC is the default for these OSes. + ;; + mingw*|os2*|pw32*) + # This hack is so that the source file can tell whether + # it is being built for inclusion in a dll (and should + # export symbols for example). + PIC_CFLAGS="-DDLL_EXPORT" + ;; + darwin*|rhapsody*) + # PIC is the default on this platform + # Common symbols not allowed in MH_DYLIB files + PIC_CFLAGS="-fno-common" + ;; + hpux*) + # PIC is the default for IA64 HP-UX and 64-bit HP-UX, + # but not for PA HP-UX. + case $host_cpu in + hppa*64*|ia64*) + ;; + *) + PIC_CFLAGS="-fPIC" + ;; + esac + ;; + *) + # Everyone else on GCC uses -fPIC + PIC_CFLAGS="-fPIC" + ;; + esac + else # !GCC + case "$host_os" in + hpux9*|hpux10*|hpux11*) + # PIC is the default for IA64 HP-UX and 64-bit HP-UX, + # but not for PA HP-UX. + case "$host_cpu" in + hppa*64*|ia64*) + # +Z the default + ;; + *) + PIC_CFLAGS="+Z" + ;; + esac + ;; + linux*|k*bsd*-gnu) + case `basename "$CC"` in + icc*|ecc*|ifort*) + PIC_CFLAGS="-KPIC" + ;; + pgcc*|pgf77*|pgf90*|pgf95*) + # Portland Group compilers (*not* the Pentium gcc + # compiler, which looks to be a dead project) + PIC_CFLAGS="-fpic" + ;; + ccc*) + # All Alpha code is PIC. + ;; + xl*) + # IBM XL C 8.0/Fortran 10.1 on PPC + PIC_CFLAGS="-qpic" + ;; + *) + case `$CC -V 2>&1 | sed 5q` in + *Sun\ C*|*Sun\ F*) + # Sun C 5.9 or Sun Fortran + PIC_CFLAGS="-KPIC" + ;; + esac + esac + ;; + solaris*) + PIC_CFLAGS="-KPIC" + ;; + sunos4*) + PIC_CFLAGS="-PIC" + ;; + esac + fi # GCC + fi # PIC_CFLAGS + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $PIC_CFLAGS" >&5 +$as_echo "$PIC_CFLAGS" >&6; } +fi + + +fi + + +# Support for POSIX multithreading (we should generally have this) +# +if test "$enable_threads" != "no"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for a sed that does not truncate output" >&5 +$as_echo_n "checking for a sed that does not truncate output... " >&6; } +if ${ac_cv_path_SED+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_script=s/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa/bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb/ + for ac_i in 1 2 3 4 5 6 7; do + ac_script="$ac_script$as_nl$ac_script" + done + echo "$ac_script" 2>/dev/null | sed 99q >conftest.sed + { ac_script=; unset ac_script;} + if test -z "$SED"; then + ac_path_SED_found=false + # Loop through the user's path and test for each of PROGNAME-LIST + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_prog in sed gsed; do + for ac_exec_ext in '' $ac_executable_extensions; do + ac_path_SED="$as_dir/$ac_prog$ac_exec_ext" + as_fn_executable_p "$ac_path_SED" || continue +# Check for GNU ac_path_SED and select it if it is found. + # Check for GNU $ac_path_SED +case `"$ac_path_SED" --version 2>&1` in +*GNU*) + ac_cv_path_SED="$ac_path_SED" ac_path_SED_found=:;; +*) + ac_count=0 + $as_echo_n 0123456789 >"conftest.in" + while : + do + cat "conftest.in" "conftest.in" >"conftest.tmp" + mv "conftest.tmp" "conftest.in" + cp "conftest.in" "conftest.nl" + $as_echo '' >> "conftest.nl" + "$ac_path_SED" -f conftest.sed < "conftest.nl" >"conftest.out" 2>/dev/null || break + diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break + as_fn_arith $ac_count + 1 && ac_count=$as_val + if test $ac_count -gt ${ac_path_SED_max-0}; then + # Best one so far, save it but keep looking for a better one + ac_cv_path_SED="$ac_path_SED" + ac_path_SED_max=$ac_count + fi + # 10*(2^10) chars as input seems more than enough + test $ac_count -gt 10 && break + done + rm -f conftest.in conftest.tmp conftest.nl conftest.out;; +esac + + $ac_path_SED_found && break 3 + done + done + done +IFS=$as_save_IFS + if test -z "$ac_cv_path_SED"; then + as_fn_error $? "no acceptable sed could be found in \$PATH" "$LINENO" 5 + fi +else + ac_cv_path_SED=$SED +fi + +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_SED" >&5 +$as_echo "$ac_cv_path_SED" >&6; } + SED="$ac_cv_path_SED" + rm -f conftest.sed + + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for grep that handles long lines and -e" >&5 +$as_echo_n "checking for grep that handles long lines and -e... " >&6; } +if ${ac_cv_path_GREP+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -z "$GREP"; then + ac_path_GREP_found=false + # Loop through the user's path and test for each of PROGNAME-LIST + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_prog in grep ggrep; do + for ac_exec_ext in '' $ac_executable_extensions; do + ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext" + as_fn_executable_p "$ac_path_GREP" || continue +# Check for GNU ac_path_GREP and select it if it is found. + # Check for GNU $ac_path_GREP +case `"$ac_path_GREP" --version 2>&1` in +*GNU*) + ac_cv_path_GREP="$ac_path_GREP" ac_path_GREP_found=:;; +*) + ac_count=0 + $as_echo_n 0123456789 >"conftest.in" + while : + do + cat "conftest.in" "conftest.in" >"conftest.tmp" + mv "conftest.tmp" "conftest.in" + cp "conftest.in" "conftest.nl" + $as_echo 'GREP' >> "conftest.nl" + "$ac_path_GREP" -e 'GREP$' -e '-(cannot match)-' < "conftest.nl" >"conftest.out" 2>/dev/null || break + diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break + as_fn_arith $ac_count + 1 && ac_count=$as_val + if test $ac_count -gt ${ac_path_GREP_max-0}; then + # Best one so far, save it but keep looking for a better one + ac_cv_path_GREP="$ac_path_GREP" + ac_path_GREP_max=$ac_count + fi + # 10*(2^10) chars as input seems more than enough + test $ac_count -gt 10 && break + done + rm -f conftest.in conftest.tmp conftest.nl conftest.out;; +esac + + $ac_path_GREP_found && break 3 + done + done + done +IFS=$as_save_IFS + if test -z "$ac_cv_path_GREP"; then + as_fn_error $? "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5 + fi +else + ac_cv_path_GREP=$GREP +fi + +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_GREP" >&5 +$as_echo "$ac_cv_path_GREP" >&6; } + GREP="$ac_cv_path_GREP" + + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for egrep" >&5 +$as_echo_n "checking for egrep... " >&6; } +if ${ac_cv_path_EGREP+:} false; then : + $as_echo_n "(cached) " >&6 +else + if echo a | $GREP -E '(a|b)' >/dev/null 2>&1 + then ac_cv_path_EGREP="$GREP -E" + else + if test -z "$EGREP"; then + ac_path_EGREP_found=false + # Loop through the user's path and test for each of PROGNAME-LIST + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_prog in egrep; do + for ac_exec_ext in '' $ac_executable_extensions; do + ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext" + as_fn_executable_p "$ac_path_EGREP" || continue +# Check for GNU ac_path_EGREP and select it if it is found. + # Check for GNU $ac_path_EGREP +case `"$ac_path_EGREP" --version 2>&1` in +*GNU*) + ac_cv_path_EGREP="$ac_path_EGREP" ac_path_EGREP_found=:;; +*) + ac_count=0 + $as_echo_n 0123456789 >"conftest.in" + while : + do + cat "conftest.in" "conftest.in" >"conftest.tmp" + mv "conftest.tmp" "conftest.in" + cp "conftest.in" "conftest.nl" + $as_echo 'EGREP' >> "conftest.nl" + "$ac_path_EGREP" 'EGREP$' < "conftest.nl" >"conftest.out" 2>/dev/null || break + diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break + as_fn_arith $ac_count + 1 && ac_count=$as_val + if test $ac_count -gt ${ac_path_EGREP_max-0}; then + # Best one so far, save it but keep looking for a better one + ac_cv_path_EGREP="$ac_path_EGREP" + ac_path_EGREP_max=$ac_count + fi + # 10*(2^10) chars as input seems more than enough + test $ac_count -gt 10 && break + done + rm -f conftest.in conftest.tmp conftest.nl conftest.out;; +esac + + $ac_path_EGREP_found && break 3 + done + done + done +IFS=$as_save_IFS + if test -z "$ac_cv_path_EGREP"; then + as_fn_error $? "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5 + fi +else + ac_cv_path_EGREP=$EGREP +fi + + fi +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_EGREP" >&5 +$as_echo "$ac_cv_path_EGREP" >&6; } + EGREP="$ac_cv_path_EGREP" + + + + + + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + +ax_pthread_ok=no + +# We used to check for pthread.h first, but this fails if pthread.h +# requires special compiler flags (e.g. on Tru64 or Sequent). +# It gets checked for in the link test anyway. + +# First of all, check if the user has set any of the PTHREAD_LIBS, +# etcetera environment variables, and if threads linking works using +# them: +if test "x$PTHREAD_CFLAGS$PTHREAD_LIBS" != "x"; then + ax_pthread_save_CC="$CC" + ax_pthread_save_CFLAGS="$CFLAGS" + ax_pthread_save_LIBS="$LIBS" + if test "x$PTHREAD_CC" != "x"; then : + CC="$PTHREAD_CC" +fi + if test "x$PTHREAD_CXX" != "x"; then : + CXX="$PTHREAD_CXX" +fi + CFLAGS="$CFLAGS $PTHREAD_CFLAGS" + LIBS="$PTHREAD_LIBS $LIBS" + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for pthread_join using $CC $PTHREAD_CFLAGS $PTHREAD_LIBS" >&5 +$as_echo_n "checking for pthread_join using $CC $PTHREAD_CFLAGS $PTHREAD_LIBS... " >&6; } + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char pthread_join (); +int +main () +{ +return pthread_join (); + ; + return 0; +} +_ACEOF +if ac_fn_c_try_link "$LINENO"; then : + ax_pthread_ok=yes +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ax_pthread_ok" >&5 +$as_echo "$ax_pthread_ok" >&6; } + if test "x$ax_pthread_ok" = "xno"; then + PTHREAD_LIBS="" + PTHREAD_CFLAGS="" + fi + CC="$ax_pthread_save_CC" + CFLAGS="$ax_pthread_save_CFLAGS" + LIBS="$ax_pthread_save_LIBS" +fi + +# We must check for the threads library under a number of different +# names; the ordering is very important because some systems +# (e.g. DEC) have both -lpthread and -lpthreads, where one of the +# libraries is broken (non-POSIX). + +# Create a list of thread flags to try. Items with a "," contain both +# C compiler flags (before ",") and linker flags (after ","). Other items +# starting with a "-" are C compiler flags, and remaining items are +# library names, except for "none" which indicates that we try without +# any flags at all, and "pthread-config" which is a program returning +# the flags for the Pth emulation library. + +ax_pthread_flags="pthreads none -Kthread -pthread -pthreads -mthreads pthread --thread-safe -mt pthread-config" + +# The ordering *is* (sometimes) important. Some notes on the +# individual items follow: + +# pthreads: AIX (must check this before -lpthread) +# none: in case threads are in libc; should be tried before -Kthread and +# other compiler flags to prevent continual compiler warnings +# -Kthread: Sequent (threads in libc, but -Kthread needed for pthread.h) +# -pthread: Linux/gcc (kernel threads), BSD/gcc (userland threads), Tru64 +# (Note: HP C rejects this with "bad form for `-t' option") +# -pthreads: Solaris/gcc (Note: HP C also rejects) +# -mt: Sun Workshop C (may only link SunOS threads [-lthread], but it +# doesn't hurt to check since this sometimes defines pthreads and +# -D_REENTRANT too), HP C (must be checked before -lpthread, which +# is present but should not be used directly; and before -mthreads, +# because the compiler interprets this as "-mt" + "-hreads") +# -mthreads: Mingw32/gcc, Lynx/gcc +# pthread: Linux, etcetera +# --thread-safe: KAI C++ +# pthread-config: use pthread-config program (for GNU Pth library) + +case $host_os in + + freebsd*) + + # -kthread: FreeBSD kernel threads (preferred to -pthread since SMP-able) + # lthread: LinuxThreads port on FreeBSD (also preferred to -pthread) + + ax_pthread_flags="-kthread lthread $ax_pthread_flags" + ;; + + hpux*) + + # From the cc(1) man page: "[-mt] Sets various -D flags to enable + # multi-threading and also sets -lpthread." + + ax_pthread_flags="-mt -pthread pthread $ax_pthread_flags" + ;; + + openedition*) + + # IBM z/OS requires a feature-test macro to be defined in order to + # enable POSIX threads at all, so give the user a hint if this is + # not set. (We don't define these ourselves, as they can affect + # other portions of the system API in unpredictable ways.) + + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +# if !defined(_OPEN_THREADS) && !defined(_UNIX03_THREADS) + AX_PTHREAD_ZOS_MISSING +# endif + +_ACEOF +if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | + $EGREP "AX_PTHREAD_ZOS_MISSING" >/dev/null 2>&1; then : + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: IBM z/OS requires -D_OPEN_THREADS or -D_UNIX03_THREADS to enable pthreads support." >&5 +$as_echo "$as_me: WARNING: IBM z/OS requires -D_OPEN_THREADS or -D_UNIX03_THREADS to enable pthreads support." >&2;} +fi +rm -f conftest* + + ;; + + solaris*) + + # On Solaris (at least, for some versions), libc contains stubbed + # (non-functional) versions of the pthreads routines, so link-based + # tests will erroneously succeed. (N.B.: The stubs are missing + # pthread_cleanup_push, or rather a function called by this macro, + # so we could check for that, but who knows whether they'll stub + # that too in a future libc.) So we'll check first for the + # standard Solaris way of linking pthreads (-mt -lpthread). + + ax_pthread_flags="-mt,-lpthread pthread $ax_pthread_flags" + ;; +esac + +# Are we compiling with Clang? + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC is Clang" >&5 +$as_echo_n "checking whether $CC is Clang... " >&6; } +if ${ax_cv_PTHREAD_CLANG+:} false; then : + $as_echo_n "(cached) " >&6 +else + ax_cv_PTHREAD_CLANG=no + # Note that Autoconf sets GCC=yes for Clang as well as GCC + if test "x$GCC" = "xyes"; then + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +/* Note: Clang 2.7 lacks __clang_[a-z]+__ */ +# if defined(__clang__) && defined(__llvm__) + AX_PTHREAD_CC_IS_CLANG +# endif + +_ACEOF +if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | + $EGREP "AX_PTHREAD_CC_IS_CLANG" >/dev/null 2>&1; then : + ax_cv_PTHREAD_CLANG=yes +fi +rm -f conftest* + + fi + +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ax_cv_PTHREAD_CLANG" >&5 +$as_echo "$ax_cv_PTHREAD_CLANG" >&6; } +ax_pthread_clang="$ax_cv_PTHREAD_CLANG" + + +# GCC generally uses -pthread, or -pthreads on some platforms (e.g. SPARC) + +# Note that for GCC and Clang -pthread generally implies -lpthread, +# except when -nostdlib is passed. +# This is problematic using libtool to build C++ shared libraries with pthread: +# [1] https://gcc.gnu.org/bugzilla/show_bug.cgi?id=25460 +# [2] https://bugzilla.redhat.com/show_bug.cgi?id=661333 +# [3] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=468555 +# To solve this, first try -pthread together with -lpthread for GCC + +if test "x$GCC" = "xyes"; then : + ax_pthread_flags="-pthread,-lpthread -pthread -pthreads $ax_pthread_flags" +fi + +# Clang takes -pthread (never supported any other flag), but we'll try with -lpthread first + +if test "x$ax_pthread_clang" = "xyes"; then : + ax_pthread_flags="-pthread,-lpthread -pthread" +fi + + +# The presence of a feature test macro requesting re-entrant function +# definitions is, on some systems, a strong hint that pthreads support is +# correctly enabled + +case $host_os in + darwin* | hpux* | linux* | osf* | solaris*) + ax_pthread_check_macro="_REENTRANT" + ;; + + aix*) + ax_pthread_check_macro="_THREAD_SAFE" + ;; + + *) + ax_pthread_check_macro="--" + ;; +esac +if test "x$ax_pthread_check_macro" = "x--"; then : + ax_pthread_check_cond=0 +else + ax_pthread_check_cond="!defined($ax_pthread_check_macro)" +fi + + +if test "x$ax_pthread_ok" = "xno"; then +for ax_pthread_try_flag in $ax_pthread_flags; do + + case $ax_pthread_try_flag in + none) + { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether pthreads work without any flags" >&5 +$as_echo_n "checking whether pthreads work without any flags... " >&6; } + ;; + + *,*) + PTHREAD_CFLAGS=`echo $ax_pthread_try_flag | sed "s/^\(.*\),\(.*\)$/\1/"` + PTHREAD_LIBS=`echo $ax_pthread_try_flag | sed "s/^\(.*\),\(.*\)$/\2/"` + { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether pthreads work with \"$PTHREAD_CFLAGS\" and \"$PTHREAD_LIBS\"" >&5 +$as_echo_n "checking whether pthreads work with \"$PTHREAD_CFLAGS\" and \"$PTHREAD_LIBS\"... " >&6; } + ;; + + -*) + { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether pthreads work with $ax_pthread_try_flag" >&5 +$as_echo_n "checking whether pthreads work with $ax_pthread_try_flag... " >&6; } + PTHREAD_CFLAGS="$ax_pthread_try_flag" + ;; + + pthread-config) + # Extract the first word of "pthread-config", so it can be a program name with args. +set dummy pthread-config; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_ax_pthread_config+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$ax_pthread_config"; then + ac_cv_prog_ax_pthread_config="$ax_pthread_config" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_ax_pthread_config="yes" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + + test -z "$ac_cv_prog_ax_pthread_config" && ac_cv_prog_ax_pthread_config="no" +fi +fi +ax_pthread_config=$ac_cv_prog_ax_pthread_config +if test -n "$ax_pthread_config"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ax_pthread_config" >&5 +$as_echo "$ax_pthread_config" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + + if test "x$ax_pthread_config" = "xno"; then : + continue +fi + PTHREAD_CFLAGS="`pthread-config --cflags`" + PTHREAD_LIBS="`pthread-config --ldflags` `pthread-config --libs`" + ;; + + *) + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for the pthreads library -l$ax_pthread_try_flag" >&5 +$as_echo_n "checking for the pthreads library -l$ax_pthread_try_flag... " >&6; } + PTHREAD_LIBS="-l$ax_pthread_try_flag" + ;; + esac + + ax_pthread_save_CFLAGS="$CFLAGS" + ax_pthread_save_LIBS="$LIBS" + CFLAGS="$CFLAGS $PTHREAD_CFLAGS" + LIBS="$PTHREAD_LIBS $LIBS" + + # Check for various functions. We must include pthread.h, + # since some functions may be macros. (On the Sequent, we + # need a special flag -Kthread to make this header compile.) + # We check for pthread_join because it is in -lpthread on IRIX + # while pthread_create is in libc. We check for pthread_attr_init + # due to DEC craziness with -lpthreads. We check for + # pthread_cleanup_push because it is one of the few pthread + # functions on Solaris that doesn't have a non-functional libc stub. + # We try pthread_create on general principles. + + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include +# if $ax_pthread_check_cond +# error "$ax_pthread_check_macro must be defined" +# endif + static void *some_global = NULL; + static void routine(void *a) + { + /* To avoid any unused-parameter or + unused-but-set-parameter warning. */ + some_global = a; + } + static void *start_routine(void *a) { return a; } +int +main () +{ +pthread_t th; pthread_attr_t attr; + pthread_create(&th, 0, start_routine, 0); + pthread_join(th, 0); + pthread_attr_init(&attr); + pthread_cleanup_push(routine, 0); + pthread_cleanup_pop(0) /* ; */ + ; + return 0; +} +_ACEOF +if ac_fn_c_try_link "$LINENO"; then : + ax_pthread_ok=yes +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext + + CFLAGS="$ax_pthread_save_CFLAGS" + LIBS="$ax_pthread_save_LIBS" + + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ax_pthread_ok" >&5 +$as_echo "$ax_pthread_ok" >&6; } + if test "x$ax_pthread_ok" = "xyes"; then : + break +fi + + PTHREAD_LIBS="" + PTHREAD_CFLAGS="" +done +fi + + +# Clang needs special handling, because older versions handle the -pthread +# option in a rather... idiosyncratic way + +if test "x$ax_pthread_clang" = "xyes"; then + + # Clang takes -pthread; it has never supported any other flag + + # (Note 1: This will need to be revisited if a system that Clang + # supports has POSIX threads in a separate library. This tends not + # to be the way of modern systems, but it's conceivable.) + + # (Note 2: On some systems, notably Darwin, -pthread is not needed + # to get POSIX threads support; the API is always present and + # active. We could reasonably leave PTHREAD_CFLAGS empty. But + # -pthread does define _REENTRANT, and while the Darwin headers + # ignore this macro, third-party headers might not.) + + # However, older versions of Clang make a point of warning the user + # that, in an invocation where only linking and no compilation is + # taking place, the -pthread option has no effect ("argument unused + # during compilation"). They expect -pthread to be passed in only + # when source code is being compiled. + # + # Problem is, this is at odds with the way Automake and most other + # C build frameworks function, which is that the same flags used in + # compilation (CFLAGS) are also used in linking. Many systems + # supported by AX_PTHREAD require exactly this for POSIX threads + # support, and in fact it is often not straightforward to specify a + # flag that is used only in the compilation phase and not in + # linking. Such a scenario is extremely rare in practice. + # + # Even though use of the -pthread flag in linking would only print + # a warning, this can be a nuisance for well-run software projects + # that build with -Werror. So if the active version of Clang has + # this misfeature, we search for an option to squash it. + + { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether Clang needs flag to prevent \"argument unused\" warning when linking with -pthread" >&5 +$as_echo_n "checking whether Clang needs flag to prevent \"argument unused\" warning when linking with -pthread... " >&6; } +if ${ax_cv_PTHREAD_CLANG_NO_WARN_FLAG+:} false; then : + $as_echo_n "(cached) " >&6 +else + ax_cv_PTHREAD_CLANG_NO_WARN_FLAG=unknown + # Create an alternate version of $ac_link that compiles and + # links in two steps (.c -> .o, .o -> exe) instead of one + # (.c -> exe), because the warning occurs only in the second + # step + ax_pthread_save_ac_link="$ac_link" + ax_pthread_sed='s/conftest\.\$ac_ext/conftest.$ac_objext/g' + ax_pthread_link_step=`$as_echo "$ac_link" | sed "$ax_pthread_sed"` + ax_pthread_2step_ac_link="($ac_compile) && (echo ==== >&5) && ($ax_pthread_link_step)" + ax_pthread_save_CFLAGS="$CFLAGS" + for ax_pthread_try in '' -Qunused-arguments -Wno-unused-command-line-argument unknown; do + if test "x$ax_pthread_try" = "xunknown"; then : + break +fi + CFLAGS="-Werror -Wunknown-warning-option $ax_pthread_try -pthread $ax_pthread_save_CFLAGS" + ac_link="$ax_pthread_save_ac_link" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +int main(void){return 0;} +_ACEOF +if ac_fn_c_try_link "$LINENO"; then : + ac_link="$ax_pthread_2step_ac_link" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +int main(void){return 0;} +_ACEOF +if ac_fn_c_try_link "$LINENO"; then : + break +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext + +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext + done + ac_link="$ax_pthread_save_ac_link" + CFLAGS="$ax_pthread_save_CFLAGS" + if test "x$ax_pthread_try" = "x"; then : + ax_pthread_try=no +fi + ax_cv_PTHREAD_CLANG_NO_WARN_FLAG="$ax_pthread_try" + +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ax_cv_PTHREAD_CLANG_NO_WARN_FLAG" >&5 +$as_echo "$ax_cv_PTHREAD_CLANG_NO_WARN_FLAG" >&6; } + + case "$ax_cv_PTHREAD_CLANG_NO_WARN_FLAG" in + no | unknown) ;; + *) PTHREAD_CFLAGS="$ax_cv_PTHREAD_CLANG_NO_WARN_FLAG $PTHREAD_CFLAGS" ;; + esac + +fi # $ax_pthread_clang = yes + + + +# Various other checks: +if test "x$ax_pthread_ok" = "xyes"; then + ax_pthread_save_CFLAGS="$CFLAGS" + ax_pthread_save_LIBS="$LIBS" + CFLAGS="$CFLAGS $PTHREAD_CFLAGS" + LIBS="$PTHREAD_LIBS $LIBS" + + # Detect AIX lossage: JOINABLE attribute is called UNDETACHED. + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for joinable pthread attribute" >&5 +$as_echo_n "checking for joinable pthread attribute... " >&6; } +if ${ax_cv_PTHREAD_JOINABLE_ATTR+:} false; then : + $as_echo_n "(cached) " >&6 +else + ax_cv_PTHREAD_JOINABLE_ATTR=unknown + for ax_pthread_attr in PTHREAD_CREATE_JOINABLE PTHREAD_CREATE_UNDETACHED; do + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include +int +main () +{ +int attr = $ax_pthread_attr; return attr /* ; */ + ; + return 0; +} +_ACEOF +if ac_fn_c_try_link "$LINENO"; then : + ax_cv_PTHREAD_JOINABLE_ATTR=$ax_pthread_attr; break +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext + done + +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ax_cv_PTHREAD_JOINABLE_ATTR" >&5 +$as_echo "$ax_cv_PTHREAD_JOINABLE_ATTR" >&6; } + if test "x$ax_cv_PTHREAD_JOINABLE_ATTR" != "xunknown" && \ + test "x$ax_cv_PTHREAD_JOINABLE_ATTR" != "xPTHREAD_CREATE_JOINABLE" && \ + test "x$ax_pthread_joinable_attr_defined" != "xyes"; then : + +cat >>confdefs.h <<_ACEOF +#define PTHREAD_CREATE_JOINABLE $ax_cv_PTHREAD_JOINABLE_ATTR +_ACEOF + + ax_pthread_joinable_attr_defined=yes + +fi + + { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether more special flags are required for pthreads" >&5 +$as_echo_n "checking whether more special flags are required for pthreads... " >&6; } +if ${ax_cv_PTHREAD_SPECIAL_FLAGS+:} false; then : + $as_echo_n "(cached) " >&6 +else + ax_cv_PTHREAD_SPECIAL_FLAGS=no + case $host_os in + solaris*) + ax_cv_PTHREAD_SPECIAL_FLAGS="-D_POSIX_PTHREAD_SEMANTICS" + ;; + esac + +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ax_cv_PTHREAD_SPECIAL_FLAGS" >&5 +$as_echo "$ax_cv_PTHREAD_SPECIAL_FLAGS" >&6; } + if test "x$ax_cv_PTHREAD_SPECIAL_FLAGS" != "xno" && \ + test "x$ax_pthread_special_flags_added" != "xyes"; then : + PTHREAD_CFLAGS="$ax_cv_PTHREAD_SPECIAL_FLAGS $PTHREAD_CFLAGS" + ax_pthread_special_flags_added=yes +fi + + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for PTHREAD_PRIO_INHERIT" >&5 +$as_echo_n "checking for PTHREAD_PRIO_INHERIT... " >&6; } +if ${ax_cv_PTHREAD_PRIO_INHERIT+:} false; then : + $as_echo_n "(cached) " >&6 +else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include +int +main () +{ +int i = PTHREAD_PRIO_INHERIT; + return i; + ; + return 0; +} +_ACEOF +if ac_fn_c_try_link "$LINENO"; then : + ax_cv_PTHREAD_PRIO_INHERIT=yes +else + ax_cv_PTHREAD_PRIO_INHERIT=no +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext + +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ax_cv_PTHREAD_PRIO_INHERIT" >&5 +$as_echo "$ax_cv_PTHREAD_PRIO_INHERIT" >&6; } + if test "x$ax_cv_PTHREAD_PRIO_INHERIT" = "xyes" && \ + test "x$ax_pthread_prio_inherit_defined" != "xyes"; then : + +$as_echo "#define HAVE_PTHREAD_PRIO_INHERIT 1" >>confdefs.h + + ax_pthread_prio_inherit_defined=yes + +fi + + CFLAGS="$ax_pthread_save_CFLAGS" + LIBS="$ax_pthread_save_LIBS" + + # More AIX lossage: compile with *_r variant + if test "x$GCC" != "xyes"; then + case $host_os in + aix*) + case "x/$CC" in #( + x*/c89|x*/c89_128|x*/c99|x*/c99_128|x*/cc|x*/cc128|x*/xlc|x*/xlc_v6|x*/xlc128|x*/xlc128_v6) : + #handle absolute path differently from PATH based program lookup + case "x$CC" in #( + x/*) : + + if as_fn_executable_p ${CC}_r; then : + PTHREAD_CC="${CC}_r" +fi + if test "x${CXX}" != "x"; then : + if as_fn_executable_p ${CXX}_r; then : + PTHREAD_CXX="${CXX}_r" +fi +fi + ;; #( + *) : + + for ac_prog in ${CC}_r +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_PTHREAD_CC+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$PTHREAD_CC"; then + ac_cv_prog_PTHREAD_CC="$PTHREAD_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_PTHREAD_CC="$ac_prog" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +fi +fi +PTHREAD_CC=$ac_cv_prog_PTHREAD_CC +if test -n "$PTHREAD_CC"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $PTHREAD_CC" >&5 +$as_echo "$PTHREAD_CC" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + + test -n "$PTHREAD_CC" && break +done +test -n "$PTHREAD_CC" || PTHREAD_CC="$CC" + + if test "x${CXX}" != "x"; then : + for ac_prog in ${CXX}_r +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_PTHREAD_CXX+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$PTHREAD_CXX"; then + ac_cv_prog_PTHREAD_CXX="$PTHREAD_CXX" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_PTHREAD_CXX="$ac_prog" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +fi +fi +PTHREAD_CXX=$ac_cv_prog_PTHREAD_CXX +if test -n "$PTHREAD_CXX"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $PTHREAD_CXX" >&5 +$as_echo "$PTHREAD_CXX" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + + test -n "$PTHREAD_CXX" && break +done +test -n "$PTHREAD_CXX" || PTHREAD_CXX="$CXX" + +fi + + ;; +esac + ;; #( + *) : + ;; +esac + ;; + esac + fi +fi + +test -n "$PTHREAD_CC" || PTHREAD_CC="$CC" +test -n "$PTHREAD_CXX" || PTHREAD_CXX="$CXX" + + + + + + +# Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND: +if test "x$ax_pthread_ok" = "xyes"; then + + +$as_echo "#define HAVE_PTHREAD 1" >>confdefs.h + + +$as_echo "#define HMMER_THREADS 1" >>confdefs.h + + + + + : +else + ax_pthread_ok=no + + if test "$enable_threads" = "yes"; then + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error $? "Unable to compile with POSIX multithreading. +See \`config.log' for more details" "$LINENO" 5; } + fi + enable_threads=no + +fi +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + + +fi + + + + +# Support for vector implementations +# +# If we were explicitly told to enable one ($enable_foo="yes") and we +# can't, fail with an error. +# +# If we're autodetecting ($enable_foo="check"), set $enable_foo to the +# result ("yes" or "no"). +# +# If vector support "foo" is enabled: +# - define preprocessor symbol eslENABLE_FOO (esl_config.h.in, p7_config.h.in) +# - set output variable FOO_CFLAGS, if needed (Makefile.in) +# - set shell variable $enable_foo to "yes" +# - set shell variable $impl_choice to "foo" +# and if vector support is available (regardless of whether we +# decide to enable it), the autoconf macros: +# - set shell variable $esl_have_foo to "yes" +# - set shell var $esl_foo_cflags to any necessary compiler flags +# +if test "$enable_vmx" = "yes" || test "$enable_vmx" = "check"; then + + { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC can compile our Altivec/VMX code" >&5 +$as_echo_n "checking whether $CC can compile our Altivec/VMX code... " >&6; } + esl_have_vmx=no + + if test "x$VMX_CFLAGS" != x; then + esl_vmx_try_flags=$VMX_CFLAGS + else + esl_vmx_try_flags="none -maltivec -faltivec" + fi + + save_CFLAGS=$CFLAGS + for esl_vmx_cflags in $esl_vmx_try_flags; do + case $esl_vmx_cflags in + none) CFLAGS=$save_CFLAGS;; + *) CFLAGS="$save_CFLAGS $esl_vmx_cflags";; + esac + + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +#include +#include +int stub_vmx(void) { +vector signed int v1,v2; +union { vector signed int v; int32_t x[4]; } v3; +v1 = vec_splat_s32(6); +v2 = vec_splat_s32(12); +v3.v = vec_add(v1,v2); +return (int) v3.x[0];} +int main(void) { if (stub_vmx() != 18) return 1; else return 0; } + +_ACEOF +if ac_fn_c_try_link "$LINENO"; then : + esl_have_vmx=yes; break; +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext + done + CFLAGS=$save_CFLAGS + + if test "$esl_have_vmx" = "no"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } + esl_vmx_cflags= + else + if test "$esl_vmx_cflags" = "none"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +$as_echo "yes" >&6; } + esl_vmx_cflags= + else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes, with $esl_vmx_cflags" >&5 +$as_echo "yes, with $esl_vmx_cflags" >&6; } + fi + fi + + if test "x$esl_have_vmx" = xyes; then : + + +$as_echo "#define eslENABLE_VMX 1" >>confdefs.h + + HMMERIMPLLIB="impl_vmx/libhmmerimpl.a" + + VMX_CFLAGS=$esl_vmx_cflags + + enable_vmx=yes + impl_choice=vmx + +else + + if test "$enable_vmx" = "yes"; then + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error $? "Unable to compile our Altivec/VMX implementations. Try another compiler? +See \`config.log' for more details" "$LINENO" 5; } + fi + enable_vmx=no + +fi + +fi + +if test "$enable_sse" = "yes" || test "$enable_sse" = "check"; then + + { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC can compile our SSE code" >&5 +$as_echo_n "checking whether $CC can compile our SSE code... " >&6; } + esl_have_sse=no + + if test "x$SSE_CFLAGS" != x; then + esl_sse_try_flags=$SSE_CFLAGS + else + esl_sse_try_flags="none -msse2" + fi + + save_CFLAGS=$CFLAGS + for esl_sse_cflags in $esl_sse_try_flags; do + case $esl_sse_cflags in + none) CFLAGS=$save_CFLAGS;; + *) CFLAGS="$save_CFLAGS $esl_sse_cflags";; + esac + + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +#include +#include +int stub_sse(void) { +__m128i v1 = _mm_set1_epi32(42); +__m128i v2 = _mm_set1_epi32(86); +union { __m128i v; int32_t x[4]; } v3; +v3.v = _mm_add_epi32(v1, v2); +return (int) v3.x[0]; +} +int main(void) { if (stub_sse() != 128) return 1; else return 0; } + +_ACEOF +if ac_fn_c_try_link "$LINENO"; then : + esl_have_sse=yes; break; +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext + done + + CFLAGS=$save_CFLAGS + if test "$esl_have_sse" = "no"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } + esl_sse_cflags= + else + if test "$esl_sse_cflags" = "none"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +$as_echo "yes" >&6; } + esl_sse_cflags= + else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes, with $esl_sse_cflags" >&5 +$as_echo "yes, with $esl_sse_cflags" >&6; } + fi + fi + + if test "x$esl_have_sse" = xyes; then : + + +$as_echo "#define eslENABLE_SSE 1" >>confdefs.h + + HMMERIMPLLIB="impl_sse/libhmmerimpl.a" + + SSE_CFLAGS=$esl_sse_cflags + + enable_sse=yes + impl_choice=sse + +else + + if test "$enable_sse" = "yes"; then + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error $? "Unable to compile our SSE implementations. Try another compiler? +See \`config.log' for more details" "$LINENO" 5; } + fi + enable_sse=no + +fi + +fi + +# If we didn't choose an implementation, die. +case "$impl_choice" in +sse) { $as_echo "$as_me:${as_lineno-$LINENO}: Activating Intel/AMD SSE vector DP implementation" >&5 +$as_echo "$as_me: Activating Intel/AMD SSE vector DP implementation" >&6;} + ;; +vmx) { $as_echo "$as_me:${as_lineno-$LINENO}: Activating Altivec/VMX vector DP implementation" >&5 +$as_echo "$as_me: Activating Altivec/VMX vector DP implementation" >&6;} + ;; +*) { $as_echo "$as_me:${as_lineno-$LINENO}: ::::::::::--- no vector instruction set ---::::::::::" >&5 +$as_echo "$as_me: ::::::::::--- no vector instruction set ---::::::::::" >&6;} + { $as_echo "$as_me:${as_lineno-$LINENO}: HMMER3 requires SSE or VMX vector instructions." >&5 +$as_echo "$as_me: HMMER3 requires SSE or VMX vector instructions." >&6;} + { $as_echo "$as_me:${as_lineno-$LINENO}: Supported platforms are x86 (Intel/AMD) and PowerPC." >&5 +$as_echo "$as_me: Supported platforms are x86 (Intel/AMD) and PowerPC." >&6;} + as_fn_error $? "No supported vectorization found for your machine." "$LINENO" 5 + ;; +esac +IMPL_CHOICE=$impl_choice + + + + +# Easel has additional vector implementations that HMMER3 does not +# support. Provide blank config for those CFLAGS. + + + + + + +# For x86 processors check if the flush to zero macro is available +# in order to avoid the performance penalty dealing with sub-normal +# values in the floating point calculations. +if test "$impl_choice" = "sse"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether _MM_SET_FLUSH_ZERO_MODE is supported" >&5 +$as_echo_n "checking whether _MM_SET_FLUSH_ZERO_MODE is supported... " >&6; } + esl_save_cflags="$CFLAGS" + CFLAGS="$CFLAGS $SSE_CFLAGS" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include +int +main () +{ +_MM_SET_FLUSH_ZERO_MODE (_MM_FLUSH_ZERO_ON); + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +$as_echo "yes" >&6; } + +$as_echo "#define HAVE_FLUSH_ZERO_MODE 1" >>confdefs.h + +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } + +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + CFLAGS="$esl_save_cflags" +fi + +# Check if the linker supports library groups for recursive libraries +if test "x$impl_choice" != xno; then : + { $as_echo "$as_me:${as_lineno-$LINENO}: checking compiler support --start-group" >&5 +$as_echo_n "checking compiler support --start-group... " >&6; } + LDFLAGS_save=$LDFLAGS + LDFLAGS="-Wl,--start-group -Wl,--end-group $LDFLAGS" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_link "$LINENO"; then : + { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +$as_echo "yes" >&6; } + GROUPHMMERLIBS="-Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group" + +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } + GROUPHMMERLIBS="-lhmmer -lhmmerimpl" + +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext + LDFLAGS=$LDFLAGS_save +else + GROUPHMMERLIBS="-lhmmer" + +fi + +# Define HAVE_GZIP if gzip is in $PATH (or if HAVE_GZIP is already set) +# Extract the first word of ""gzip"", so it can be a program name with args. +set dummy "gzip"; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_path_HAVE_GZIP+:} false; then : + $as_echo_n "(cached) " >&6 +else + case $HAVE_GZIP in + [\\/]* | ?:[\\/]*) + ac_cv_path_HAVE_GZIP="$HAVE_GZIP" # Let the user override the test with a path. + ;; + *) + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_path_HAVE_GZIP="$as_dir/$ac_word$ac_exec_ext" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + + test -z "$ac_cv_path_HAVE_GZIP" && ac_cv_path_HAVE_GZIP=""no"" + ;; +esac +fi +HAVE_GZIP=$ac_cv_path_HAVE_GZIP +if test -n "$HAVE_GZIP"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $HAVE_GZIP" >&5 +$as_echo "$HAVE_GZIP" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + +if test "${HAVE_GZIP}" = "no"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: gzip not found" >&5 +$as_echo "$as_me: WARNING: gzip not found" >&2;} +else + +$as_echo "#define HAVE_GZIP 1" >>confdefs.h + +fi + +# We need python 3 for 'make check' and some dev tools. sqc checks +# too, as does the Makefile, but we also check in ./configure, so we +# don't recommend 'make check' to the user if they can't use it. +# +# Extract the first word of "python3", so it can be a program name with args. +set dummy python3; ac_word=$2 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if ${ac_cv_prog_HAVE_PYTHON3+:} false; then : + $as_echo_n "(cached) " >&6 +else + if test -n "$HAVE_PYTHON3"; then + ac_cv_prog_HAVE_PYTHON3="$HAVE_PYTHON3" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then + ac_cv_prog_HAVE_PYTHON3="yes" + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done + done +IFS=$as_save_IFS + +fi +fi +HAVE_PYTHON3=$ac_cv_prog_HAVE_PYTHON3 +if test -n "$HAVE_PYTHON3"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $HAVE_PYTHON3" >&5 +$as_echo "$HAVE_PYTHON3" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + + + +################################################################ +# 6. Checks for libraries +################################################################# +LIBGSL= +if test "x$with_gsl" != xno; then : + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for gsl_expm1 in -lgsl" >&5 +$as_echo_n "checking for gsl_expm1 in -lgsl... " >&6; } +if ${ac_cv_lib_gsl_gsl_expm1+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lgsl -lgslcblas + $LIBS" +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char gsl_expm1 (); +int +main () +{ +return gsl_expm1 (); + ; + return 0; +} +_ACEOF +if ac_fn_c_try_link "$LINENO"; then : + ac_cv_lib_gsl_gsl_expm1=yes +else + ac_cv_lib_gsl_gsl_expm1=no +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_gsl_gsl_expm1" >&5 +$as_echo "$ac_cv_lib_gsl_gsl_expm1" >&6; } +if test "x$ac_cv_lib_gsl_gsl_expm1" = xyes; then : + LIBGSL="-lgsl -lgslcblas" + + +$as_echo "#define HAVE_LIBGSL 1" >>confdefs.h + + +else + if test "x$with_gsl" != xcheck; then + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error $? "--with-gsl was given, but GSL library was not found +See \`config.log' for more details" "$LINENO" 5; } + fi + +fi + +fi + +# Easel stopwatch high-res timer may try to use clock_gettime, +# which may be in librt +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing clock_gettime" >&5 +$as_echo_n "checking for library containing clock_gettime... " >&6; } +if ${ac_cv_search_clock_gettime+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_func_search_save_LIBS=$LIBS +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char clock_gettime (); +int +main () +{ +return clock_gettime (); + ; + return 0; +} +_ACEOF +for ac_lib in '' rt posix4; do + if test -z "$ac_lib"; then + ac_res="none required" + else + ac_res=-l$ac_lib + LIBS="-l$ac_lib $ac_func_search_save_LIBS" + fi + if ac_fn_c_try_link "$LINENO"; then : + ac_cv_search_clock_gettime=$ac_res +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext + if ${ac_cv_search_clock_gettime+:} false; then : + break +fi +done +if ${ac_cv_search_clock_gettime+:} false; then : + +else + ac_cv_search_clock_gettime=no +fi +rm conftest.$ac_ext +LIBS=$ac_func_search_save_LIBS +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_clock_gettime" >&5 +$as_echo "$ac_cv_search_clock_gettime" >&6; } +ac_res=$ac_cv_search_clock_gettime +if test "$ac_res" != no; then : + test "$ac_res" = "none required" || LIBS="$ac_res $LIBS" + +fi + + +# mingw mmap +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing mmap" >&5 +$as_echo_n "checking for library containing mmap... " >&6; } +if ${ac_cv_search_mmap+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_func_search_save_LIBS=$LIBS +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char mmap (); +int +main () +{ +return mmap (); + ; + return 0; +} +_ACEOF +for ac_lib in '' mman; do + if test -z "$ac_lib"; then + ac_res="none required" + else + ac_res=-l$ac_lib + LIBS="-l$ac_lib $ac_func_search_save_LIBS" + fi + if ac_fn_c_try_link "$LINENO"; then : + ac_cv_search_mmap=$ac_res +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext + if ${ac_cv_search_mmap+:} false; then : + break +fi +done +if ${ac_cv_search_mmap+:} false; then : + +else + ac_cv_search_mmap=no +fi +rm conftest.$ac_ext +LIBS=$ac_func_search_save_LIBS +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_mmap" >&5 +$as_echo "$ac_cv_search_mmap" >&6; } +ac_res=$ac_cv_search_mmap +if test "$ac_res" != no; then : + test "$ac_res" = "none required" || LIBS="$ac_res $LIBS" + +fi + + +################################################################ +# 7. Checks for headers +################################################################# + +# Defines HAVE_SYS_TYPES_H, HAVE_STDINT_H, etc. +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5 +$as_echo_n "checking for ANSI C header files... " >&6; } +if ${ac_cv_header_stdc+:} false; then : + $as_echo_n "(cached) " >&6 +else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include +#include +#include +#include + +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_header_stdc=yes +else + ac_cv_header_stdc=no +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + +if test $ac_cv_header_stdc = yes; then + # SunOS 4.x string.h does not declare mem*, contrary to ANSI. + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include + +_ACEOF +if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | + $EGREP "memchr" >/dev/null 2>&1; then : + +else + ac_cv_header_stdc=no +fi +rm -f conftest* + +fi + +if test $ac_cv_header_stdc = yes; then + # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI. + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include + +_ACEOF +if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | + $EGREP "free" >/dev/null 2>&1; then : + +else + ac_cv_header_stdc=no +fi +rm -f conftest* + +fi + +if test $ac_cv_header_stdc = yes; then + # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi. + if test "$cross_compiling" = yes; then : + : +else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include +#include +#if ((' ' & 0x0FF) == 0x020) +# define ISLOWER(c) ('a' <= (c) && (c) <= 'z') +# define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) +#else +# define ISLOWER(c) \ + (('a' <= (c) && (c) <= 'i') \ + || ('j' <= (c) && (c) <= 'r') \ + || ('s' <= (c) && (c) <= 'z')) +# define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c)) +#endif + +#define XOR(e, f) (((e) && !(f)) || (!(e) && (f))) +int +main () +{ + int i; + for (i = 0; i < 256; i++) + if (XOR (islower (i), ISLOWER (i)) + || toupper (i) != TOUPPER (i)) + return 2; + return 0; +} +_ACEOF +if ac_fn_c_try_run "$LINENO"; then : + +else + ac_cv_header_stdc=no +fi +rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ + conftest.$ac_objext conftest.beam conftest.$ac_ext +fi + +fi +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5 +$as_echo "$ac_cv_header_stdc" >&6; } +if test $ac_cv_header_stdc = yes; then + +$as_echo "#define STDC_HEADERS 1" >>confdefs.h + +fi + +# On IRIX 5.3, sys/types and inttypes.h are conflicting. +for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \ + inttypes.h stdint.h unistd.h +do : + as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` +ac_fn_c_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default +" +if eval test \"x\$"$as_ac_Header"\" = x"yes"; then : + cat >>confdefs.h <<_ACEOF +#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 +_ACEOF + +fi + +done + + +for ac_header in \ + endian.h\ + inttypes.h\ + stdint.h\ + unistd.h\ + sys/types.h\ + netinet/in.h + +do : + as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` +ac_fn_c_check_header_mongrel "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default" +if eval test \"x\$"$as_ac_Header"\" = x"yes"; then : + cat >>confdefs.h <<_ACEOF +#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 +_ACEOF + +fi + +done + + +# Check for sysctl.h separately. On OpenBSD, it requires +# and autoconf needs special logic to deal w. this as +# follows. +for ac_header in sys/param.h +do : + ac_fn_c_check_header_mongrel "$LINENO" "sys/param.h" "ac_cv_header_sys_param_h" "$ac_includes_default" +if test "x$ac_cv_header_sys_param_h" = xyes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_SYS_PARAM_H 1 +_ACEOF + +fi + +done + +for ac_header in sys/sysctl.h +do : + ac_fn_c_check_header_compile "$LINENO" "sys/sysctl.h" "ac_cv_header_sys_sysctl_h" "#ifdef HAVE_SYS_PARAM_H +#include +#endif + +" +if test "x$ac_cv_header_sys_sysctl_h" = xyes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_SYS_SYSCTL_H 1 +_ACEOF + +fi + +done + + + +# altivec.h requires the simd cflags +# For reasons I don't understand, this needs to come after any other CHECK_HEADERS(). +if test "$impl_choice" = "vmx"; then + esl_save_CFLAGS="$CFLAGS" + esl_save_CPPFLAGS="$CPPFLAGS" + CFLAGS="$CFLAGS $VMX_CFLAGS" + CPPFLAGS="$CPPFLAGS $VMX_CFLAGS" + for ac_header in altivec.h +do : + ac_fn_c_check_header_mongrel "$LINENO" "altivec.h" "ac_cv_header_altivec_h" "$ac_includes_default" +if test "x$ac_cv_header_altivec_h" = xyes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_ALTIVEC_H 1 +_ACEOF + +fi + +done + + CFLAGS="$esl_save_CFLAGS" + CPPFLAGS="$esl_save_CPPFLAGS" +fi + +################################################################ +# 8. Checks for types +################################################################# +ac_fn_c_find_uintX_t "$LINENO" "8" "ac_cv_c_uint8_t" +case $ac_cv_c_uint8_t in #( + no|yes) ;; #( + *) + +$as_echo "#define _UINT8_T 1" >>confdefs.h + + +cat >>confdefs.h <<_ACEOF +#define uint8_t $ac_cv_c_uint8_t +_ACEOF +;; + esac + +ac_fn_c_find_uintX_t "$LINENO" "16" "ac_cv_c_uint16_t" +case $ac_cv_c_uint16_t in #( + no|yes) ;; #( + *) + + +cat >>confdefs.h <<_ACEOF +#define uint16_t $ac_cv_c_uint16_t +_ACEOF +;; + esac + +ac_fn_c_find_uintX_t "$LINENO" "32" "ac_cv_c_uint32_t" +case $ac_cv_c_uint32_t in #( + no|yes) ;; #( + *) + +$as_echo "#define _UINT32_T 1" >>confdefs.h + + +cat >>confdefs.h <<_ACEOF +#define uint32_t $ac_cv_c_uint32_t +_ACEOF +;; + esac + +ac_fn_c_find_uintX_t "$LINENO" "64" "ac_cv_c_uint64_t" +case $ac_cv_c_uint64_t in #( + no|yes) ;; #( + *) + +$as_echo "#define _UINT64_T 1" >>confdefs.h + + +cat >>confdefs.h <<_ACEOF +#define uint64_t $ac_cv_c_uint64_t +_ACEOF +;; + esac + + + ac_fn_c_check_type "$LINENO" "uintptr_t" "ac_cv_type_uintptr_t" "$ac_includes_default" +if test "x$ac_cv_type_uintptr_t" = xyes; then : + +$as_echo "#define HAVE_UINTPTR_T 1" >>confdefs.h + +else + for ac_type in 'unsigned int' 'unsigned long int' \ + 'unsigned long long int'; do + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(sizeof (void *) <= sizeof ($ac_type))]; +test_array [0] = 0; +return test_array [0]; + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + +cat >>confdefs.h <<_ACEOF +#define uintptr_t $ac_type +_ACEOF + + ac_type= +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + test -z "$ac_type" && break + done +fi + + +ac_fn_c_check_type "$LINENO" "off_t" "ac_cv_type_off_t" "$ac_includes_default" +if test "x$ac_cv_type_off_t" = xyes; then : + +else + +cat >>confdefs.h <<_ACEOF +#define off_t long int +_ACEOF + +fi + + + +################################################################ +# 9. Checks for structures - currently none +################################################################ + + +################################################################ +# 10. Checks for compiler characteristics +################################################################ + + { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether byte ordering is bigendian" >&5 +$as_echo_n "checking whether byte ordering is bigendian... " >&6; } +if ${ac_cv_c_bigendian+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_cv_c_bigendian=unknown + # See if we're dealing with a universal compiler. + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#ifndef __APPLE_CC__ + not a universal capable compiler + #endif + typedef int dummy; + +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + + # Check for potential -arch flags. It is not universal unless + # there are at least two -arch flags with different values. + ac_arch= + ac_prev= + for ac_word in $CC $CFLAGS $CPPFLAGS $LDFLAGS; do + if test -n "$ac_prev"; then + case $ac_word in + i?86 | x86_64 | ppc | ppc64) + if test -z "$ac_arch" || test "$ac_arch" = "$ac_word"; then + ac_arch=$ac_word + else + ac_cv_c_bigendian=universal + break + fi + ;; + esac + ac_prev= + elif test "x$ac_word" = "x-arch"; then + ac_prev=arch + fi + done +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + if test $ac_cv_c_bigendian = unknown; then + # See if sys/param.h defines the BYTE_ORDER macro. + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include + #include + +int +main () +{ +#if ! (defined BYTE_ORDER && defined BIG_ENDIAN \ + && defined LITTLE_ENDIAN && BYTE_ORDER && BIG_ENDIAN \ + && LITTLE_ENDIAN) + bogus endian macros + #endif + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + # It does; now see whether it defined to BIG_ENDIAN or not. + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include + #include + +int +main () +{ +#if BYTE_ORDER != BIG_ENDIAN + not big endian + #endif + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_c_bigendian=yes +else + ac_cv_c_bigendian=no +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + fi + if test $ac_cv_c_bigendian = unknown; then + # See if defines _LITTLE_ENDIAN or _BIG_ENDIAN (e.g., Solaris). + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include + +int +main () +{ +#if ! (defined _LITTLE_ENDIAN || defined _BIG_ENDIAN) + bogus endian macros + #endif + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + # It does; now see whether it defined to _BIG_ENDIAN or not. + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include + +int +main () +{ +#ifndef _BIG_ENDIAN + not big endian + #endif + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_c_bigendian=yes +else + ac_cv_c_bigendian=no +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + fi + if test $ac_cv_c_bigendian = unknown; then + # Compile a test program. + if test "$cross_compiling" = yes; then : + # Try to guess by grepping values from an object file. + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +short int ascii_mm[] = + { 0x4249, 0x4765, 0x6E44, 0x6961, 0x6E53, 0x7953, 0 }; + short int ascii_ii[] = + { 0x694C, 0x5454, 0x656C, 0x6E45, 0x6944, 0x6E61, 0 }; + int use_ascii (int i) { + return ascii_mm[i] + ascii_ii[i]; + } + short int ebcdic_ii[] = + { 0x89D3, 0xE3E3, 0x8593, 0x95C5, 0x89C4, 0x9581, 0 }; + short int ebcdic_mm[] = + { 0xC2C9, 0xC785, 0x95C4, 0x8981, 0x95E2, 0xA8E2, 0 }; + int use_ebcdic (int i) { + return ebcdic_mm[i] + ebcdic_ii[i]; + } + extern int foo; + +int +main () +{ +return use_ascii (foo) == use_ebcdic (foo); + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + if grep BIGenDianSyS conftest.$ac_objext >/dev/null; then + ac_cv_c_bigendian=yes + fi + if grep LiTTleEnDian conftest.$ac_objext >/dev/null ; then + if test "$ac_cv_c_bigendian" = unknown; then + ac_cv_c_bigendian=no + else + # finding both strings is unlikely to happen, but who knows? + ac_cv_c_bigendian=unknown + fi + fi +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ + + /* Are we little or big endian? From Harbison&Steele. */ + union + { + long int l; + char c[sizeof (long int)]; + } u; + u.l = 1; + return u.c[sizeof (long int) - 1] == 1; + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_run "$LINENO"; then : + ac_cv_c_bigendian=no +else + ac_cv_c_bigendian=yes +fi +rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ + conftest.$ac_objext conftest.beam conftest.$ac_ext +fi + + fi +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_bigendian" >&5 +$as_echo "$ac_cv_c_bigendian" >&6; } + case $ac_cv_c_bigendian in #( + yes) + + +$as_echo "#define WORDS_BIGENDIAN 1" >>confdefs.h + + ;; #( + no) + + if test "$enable_vmx" = "yes"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: ::::::::::--- no vector instruction set ---::::::::::" >&5 +$as_echo "$as_me: ::::::::::--- no vector instruction set ---::::::::::" >&6;} + { $as_echo "$as_me:${as_lineno-$LINENO}: HMMER3 Altivec/VMX only supports bigendian platforms: e.g. ppc64 not ppc64le" >&5 +$as_echo "$as_me: HMMER3 Altivec/VMX only supports bigendian platforms: e.g. ppc64 not ppc64le" >&6;} + as_fn_error $? "No supported vectorization found for your machine." "$LINENO" 5 + fi + ;; #( + universal) + +$as_echo "#define AC_APPLE_UNIVERSAL_BUILD 1" >>confdefs.h + + ;; #( + *) + + { $as_echo "$as_me:${as_lineno-$LINENO}: ::::::::::--- no vector instruction set ---::::::::::" >&5 +$as_echo "$as_me: ::::::::::--- no vector instruction set ---::::::::::" >&6;} + { $as_echo "$as_me:${as_lineno-$LINENO}: Couldn't determine byte order for your platform." >&5 +$as_echo "$as_me: Couldn't determine byte order for your platform." >&6;} + { $as_echo "$as_me:${as_lineno-$LINENO}: HMMER3 vector code is sensitive to byte order." >&5 +$as_echo "$as_me: HMMER3 vector code is sensitive to byte order." >&6;} + as_fn_error $? "No supported vectorization found for your machine." "$LINENO" 5 + ;; + esac + + +# __attribute__() tags on function declarations +# HAVE_FUNC_ATTRIBUTE_NORETURN +# +# The clang static analyzer can't figure out that some of our +# varargs-dependent fatal error handlers (esl_fatal(), for example) +# cannot return. To tell it so, we take advantage of __attribute__ +# tags on function declarations, a non-ISO gcc extension, when +# available. gcc, clang, and other gcc-like compilers support this. +# +# This gets set in the Easel esl_config.h. +# + + + + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for __attribute__((noreturn))" >&5 +$as_echo_n "checking for __attribute__((noreturn))... " >&6; } +if ${ax_cv_have_func_attribute_noreturn+:} false; then : + $as_echo_n "(cached) " >&6 +else + + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + + + void foo( void ) __attribute__((noreturn)); + +int +main () +{ + + ; + return 0; +} + +_ACEOF +if ac_fn_c_try_link "$LINENO"; then : + if test -s conftest.err; then : + ax_cv_have_func_attribute_noreturn=no +else + ax_cv_have_func_attribute_noreturn=yes +fi +else + ax_cv_have_func_attribute_noreturn=no +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext + +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ax_cv_have_func_attribute_noreturn" >&5 +$as_echo "$ax_cv_have_func_attribute_noreturn" >&6; } + + if test yes = $ax_cv_have_func_attribute_noreturn; then : + +cat >>confdefs.h <<_ACEOF +#define HAVE_FUNC_ATTRIBUTE_NORETURN 1 +_ACEOF + +fi + + + + +# HAVE_FUNC_ATTRIBUTE_FORMAT +# +# We have some printf()-style functions that use varargs. +# Apparently when you do something like +# int64_t bigint; +# my_printf("%d", bigint); +# a compiler can't normally detect the size mismatch between the +# specifier (%d) and the argument (bigint). Usually this isn't a +# problem (apparently most platforms cast appropriately) but we had +# problems on ARM. gcc-like compilers allow declaring an attribute +# of format(printf, , ), enabling the +# compiler to typecheck printf()-like arguments, and warn appropriately. +# We only need or use this in development. +# +# This gets set in the Easel esl_config.h. + + + + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for __attribute__((format))" >&5 +$as_echo_n "checking for __attribute__((format))... " >&6; } +if ${ax_cv_have_func_attribute_format+:} false; then : + $as_echo_n "(cached) " >&6 +else + + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + + + int foo(const char *p, ...) __attribute__((format(printf, 1, 2))); + +int +main () +{ + + ; + return 0; +} + +_ACEOF +if ac_fn_c_try_link "$LINENO"; then : + if test -s conftest.err; then : + ax_cv_have_func_attribute_format=no +else + ax_cv_have_func_attribute_format=yes +fi +else + ax_cv_have_func_attribute_format=no +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext + +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ax_cv_have_func_attribute_format" >&5 +$as_echo "$ax_cv_have_func_attribute_format" >&6; } + + if test yes = $ax_cv_have_func_attribute_format; then : + +cat >>confdefs.h <<_ACEOF +#define HAVE_FUNC_ATTRIBUTE_FORMAT 1 +_ACEOF + +fi + + + + + + +################################################################ +# 11. Checks for functions, defining HAVE_FOO when foo is found +################################################################ + +for ac_func in mkstemp +do : + ac_fn_c_check_func "$LINENO" "mkstemp" "ac_cv_func_mkstemp" +if test "x$ac_cv_func_mkstemp" = xyes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_MKSTEMP 1 +_ACEOF + +fi +done + +for ac_func in popen +do : + ac_fn_c_check_func "$LINENO" "popen" "ac_cv_func_popen" +if test "x$ac_cv_func_popen" = xyes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_POPEN 1 +_ACEOF + +fi +done + +for ac_func in putenv +do : + ac_fn_c_check_func "$LINENO" "putenv" "ac_cv_func_putenv" +if test "x$ac_cv_func_putenv" = xyes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_PUTENV 1 +_ACEOF + +fi +done + +for ac_func in strcasecmp +do : + ac_fn_c_check_func "$LINENO" "strcasecmp" "ac_cv_func_strcasecmp" +if test "x$ac_cv_func_strcasecmp" = xyes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_STRCASECMP 1 +_ACEOF + +fi +done + +for ac_func in strsep +do : + ac_fn_c_check_func "$LINENO" "strsep" "ac_cv_func_strsep" +if test "x$ac_cv_func_strsep" = xyes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_STRSEP 1 +_ACEOF + +fi +done + +for ac_func in times +do : + ac_fn_c_check_func "$LINENO" "times" "ac_cv_func_times" +if test "x$ac_cv_func_times" = xyes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_TIMES 1 +_ACEOF + +fi +done + +for ac_func in getpid +do : + ac_fn_c_check_func "$LINENO" "getpid" "ac_cv_func_getpid" +if test "x$ac_cv_func_getpid" = xyes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_GETPID 1 +_ACEOF + +fi +done + +for ac_func in sysctl +do : + ac_fn_c_check_func "$LINENO" "sysctl" "ac_cv_func_sysctl" +if test "x$ac_cv_func_sysctl" = xyes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_SYSCTL 1 +_ACEOF + +fi +done + +for ac_func in sysconf +do : + ac_fn_c_check_func "$LINENO" "sysconf" "ac_cv_func_sysconf" +if test "x$ac_cv_func_sysconf" = xyes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_SYSCONF 1 +_ACEOF + +fi +done + +for ac_func in getcwd +do : + ac_fn_c_check_func "$LINENO" "getcwd" "ac_cv_func_getcwd" +if test "x$ac_cv_func_getcwd" = xyes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_GETCWD 1 +_ACEOF + +fi +done + +for ac_func in chmod +do : + ac_fn_c_check_func "$LINENO" "chmod" "ac_cv_func_chmod" +if test "x$ac_cv_func_chmod" = xyes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_CHMOD 1 +_ACEOF + +fi +done + +for ac_func in stat +do : + ac_fn_c_check_func "$LINENO" "stat" "ac_cv_func_stat" +if test "x$ac_cv_func_stat" = xyes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_STAT 1 +_ACEOF + +fi +done + +for ac_func in fstat +do : + ac_fn_c_check_func "$LINENO" "fstat" "ac_cv_func_fstat" +if test "x$ac_cv_func_fstat" = xyes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_FSTAT 1 +_ACEOF + +fi +done + +for ac_func in erfc +do : + ac_fn_c_check_func "$LINENO" "erfc" "ac_cv_func_erfc" +if test "x$ac_cv_func_erfc" = xyes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_ERFC 1 +_ACEOF + +fi +done + + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing ntohs" >&5 +$as_echo_n "checking for library containing ntohs... " >&6; } +if ${ac_cv_search_ntohs+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_func_search_save_LIBS=$LIBS +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char ntohs (); +int +main () +{ +return ntohs (); + ; + return 0; +} +_ACEOF +for ac_lib in '' socket; do + if test -z "$ac_lib"; then + ac_res="none required" + else + ac_res=-l$ac_lib + LIBS="-l$ac_lib $ac_func_search_save_LIBS" + fi + if ac_fn_c_try_link "$LINENO"; then : + ac_cv_search_ntohs=$ac_res +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext + if ${ac_cv_search_ntohs+:} false; then : + break +fi +done +if ${ac_cv_search_ntohs+:} false; then : + +else + ac_cv_search_ntohs=no +fi +rm conftest.$ac_ext +LIBS=$ac_func_search_save_LIBS +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_ntohs" >&5 +$as_echo "$ac_cv_search_ntohs" >&6; } +ac_res=$ac_cv_search_ntohs +if test "$ac_res" != no; then : + test "$ac_res" = "none required" || LIBS="$ac_res $LIBS" + +fi + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing ntohl" >&5 +$as_echo_n "checking for library containing ntohl... " >&6; } +if ${ac_cv_search_ntohl+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_func_search_save_LIBS=$LIBS +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char ntohl (); +int +main () +{ +return ntohl (); + ; + return 0; +} +_ACEOF +for ac_lib in '' socket; do + if test -z "$ac_lib"; then + ac_res="none required" + else + ac_res=-l$ac_lib + LIBS="-l$ac_lib $ac_func_search_save_LIBS" + fi + if ac_fn_c_try_link "$LINENO"; then : + ac_cv_search_ntohl=$ac_res +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext + if ${ac_cv_search_ntohl+:} false; then : + break +fi +done +if ${ac_cv_search_ntohl+:} false; then : + +else + ac_cv_search_ntohl=no +fi +rm conftest.$ac_ext +LIBS=$ac_func_search_save_LIBS +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_ntohl" >&5 +$as_echo "$ac_cv_search_ntohl" >&6; } +ac_res=$ac_cv_search_ntohl +if test "$ac_res" != no; then : + test "$ac_res" = "none required" || LIBS="$ac_res $LIBS" + +fi + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing htons" >&5 +$as_echo_n "checking for library containing htons... " >&6; } +if ${ac_cv_search_htons+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_func_search_save_LIBS=$LIBS +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char htons (); +int +main () +{ +return htons (); + ; + return 0; +} +_ACEOF +for ac_lib in '' socket; do + if test -z "$ac_lib"; then + ac_res="none required" + else + ac_res=-l$ac_lib + LIBS="-l$ac_lib $ac_func_search_save_LIBS" + fi + if ac_fn_c_try_link "$LINENO"; then : + ac_cv_search_htons=$ac_res +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext + if ${ac_cv_search_htons+:} false; then : + break +fi +done +if ${ac_cv_search_htons+:} false; then : + +else + ac_cv_search_htons=no +fi +rm conftest.$ac_ext +LIBS=$ac_func_search_save_LIBS +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_htons" >&5 +$as_echo "$ac_cv_search_htons" >&6; } +ac_res=$ac_cv_search_htons +if test "$ac_res" != no; then : + test "$ac_res" = "none required" || LIBS="$ac_res $LIBS" + +fi + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing htonl" >&5 +$as_echo_n "checking for library containing htonl... " >&6; } +if ${ac_cv_search_htonl+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_func_search_save_LIBS=$LIBS +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char htonl (); +int +main () +{ +return htonl (); + ; + return 0; +} +_ACEOF +for ac_lib in '' socket; do + if test -z "$ac_lib"; then + ac_res="none required" + else + ac_res=-l$ac_lib + LIBS="-l$ac_lib $ac_func_search_save_LIBS" + fi + if ac_fn_c_try_link "$LINENO"; then : + ac_cv_search_htonl=$ac_res +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext + if ${ac_cv_search_htonl+:} false; then : + break +fi +done +if ${ac_cv_search_htonl+:} false; then : + +else + ac_cv_search_htonl=no +fi +rm conftest.$ac_ext +LIBS=$ac_func_search_save_LIBS +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_htonl" >&5 +$as_echo "$ac_cv_search_htonl" >&6; } +ac_res=$ac_cv_search_htonl +if test "$ac_res" != no; then : + test "$ac_res" = "none required" || LIBS="$ac_res $LIBS" + +fi + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing socket" >&5 +$as_echo_n "checking for library containing socket... " >&6; } +if ${ac_cv_search_socket+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_func_search_save_LIBS=$LIBS +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char socket (); +int +main () +{ +return socket (); + ; + return 0; +} +_ACEOF +for ac_lib in '' socket; do + if test -z "$ac_lib"; then + ac_res="none required" + else + ac_res=-l$ac_lib + LIBS="-l$ac_lib $ac_func_search_save_LIBS" + fi + if ac_fn_c_try_link "$LINENO"; then : + ac_cv_search_socket=$ac_res +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext + if ${ac_cv_search_socket+:} false; then : + break +fi +done +if ${ac_cv_search_socket+:} false; then : + +else + ac_cv_search_socket=no +fi +rm conftest.$ac_ext +LIBS=$ac_func_search_save_LIBS +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_socket" >&5 +$as_echo "$ac_cv_search_socket" >&6; } +ac_res=$ac_cv_search_socket +if test "$ac_res" != no; then : + test "$ac_res" = "none required" || LIBS="$ac_res $LIBS" + +fi + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing inet_pton" >&5 +$as_echo_n "checking for library containing inet_pton... " >&6; } +if ${ac_cv_search_inet_pton+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_func_search_save_LIBS=$LIBS +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char inet_pton (); +int +main () +{ +return inet_pton (); + ; + return 0; +} +_ACEOF +for ac_lib in '' nsl; do + if test -z "$ac_lib"; then + ac_res="none required" + else + ac_res=-l$ac_lib + LIBS="-l$ac_lib $ac_func_search_save_LIBS" + fi + if ac_fn_c_try_link "$LINENO"; then : + ac_cv_search_inet_pton=$ac_res +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext + if ${ac_cv_search_inet_pton+:} false; then : + break +fi +done +if ${ac_cv_search_inet_pton+:} false; then : + +else + ac_cv_search_inet_pton=no +fi +rm conftest.$ac_ext +LIBS=$ac_func_search_save_LIBS +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_inet_pton" >&5 +$as_echo "$ac_cv_search_inet_pton" >&6; } +ac_res=$ac_cv_search_inet_pton +if test "$ac_res" != no; then : + test "$ac_res" = "none required" || LIBS="$ac_res $LIBS" + +fi + + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for _LARGEFILE_SOURCE value needed for large files" >&5 +$as_echo_n "checking for _LARGEFILE_SOURCE value needed for large files... " >&6; } +if ${ac_cv_sys_largefile_source+:} false; then : + $as_echo_n "(cached) " >&6 +else + while :; do + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include /* for off_t */ + #include +int +main () +{ +int (*fp) (FILE *, off_t, int) = fseeko; + return fseeko (stdin, 0, 0) && fp (stdin, 0, 0); + ; + return 0; +} +_ACEOF +if ac_fn_c_try_link "$LINENO"; then : + ac_cv_sys_largefile_source=no; break +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#define _LARGEFILE_SOURCE 1 +#include /* for off_t */ + #include +int +main () +{ +int (*fp) (FILE *, off_t, int) = fseeko; + return fseeko (stdin, 0, 0) && fp (stdin, 0, 0); + ; + return 0; +} +_ACEOF +if ac_fn_c_try_link "$LINENO"; then : + ac_cv_sys_largefile_source=1; break +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext + ac_cv_sys_largefile_source=unknown + break +done +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sys_largefile_source" >&5 +$as_echo "$ac_cv_sys_largefile_source" >&6; } +case $ac_cv_sys_largefile_source in #( + no | unknown) ;; + *) +cat >>confdefs.h <<_ACEOF +#define _LARGEFILE_SOURCE $ac_cv_sys_largefile_source +_ACEOF +;; +esac +rm -rf conftest* + +# We used to try defining _XOPEN_SOURCE=500 too, to work around a bug +# in glibc 2.1.3, but that breaks too many other things. +# If you want fseeko and ftello with glibc, upgrade to a fixed glibc. +if test $ac_cv_sys_largefile_source != unknown; then + +$as_echo "#define HAVE_FSEEKO 1" >>confdefs.h + +fi + + + +################################################################# +# 12. System services +################################################################# +# Check whether --enable-largefile was given. +if test "${enable_largefile+set}" = set; then : + enableval=$enable_largefile; +fi + +if test "$enable_largefile" != no; then + + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for special C compiler options needed for large files" >&5 +$as_echo_n "checking for special C compiler options needed for large files... " >&6; } +if ${ac_cv_sys_largefile_CC+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_cv_sys_largefile_CC=no + if test "$GCC" != yes; then + ac_save_CC=$CC + while :; do + # IRIX 6.2 and later do not support large files by default, + # so use the C compiler's -n32 option if that helps. + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include + /* Check that off_t can represent 2**63 - 1 correctly. + We can't simply define LARGE_OFF_T to be 9223372036854775807, + since some C++ compilers masquerading as C compilers + incorrectly reject 9223372036854775807. */ +#define LARGE_OFF_T ((((off_t) 1 << 31) << 31) - 1 + (((off_t) 1 << 31) << 31)) + int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721 + && LARGE_OFF_T % 2147483647 == 1) + ? 1 : -1]; +int +main () +{ + + ; + return 0; +} +_ACEOF + if ac_fn_c_try_compile "$LINENO"; then : + break +fi +rm -f core conftest.err conftest.$ac_objext + CC="$CC -n32" + if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_sys_largefile_CC=' -n32'; break +fi +rm -f core conftest.err conftest.$ac_objext + break + done + CC=$ac_save_CC + rm -f conftest.$ac_ext + fi +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sys_largefile_CC" >&5 +$as_echo "$ac_cv_sys_largefile_CC" >&6; } + if test "$ac_cv_sys_largefile_CC" != no; then + CC=$CC$ac_cv_sys_largefile_CC + fi + + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for _FILE_OFFSET_BITS value needed for large files" >&5 +$as_echo_n "checking for _FILE_OFFSET_BITS value needed for large files... " >&6; } +if ${ac_cv_sys_file_offset_bits+:} false; then : + $as_echo_n "(cached) " >&6 +else + while :; do + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include + /* Check that off_t can represent 2**63 - 1 correctly. + We can't simply define LARGE_OFF_T to be 9223372036854775807, + since some C++ compilers masquerading as C compilers + incorrectly reject 9223372036854775807. */ +#define LARGE_OFF_T ((((off_t) 1 << 31) << 31) - 1 + (((off_t) 1 << 31) << 31)) + int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721 + && LARGE_OFF_T % 2147483647 == 1) + ? 1 : -1]; +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_sys_file_offset_bits=no; break +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#define _FILE_OFFSET_BITS 64 +#include + /* Check that off_t can represent 2**63 - 1 correctly. + We can't simply define LARGE_OFF_T to be 9223372036854775807, + since some C++ compilers masquerading as C compilers + incorrectly reject 9223372036854775807. */ +#define LARGE_OFF_T ((((off_t) 1 << 31) << 31) - 1 + (((off_t) 1 << 31) << 31)) + int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721 + && LARGE_OFF_T % 2147483647 == 1) + ? 1 : -1]; +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_sys_file_offset_bits=64; break +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + ac_cv_sys_file_offset_bits=unknown + break +done +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sys_file_offset_bits" >&5 +$as_echo "$ac_cv_sys_file_offset_bits" >&6; } +case $ac_cv_sys_file_offset_bits in #( + no | unknown) ;; + *) +cat >>confdefs.h <<_ACEOF +#define _FILE_OFFSET_BITS $ac_cv_sys_file_offset_bits +_ACEOF +;; +esac +rm -rf conftest* + if test $ac_cv_sys_file_offset_bits = unknown; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for _LARGE_FILES value needed for large files" >&5 +$as_echo_n "checking for _LARGE_FILES value needed for large files... " >&6; } +if ${ac_cv_sys_large_files+:} false; then : + $as_echo_n "(cached) " >&6 +else + while :; do + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include + /* Check that off_t can represent 2**63 - 1 correctly. + We can't simply define LARGE_OFF_T to be 9223372036854775807, + since some C++ compilers masquerading as C compilers + incorrectly reject 9223372036854775807. */ +#define LARGE_OFF_T ((((off_t) 1 << 31) << 31) - 1 + (((off_t) 1 << 31) << 31)) + int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721 + && LARGE_OFF_T % 2147483647 == 1) + ? 1 : -1]; +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_sys_large_files=no; break +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#define _LARGE_FILES 1 +#include + /* Check that off_t can represent 2**63 - 1 correctly. + We can't simply define LARGE_OFF_T to be 9223372036854775807, + since some C++ compilers masquerading as C compilers + incorrectly reject 9223372036854775807. */ +#define LARGE_OFF_T ((((off_t) 1 << 31) << 31) - 1 + (((off_t) 1 << 31) << 31)) + int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721 + && LARGE_OFF_T % 2147483647 == 1) + ? 1 : -1]; +int +main () +{ + + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_sys_large_files=1; break +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + ac_cv_sys_large_files=unknown + break +done +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sys_large_files" >&5 +$as_echo "$ac_cv_sys_large_files" >&6; } +case $ac_cv_sys_large_files in #( + no | unknown) ;; + *) +cat >>confdefs.h <<_ACEOF +#define _LARGE_FILES $ac_cv_sys_large_files +_ACEOF +;; +esac +rm -rf conftest* + fi + + +fi + + + + +################################################################ +# 13. Config subdirs and files +################################################################ + +# HMMER Makefiles. +ac_config_files="$ac_config_files Makefile src/Makefile testsuite/Makefile profmark/Makefile src/impl_${impl_choice}/Makefile documentation/Makefile documentation/man/Makefile documentation/userguide/Makefile documentation/userguide/inclusions/Makefile libdivsufsort/Makefile" + + +# Easel Makefiles. +ac_config_files="$ac_config_files easel/Makefile easel/miniapps/Makefile easel/testsuite/Makefile easel/documentation/Makefile" + + +# Substitutions in Userguide .tex files +# HMMER_VERSION, HMMER_DATE, HMMER_COPYRIGHT +ac_config_files="$ac_config_files documentation/userguide/titlepage.tex documentation/userguide/titlepage_daemon.tex documentation/userguide/copyright.tex" + + +# Substitutions in HMMER man pages: +# HMMER_VERSION, HMMER_DATE, HMMER_COPYRIGHT, HMMER_LICENSE, HMMER_URL +ac_config_files="$ac_config_files documentation/man/alimask.man documentation/man/hmmalign.man documentation/man/hmmbuild.man documentation/man/hmmc2.man documentation/man/hmmconvert.man documentation/man/hmmemit.man documentation/man/hmmer.man documentation/man/hmmfetch.man documentation/man/hmmlogo.man documentation/man/hmmpgmd.man documentation/man/hmmpgmd_shard.man documentation/man/hmmpress.man documentation/man/hmmscan.man documentation/man/hmmsearch.man documentation/man/hmmsim.man documentation/man/hmmstat.man documentation/man/jackhmmer.man documentation/man/makehmmerdb.man documentation/man/nhmmer.man documentation/man/nhmmscan.man documentation/man/phmmer.man" + + +# Substitutions in Easel man pages: +# EASEL_VERSION, EASEL_DATE, EASEL_COPYRIGHT, EASEL_LICENSE, EASEL_URL +ac_config_files="$ac_config_files easel/miniapps/esl-afetch.man easel/miniapps/esl-alimanip.man easel/miniapps/esl-alimap.man easel/miniapps/esl-alimask.man easel/miniapps/esl-alimerge.man easel/miniapps/esl-alipid.man easel/miniapps/esl-alirev.man easel/miniapps/esl-alistat.man easel/miniapps/esl-compalign.man easel/miniapps/esl-compstruct.man easel/miniapps/esl-construct.man easel/miniapps/esl-histplot.man easel/miniapps/esl-mask.man easel/miniapps/esl-mixdchlet.man easel/miniapps/esl-reformat.man easel/miniapps/esl-selectn.man easel/miniapps/esl-seqrange.man easel/miniapps/esl-seqstat.man easel/miniapps/esl-sfetch.man easel/miniapps/esl-shuffle.man easel/miniapps/esl-ssdraw.man easel/miniapps/esl-translate.man easel/miniapps/esl-weight.man" + + +ac_config_headers="$ac_config_headers easel/decoy_config.h" + # Put this first to keep gnu 'autoheader' from overwriting a real config file. +ac_config_headers="$ac_config_headers src/p7_config.h" + +ac_config_headers="$ac_config_headers easel/esl_config.h" + +ac_config_headers="$ac_config_headers libdivsufsort/divsufsort.h" + + +# the following incantation establishes a symlink of +# src/impl_{whatever} to src/impl in the *build* directory. +# Testsuite sqc tests rely on it. +ac_config_links="$ac_config_links src/impl:${ac_top_build_prefix}src/impl_${impl_choice}" + + +# Windows does not support symlinks so this command prevents the previous +# throwing an error on subsequent configures. However, you will need to do +# a manual copy prior to running tests. The copy should be done during make. + + + +################################################################ +# 14. AC_OUTPUT +################################################################ +cat >confcache <<\_ACEOF +# This file is a shell script that caches the results of configure +# tests run on this system so they can be shared between configure +# scripts and configure runs, see configure's option --config-cache. +# It is not useful on other systems. If it contains results you don't +# want to keep, you may remove or edit it. +# +# config.status only pays attention to the cache file if you give it +# the --recheck option to rerun configure. +# +# `ac_cv_env_foo' variables (set or unset) will be overridden when +# loading this file, other *unset* `ac_cv_foo' will be assigned the +# following values. + +_ACEOF + +# The following way of writing the cache mishandles newlines in values, +# but we know of no workaround that is simple, portable, and efficient. +# So, we kill variables containing newlines. +# Ultrix sh set writes to stderr and can't be redirected directly, +# and sets the high bit in the cache file unless we assign to the vars. +( + for ac_var in `(set) 2>&1 | sed -n 's/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'`; do + eval ac_val=\$$ac_var + case $ac_val in #( + *${as_nl}*) + case $ac_var in #( + *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5 +$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; + esac + case $ac_var in #( + _ | IFS | as_nl) ;; #( + BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #( + *) { eval $ac_var=; unset $ac_var;} ;; + esac ;; + esac + done + + (set) 2>&1 | + case $as_nl`(ac_space=' '; set) 2>&1` in #( + *${as_nl}ac_space=\ *) + # `set' does not quote correctly, so add quotes: double-quote + # substitution turns \\\\ into \\, and sed turns \\ into \. + sed -n \ + "s/'/'\\\\''/g; + s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p" + ;; #( + *) + # `set' quotes correctly as required by POSIX, so do not add quotes. + sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p" + ;; + esac | + sort +) | + sed ' + /^ac_cv_env_/b end + t clear + :clear + s/^\([^=]*\)=\(.*[{}].*\)$/test "${\1+set}" = set || &/ + t end + s/^\([^=]*\)=\(.*\)$/\1=${\1=\2}/ + :end' >>confcache +if diff "$cache_file" confcache >/dev/null 2>&1; then :; else + if test -w "$cache_file"; then + if test "x$cache_file" != "x/dev/null"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5 +$as_echo "$as_me: updating cache $cache_file" >&6;} + if test ! -f "$cache_file" || test -h "$cache_file"; then + cat confcache >"$cache_file" + else + case $cache_file in #( + */* | ?:*) + mv -f confcache "$cache_file"$$ && + mv -f "$cache_file"$$ "$cache_file" ;; #( + *) + mv -f confcache "$cache_file" ;; + esac + fi + fi + else + { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5 +$as_echo "$as_me: not updating unwritable cache $cache_file" >&6;} + fi +fi +rm -f confcache + +test "x$prefix" = xNONE && prefix=$ac_default_prefix +# Let make expand exec_prefix. +test "x$exec_prefix" = xNONE && exec_prefix='${prefix}' + +DEFS=-DHAVE_CONFIG_H + +ac_libobjs= +ac_ltlibobjs= +U= +for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue + # 1. Remove the extension, and $U if already installed. + ac_script='s/\$U\././;s/\.o$//;s/\.obj$//' + ac_i=`$as_echo "$ac_i" | sed "$ac_script"` + # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR + # will be set to the directory where LIBOBJS objects are built. + as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext" + as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo' +done +LIBOBJS=$ac_libobjs + +LTLIBOBJS=$ac_ltlibobjs + + + +test -d src/impl && rm -rf src/impl + +: "${CONFIG_STATUS=./config.status}" +ac_write_fail=0 +ac_clean_files_save=$ac_clean_files +ac_clean_files="$ac_clean_files $CONFIG_STATUS" +{ $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5 +$as_echo "$as_me: creating $CONFIG_STATUS" >&6;} +as_write_fail=0 +cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1 +#! $SHELL +# Generated by $as_me. +# Run this file to recreate the current configuration. +# Compiler output produced by configure, useful for debugging +# configure, is in config.log if it exists. + +debug=false +ac_cs_recheck=false +ac_cs_silent=false + +SHELL=\${CONFIG_SHELL-$SHELL} +export SHELL +_ASEOF +cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1 +## -------------------- ## +## M4sh Initialization. ## +## -------------------- ## + +# Be more Bourne compatible +DUALCASE=1; export DUALCASE # for MKS sh +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : + emulate sh + NULLCMD=: + # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which + # is contrary to our usage. Disable this feature. + alias -g '${1+"$@"}'='"$@"' + setopt NO_GLOB_SUBST +else + case `(set -o) 2>/dev/null` in #( + *posix*) : + set -o posix ;; #( + *) : + ;; +esac +fi + + +as_nl=' +' +export as_nl +# Printing a long string crashes Solaris 7 /usr/bin/printf. +as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\' +as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo +as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo +# Prefer a ksh shell builtin over an external printf program on Solaris, +# but without wasting forks for bash or zsh. +if test -z "$BASH_VERSION$ZSH_VERSION" \ + && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then + as_echo='print -r --' + as_echo_n='print -rn --' +elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then + as_echo='printf %s\n' + as_echo_n='printf %s' +else + if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then + as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"' + as_echo_n='/usr/ucb/echo -n' + else + as_echo_body='eval expr "X$1" : "X\\(.*\\)"' + as_echo_n_body='eval + arg=$1; + case $arg in #( + *"$as_nl"*) + expr "X$arg" : "X\\(.*\\)$as_nl"; + arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;; + esac; + expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl" + ' + export as_echo_n_body + as_echo_n='sh -c $as_echo_n_body as_echo' + fi + export as_echo_body + as_echo='sh -c $as_echo_body as_echo' +fi + +# The user is always right. +if test "${PATH_SEPARATOR+set}" != set; then + PATH_SEPARATOR=: + (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && { + (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 || + PATH_SEPARATOR=';' + } +fi + + +# IFS +# We need space, tab and new line, in precisely that order. Quoting is +# there to prevent editors from complaining about space-tab. +# (If _AS_PATH_WALK were called with IFS unset, it would disable word +# splitting by setting IFS to empty value.) +IFS=" "" $as_nl" + +# Find who we are. Look in the path if we contain no directory separator. +as_myself= +case $0 in #(( + *[\\/]* ) as_myself=$0 ;; + *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break + done +IFS=$as_save_IFS + + ;; +esac +# We did not find ourselves, most probably we were run as `sh COMMAND' +# in which case we are not to be found in the path. +if test "x$as_myself" = x; then + as_myself=$0 +fi +if test ! -f "$as_myself"; then + $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2 + exit 1 +fi + +# Unset variables that we do not need and which cause bugs (e.g. in +# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1" +# suppresses any "Segmentation fault" message there. '((' could +# trigger a bug in pdksh 5.2.14. +for as_var in BASH_ENV ENV MAIL MAILPATH +do eval test x\${$as_var+set} = xset \ + && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || : +done +PS1='$ ' +PS2='> ' +PS4='+ ' + +# NLS nuisances. +LC_ALL=C +export LC_ALL +LANGUAGE=C +export LANGUAGE + +# CDPATH. +(unset CDPATH) >/dev/null 2>&1 && unset CDPATH + + +# as_fn_error STATUS ERROR [LINENO LOG_FD] +# ---------------------------------------- +# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are +# provided, also output the error to LOG_FD, referencing LINENO. Then exit the +# script with STATUS, using 1 if that was 0. +as_fn_error () +{ + as_status=$1; test $as_status -eq 0 && as_status=1 + if test "$4"; then + as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4 + fi + $as_echo "$as_me: error: $2" >&2 + as_fn_exit $as_status +} # as_fn_error + + +# as_fn_set_status STATUS +# ----------------------- +# Set $? to STATUS, without forking. +as_fn_set_status () +{ + return $1 +} # as_fn_set_status + +# as_fn_exit STATUS +# ----------------- +# Exit the shell with STATUS, even in a "trap 0" or "set -e" context. +as_fn_exit () +{ + set +e + as_fn_set_status $1 + exit $1 +} # as_fn_exit + +# as_fn_unset VAR +# --------------- +# Portably unset VAR. +as_fn_unset () +{ + { eval $1=; unset $1;} +} +as_unset=as_fn_unset +# as_fn_append VAR VALUE +# ---------------------- +# Append the text in VALUE to the end of the definition contained in VAR. Take +# advantage of any shell optimizations that allow amortized linear growth over +# repeated appends, instead of the typical quadratic growth present in naive +# implementations. +if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then : + eval 'as_fn_append () + { + eval $1+=\$2 + }' +else + as_fn_append () + { + eval $1=\$$1\$2 + } +fi # as_fn_append + +# as_fn_arith ARG... +# ------------------ +# Perform arithmetic evaluation on the ARGs, and store the result in the +# global $as_val. Take advantage of shells that can avoid forks. The arguments +# must be portable across $(()) and expr. +if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then : + eval 'as_fn_arith () + { + as_val=$(( $* )) + }' +else + as_fn_arith () + { + as_val=`expr "$@" || test $? -eq 1` + } +fi # as_fn_arith + + +if expr a : '\(a\)' >/dev/null 2>&1 && + test "X`expr 00001 : '.*\(...\)'`" = X001; then + as_expr=expr +else + as_expr=false +fi + +if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then + as_basename=basename +else + as_basename=false +fi + +if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then + as_dirname=dirname +else + as_dirname=false +fi + +as_me=`$as_basename -- "$0" || +$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ + X"$0" : 'X\(//\)$' \| \ + X"$0" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X/"$0" | + sed '/^.*\/\([^/][^/]*\)\/*$/{ + s//\1/ + q + } + /^X\/\(\/\/\)$/{ + s//\1/ + q + } + /^X\/\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` + +# Avoid depending upon Character Ranges. +as_cr_letters='abcdefghijklmnopqrstuvwxyz' +as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' +as_cr_Letters=$as_cr_letters$as_cr_LETTERS +as_cr_digits='0123456789' +as_cr_alnum=$as_cr_Letters$as_cr_digits + +ECHO_C= ECHO_N= ECHO_T= +case `echo -n x` in #((((( +-n*) + case `echo 'xy\c'` in + *c*) ECHO_T=' ';; # ECHO_T is single tab character. + xy) ECHO_C='\c';; + *) echo `echo ksh88 bug on AIX 6.1` > /dev/null + ECHO_T=' ';; + esac;; +*) + ECHO_N='-n';; +esac + +rm -f conf$$ conf$$.exe conf$$.file +if test -d conf$$.dir; then + rm -f conf$$.dir/conf$$.file +else + rm -f conf$$.dir + mkdir conf$$.dir 2>/dev/null +fi +if (echo >conf$$.file) 2>/dev/null; then + if ln -s conf$$.file conf$$ 2>/dev/null; then + as_ln_s='ln -s' + # ... but there are two gotchas: + # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail. + # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable. + # In both cases, we have to default to `cp -pR'. + ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe || + as_ln_s='cp -pR' + elif ln conf$$.file conf$$ 2>/dev/null; then + as_ln_s=ln + else + as_ln_s='cp -pR' + fi +else + as_ln_s='cp -pR' +fi +rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file +rmdir conf$$.dir 2>/dev/null + + +# as_fn_mkdir_p +# ------------- +# Create "$as_dir" as a directory, including parents if necessary. +as_fn_mkdir_p () +{ + + case $as_dir in #( + -*) as_dir=./$as_dir;; + esac + test -d "$as_dir" || eval $as_mkdir_p || { + as_dirs= + while :; do + case $as_dir in #( + *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( + *) as_qdir=$as_dir;; + esac + as_dirs="'$as_qdir' $as_dirs" + as_dir=`$as_dirname -- "$as_dir" || +$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$as_dir" : 'X\(//\)[^/]' \| \ + X"$as_dir" : 'X\(//\)$' \| \ + X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X"$as_dir" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ + s//\1/ + q + } + /^X\(\/\/\)[^/].*/{ + s//\1/ + q + } + /^X\(\/\/\)$/{ + s//\1/ + q + } + /^X\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` + test -d "$as_dir" && break + done + test -z "$as_dirs" || eval "mkdir $as_dirs" + } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir" + + +} # as_fn_mkdir_p +if mkdir -p . 2>/dev/null; then + as_mkdir_p='mkdir -p "$as_dir"' +else + test -d ./-p && rmdir ./-p + as_mkdir_p=false +fi + + +# as_fn_executable_p FILE +# ----------------------- +# Test if FILE is an executable regular file. +as_fn_executable_p () +{ + test -f "$1" && test -x "$1" +} # as_fn_executable_p +as_test_x='test -x' +as_executable_p=as_fn_executable_p + +# Sed expression to map a string onto a valid CPP name. +as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'" + +# Sed expression to map a string onto a valid variable name. +as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'" + + +exec 6>&1 +## ----------------------------------- ## +## Main body of $CONFIG_STATUS script. ## +## ----------------------------------- ## +_ASEOF +test $as_write_fail = 0 && chmod +x $CONFIG_STATUS || ac_write_fail=1 + +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 +# Save the log message, to keep $0 and so on meaningful, and to +# report actual input values of CONFIG_FILES etc. instead of their +# values after options handling. +ac_log=" +This file was extended by HMMER $as_me 3.3.2, which was +generated by GNU Autoconf 2.69. Invocation command line was + + CONFIG_FILES = $CONFIG_FILES + CONFIG_HEADERS = $CONFIG_HEADERS + CONFIG_LINKS = $CONFIG_LINKS + CONFIG_COMMANDS = $CONFIG_COMMANDS + $ $0 $@ + +on `(hostname || uname -n) 2>/dev/null | sed 1q` +" + +_ACEOF + +case $ac_config_files in *" +"*) set x $ac_config_files; shift; ac_config_files=$*;; +esac + +case $ac_config_headers in *" +"*) set x $ac_config_headers; shift; ac_config_headers=$*;; +esac + + +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 +# Files that config.status was made for. +config_files="$ac_config_files" +config_headers="$ac_config_headers" +config_links="$ac_config_links" + +_ACEOF + +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 +ac_cs_usage="\ +\`$as_me' instantiates files and other configuration actions +from templates according to the current configuration. Unless the files +and actions are specified as TAGs, all are instantiated by default. + +Usage: $0 [OPTION]... [TAG]... + + -h, --help print this help, then exit + -V, --version print version number and configuration settings, then exit + --config print configuration, then exit + -q, --quiet, --silent + do not print progress messages + -d, --debug don't remove temporary files + --recheck update $as_me by reconfiguring in the same conditions + --file=FILE[:TEMPLATE] + instantiate the configuration file FILE + --header=FILE[:TEMPLATE] + instantiate the configuration header FILE + +Configuration files: +$config_files + +Configuration headers: +$config_headers + +Configuration links: +$config_links + +Report bugs to ." + +_ACEOF +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 +ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" +ac_cs_version="\\ +HMMER config.status 3.3.2 +configured by $0, generated by GNU Autoconf 2.69, + with options \\"\$ac_cs_config\\" + +Copyright (C) 2012 Free Software Foundation, Inc. +This config.status script is free software; the Free Software Foundation +gives unlimited permission to copy, distribute and modify it." + +ac_pwd='$ac_pwd' +srcdir='$srcdir' +INSTALL='$INSTALL' +test -n "\$AWK" || AWK=awk +_ACEOF + +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 +# The default lists apply if the user does not specify any file. +ac_need_defaults=: +while test $# != 0 +do + case $1 in + --*=?*) + ac_option=`expr "X$1" : 'X\([^=]*\)='` + ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'` + ac_shift=: + ;; + --*=) + ac_option=`expr "X$1" : 'X\([^=]*\)='` + ac_optarg= + ac_shift=: + ;; + *) + ac_option=$1 + ac_optarg=$2 + ac_shift=shift + ;; + esac + + case $ac_option in + # Handling of the options. + -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r) + ac_cs_recheck=: ;; + --version | --versio | --versi | --vers | --ver | --ve | --v | -V ) + $as_echo "$ac_cs_version"; exit ;; + --config | --confi | --conf | --con | --co | --c ) + $as_echo "$ac_cs_config"; exit ;; + --debug | --debu | --deb | --de | --d | -d ) + debug=: ;; + --file | --fil | --fi | --f ) + $ac_shift + case $ac_optarg in + *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;; + '') as_fn_error $? "missing file argument" ;; + esac + as_fn_append CONFIG_FILES " '$ac_optarg'" + ac_need_defaults=false;; + --header | --heade | --head | --hea ) + $ac_shift + case $ac_optarg in + *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;; + esac + as_fn_append CONFIG_HEADERS " '$ac_optarg'" + ac_need_defaults=false;; + --he | --h) + # Conflict between --help and --header + as_fn_error $? "ambiguous option: \`$1' +Try \`$0 --help' for more information.";; + --help | --hel | -h ) + $as_echo "$ac_cs_usage"; exit ;; + -q | -quiet | --quiet | --quie | --qui | --qu | --q \ + | -silent | --silent | --silen | --sile | --sil | --si | --s) + ac_cs_silent=: ;; + + # This is an error. + -*) as_fn_error $? "unrecognized option: \`$1' +Try \`$0 --help' for more information." ;; + + *) as_fn_append ac_config_targets " $1" + ac_need_defaults=false ;; + + esac + shift +done + +ac_configure_extra_args= + +if $ac_cs_silent; then + exec 6>/dev/null + ac_configure_extra_args="$ac_configure_extra_args --silent" +fi + +_ACEOF +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 +if \$ac_cs_recheck; then + set X $SHELL '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion + shift + \$as_echo "running CONFIG_SHELL=$SHELL \$*" >&6 + CONFIG_SHELL='$SHELL' + export CONFIG_SHELL + exec "\$@" +fi + +_ACEOF +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 +exec 5>>config.log +{ + echo + sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX +## Running $as_me. ## +_ASBOX + $as_echo "$ac_log" +} >&5 + +_ACEOF +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 +_ACEOF + +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 + +# Handling of arguments. +for ac_config_target in $ac_config_targets +do + case $ac_config_target in + "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;; + "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;; + "testsuite/Makefile") CONFIG_FILES="$CONFIG_FILES testsuite/Makefile" ;; + "profmark/Makefile") CONFIG_FILES="$CONFIG_FILES profmark/Makefile" ;; + "src/impl_${impl_choice}/Makefile") CONFIG_FILES="$CONFIG_FILES src/impl_${impl_choice}/Makefile" ;; + "documentation/Makefile") CONFIG_FILES="$CONFIG_FILES documentation/Makefile" ;; + "documentation/man/Makefile") CONFIG_FILES="$CONFIG_FILES documentation/man/Makefile" ;; + "documentation/userguide/Makefile") CONFIG_FILES="$CONFIG_FILES documentation/userguide/Makefile" ;; + "documentation/userguide/inclusions/Makefile") CONFIG_FILES="$CONFIG_FILES documentation/userguide/inclusions/Makefile" ;; + "libdivsufsort/Makefile") CONFIG_FILES="$CONFIG_FILES libdivsufsort/Makefile" ;; + "easel/Makefile") CONFIG_FILES="$CONFIG_FILES easel/Makefile" ;; + "easel/miniapps/Makefile") CONFIG_FILES="$CONFIG_FILES easel/miniapps/Makefile" ;; + "easel/testsuite/Makefile") CONFIG_FILES="$CONFIG_FILES easel/testsuite/Makefile" ;; + "easel/documentation/Makefile") CONFIG_FILES="$CONFIG_FILES easel/documentation/Makefile" ;; + "documentation/userguide/titlepage.tex") CONFIG_FILES="$CONFIG_FILES documentation/userguide/titlepage.tex" ;; + "documentation/userguide/titlepage_daemon.tex") CONFIG_FILES="$CONFIG_FILES documentation/userguide/titlepage_daemon.tex" ;; + "documentation/userguide/copyright.tex") CONFIG_FILES="$CONFIG_FILES documentation/userguide/copyright.tex" ;; + "documentation/man/alimask.man") CONFIG_FILES="$CONFIG_FILES documentation/man/alimask.man" ;; + "documentation/man/hmmalign.man") CONFIG_FILES="$CONFIG_FILES documentation/man/hmmalign.man" ;; + "documentation/man/hmmbuild.man") CONFIG_FILES="$CONFIG_FILES documentation/man/hmmbuild.man" ;; + "documentation/man/hmmc2.man") CONFIG_FILES="$CONFIG_FILES documentation/man/hmmc2.man" ;; + "documentation/man/hmmconvert.man") CONFIG_FILES="$CONFIG_FILES documentation/man/hmmconvert.man" ;; + "documentation/man/hmmemit.man") CONFIG_FILES="$CONFIG_FILES documentation/man/hmmemit.man" ;; + "documentation/man/hmmer.man") CONFIG_FILES="$CONFIG_FILES documentation/man/hmmer.man" ;; + "documentation/man/hmmfetch.man") CONFIG_FILES="$CONFIG_FILES documentation/man/hmmfetch.man" ;; + "documentation/man/hmmlogo.man") CONFIG_FILES="$CONFIG_FILES documentation/man/hmmlogo.man" ;; + "documentation/man/hmmpgmd.man") CONFIG_FILES="$CONFIG_FILES documentation/man/hmmpgmd.man" ;; + "documentation/man/hmmpgmd_shard.man") CONFIG_FILES="$CONFIG_FILES documentation/man/hmmpgmd_shard.man" ;; + "documentation/man/hmmpress.man") CONFIG_FILES="$CONFIG_FILES documentation/man/hmmpress.man" ;; + "documentation/man/hmmscan.man") CONFIG_FILES="$CONFIG_FILES documentation/man/hmmscan.man" ;; + "documentation/man/hmmsearch.man") CONFIG_FILES="$CONFIG_FILES documentation/man/hmmsearch.man" ;; + "documentation/man/hmmsim.man") CONFIG_FILES="$CONFIG_FILES documentation/man/hmmsim.man" ;; + "documentation/man/hmmstat.man") CONFIG_FILES="$CONFIG_FILES documentation/man/hmmstat.man" ;; + "documentation/man/jackhmmer.man") CONFIG_FILES="$CONFIG_FILES documentation/man/jackhmmer.man" ;; + "documentation/man/makehmmerdb.man") CONFIG_FILES="$CONFIG_FILES documentation/man/makehmmerdb.man" ;; + "documentation/man/nhmmer.man") CONFIG_FILES="$CONFIG_FILES documentation/man/nhmmer.man" ;; + "documentation/man/nhmmscan.man") CONFIG_FILES="$CONFIG_FILES documentation/man/nhmmscan.man" ;; + "documentation/man/phmmer.man") CONFIG_FILES="$CONFIG_FILES documentation/man/phmmer.man" ;; + "easel/miniapps/esl-afetch.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-afetch.man" ;; + "easel/miniapps/esl-alimanip.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-alimanip.man" ;; + "easel/miniapps/esl-alimap.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-alimap.man" ;; + "easel/miniapps/esl-alimask.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-alimask.man" ;; + "easel/miniapps/esl-alimerge.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-alimerge.man" ;; + "easel/miniapps/esl-alipid.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-alipid.man" ;; + "easel/miniapps/esl-alirev.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-alirev.man" ;; + "easel/miniapps/esl-alistat.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-alistat.man" ;; + "easel/miniapps/esl-compalign.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-compalign.man" ;; + "easel/miniapps/esl-compstruct.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-compstruct.man" ;; + "easel/miniapps/esl-construct.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-construct.man" ;; + "easel/miniapps/esl-histplot.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-histplot.man" ;; + "easel/miniapps/esl-mask.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-mask.man" ;; + "easel/miniapps/esl-mixdchlet.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-mixdchlet.man" ;; + "easel/miniapps/esl-reformat.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-reformat.man" ;; + "easel/miniapps/esl-selectn.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-selectn.man" ;; + "easel/miniapps/esl-seqrange.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-seqrange.man" ;; + "easel/miniapps/esl-seqstat.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-seqstat.man" ;; + "easel/miniapps/esl-sfetch.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-sfetch.man" ;; + "easel/miniapps/esl-shuffle.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-shuffle.man" ;; + "easel/miniapps/esl-ssdraw.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-ssdraw.man" ;; + "easel/miniapps/esl-translate.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-translate.man" ;; + "easel/miniapps/esl-weight.man") CONFIG_FILES="$CONFIG_FILES easel/miniapps/esl-weight.man" ;; + "easel/decoy_config.h") CONFIG_HEADERS="$CONFIG_HEADERS easel/decoy_config.h" ;; + "src/p7_config.h") CONFIG_HEADERS="$CONFIG_HEADERS src/p7_config.h" ;; + "easel/esl_config.h") CONFIG_HEADERS="$CONFIG_HEADERS easel/esl_config.h" ;; + "libdivsufsort/divsufsort.h") CONFIG_HEADERS="$CONFIG_HEADERS libdivsufsort/divsufsort.h" ;; + "src/impl") CONFIG_LINKS="$CONFIG_LINKS src/impl:${ac_top_build_prefix}src/impl_${impl_choice}" ;; + + *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;; + esac +done + + +# If the user did not use the arguments to specify the items to instantiate, +# then the envvar interface is used. Set only those that are not. +# We use the long form for the default assignment because of an extremely +# bizarre bug on SunOS 4.1.3. +if $ac_need_defaults; then + test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files + test "${CONFIG_HEADERS+set}" = set || CONFIG_HEADERS=$config_headers + test "${CONFIG_LINKS+set}" = set || CONFIG_LINKS=$config_links +fi + +# Have a temporary directory for convenience. Make it in the build tree +# simply because there is no reason against having it here, and in addition, +# creating and moving files from /tmp can sometimes cause problems. +# Hook for its removal unless debugging. +# Note that there is a small window in which the directory will not be cleaned: +# after its creation but before its name has been assigned to `$tmp'. +$debug || +{ + tmp= ac_tmp= + trap 'exit_status=$? + : "${ac_tmp:=$tmp}" + { test ! -d "$ac_tmp" || rm -fr "$ac_tmp"; } && exit $exit_status +' 0 + trap 'as_fn_exit 1' 1 2 13 15 +} +# Create a (secure) tmp directory for tmp files. + +{ + tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` && + test -d "$tmp" +} || +{ + tmp=./conf$$-$RANDOM + (umask 077 && mkdir "$tmp") +} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5 +ac_tmp=$tmp + +# Set up the scripts for CONFIG_FILES section. +# No need to generate them if there are no CONFIG_FILES. +# This happens for instance with `./config.status config.h'. +if test -n "$CONFIG_FILES"; then + + +ac_cr=`echo X | tr X '\015'` +# On cygwin, bash can eat \r inside `` if the user requested igncr. +# But we know of no other shell where ac_cr would be empty at this +# point, so we can use a bashism as a fallback. +if test "x$ac_cr" = x; then + eval ac_cr=\$\'\\r\' +fi +ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' /dev/null` +if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then + ac_cs_awk_cr='\\r' +else + ac_cs_awk_cr=$ac_cr +fi + +echo 'BEGIN {' >"$ac_tmp/subs1.awk" && +_ACEOF + + +{ + echo "cat >conf$$subs.awk <<_ACEOF" && + echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' && + echo "_ACEOF" +} >conf$$subs.sh || + as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 +ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'` +ac_delim='%!_!# ' +for ac_last_try in false false false false false :; do + . ./conf$$subs.sh || + as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 + + ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X` + if test $ac_delim_n = $ac_delim_num; then + break + elif $ac_last_try; then + as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 + else + ac_delim="$ac_delim!$ac_delim _$ac_delim!! " + fi +done +rm -f conf$$subs.sh + +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 +cat >>"\$ac_tmp/subs1.awk" <<\\_ACAWK && +_ACEOF +sed -n ' +h +s/^/S["/; s/!.*/"]=/ +p +g +s/^[^!]*!// +:repl +t repl +s/'"$ac_delim"'$// +t delim +:nl +h +s/\(.\{148\}\)..*/\1/ +t more1 +s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/ +p +n +b repl +:more1 +s/["\\]/\\&/g; s/^/"/; s/$/"\\/ +p +g +s/.\{148\}// +t nl +:delim +h +s/\(.\{148\}\)..*/\1/ +t more2 +s/["\\]/\\&/g; s/^/"/; s/$/"/ +p +b +:more2 +s/["\\]/\\&/g; s/^/"/; s/$/"\\/ +p +g +s/.\{148\}// +t delim +' >$CONFIG_STATUS || ac_write_fail=1 +rm -f conf$$subs.awk +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 +_ACAWK +cat >>"\$ac_tmp/subs1.awk" <<_ACAWK && + for (key in S) S_is_set[key] = 1 + FS = "" + +} +{ + line = $ 0 + nfields = split(line, field, "@") + substed = 0 + len = length(field[1]) + for (i = 2; i < nfields; i++) { + key = field[i] + keylen = length(key) + if (S_is_set[key]) { + value = S[key] + line = substr(line, 1, len) "" value "" substr(line, len + keylen + 3) + len += length(value) + length(field[++i]) + substed = 1 + } else + len += 1 + keylen + } + + print line +} + +_ACAWK +_ACEOF +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 +if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then + sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g" +else + cat +fi < "$ac_tmp/subs1.awk" > "$ac_tmp/subs.awk" \ + || as_fn_error $? "could not setup config files machinery" "$LINENO" 5 +_ACEOF + +# VPATH may cause trouble with some makes, so we remove sole $(srcdir), +# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and +# trailing colons and then remove the whole line if VPATH becomes empty +# (actually we leave an empty line to preserve line numbers). +if test "x$srcdir" = x.; then + ac_vpsub='/^[ ]*VPATH[ ]*=[ ]*/{ +h +s/// +s/^/:/ +s/[ ]*$/:/ +s/:\$(srcdir):/:/g +s/:\${srcdir}:/:/g +s/:@srcdir@:/:/g +s/^:*// +s/:*$// +x +s/\(=[ ]*\).*/\1/ +G +s/\n// +s/^[^=]*=[ ]*$// +}' +fi + +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 +fi # test -n "$CONFIG_FILES" + +# Set up the scripts for CONFIG_HEADERS section. +# No need to generate them if there are no CONFIG_HEADERS. +# This happens for instance with `./config.status Makefile'. +if test -n "$CONFIG_HEADERS"; then +cat >"$ac_tmp/defines.awk" <<\_ACAWK || +BEGIN { +_ACEOF + +# Transform confdefs.h into an awk script `defines.awk', embedded as +# here-document in config.status, that substitutes the proper values into +# config.h.in to produce config.h. + +# Create a delimiter string that does not exist in confdefs.h, to ease +# handling of long lines. +ac_delim='%!_!# ' +for ac_last_try in false false :; do + ac_tt=`sed -n "/$ac_delim/p" confdefs.h` + if test -z "$ac_tt"; then + break + elif $ac_last_try; then + as_fn_error $? "could not make $CONFIG_HEADERS" "$LINENO" 5 + else + ac_delim="$ac_delim!$ac_delim _$ac_delim!! " + fi +done + +# For the awk script, D is an array of macro values keyed by name, +# likewise P contains macro parameters if any. Preserve backslash +# newline sequences. + +ac_word_re=[_$as_cr_Letters][_$as_cr_alnum]* +sed -n ' +s/.\{148\}/&'"$ac_delim"'/g +t rset +:rset +s/^[ ]*#[ ]*define[ ][ ]*/ / +t def +d +:def +s/\\$// +t bsnl +s/["\\]/\\&/g +s/^ \('"$ac_word_re"'\)\(([^()]*)\)[ ]*\(.*\)/P["\1"]="\2"\ +D["\1"]=" \3"/p +s/^ \('"$ac_word_re"'\)[ ]*\(.*\)/D["\1"]=" \2"/p +d +:bsnl +s/["\\]/\\&/g +s/^ \('"$ac_word_re"'\)\(([^()]*)\)[ ]*\(.*\)/P["\1"]="\2"\ +D["\1"]=" \3\\\\\\n"\\/p +t cont +s/^ \('"$ac_word_re"'\)[ ]*\(.*\)/D["\1"]=" \2\\\\\\n"\\/p +t cont +d +:cont +n +s/.\{148\}/&'"$ac_delim"'/g +t clear +:clear +s/\\$// +t bsnlc +s/["\\]/\\&/g; s/^/"/; s/$/"/p +d +:bsnlc +s/["\\]/\\&/g; s/^/"/; s/$/\\\\\\n"\\/p +b cont +' >$CONFIG_STATUS || ac_write_fail=1 + +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 + for (key in D) D_is_set[key] = 1 + FS = "" +} +/^[\t ]*#[\t ]*(define|undef)[\t ]+$ac_word_re([\t (]|\$)/ { + line = \$ 0 + split(line, arg, " ") + if (arg[1] == "#") { + defundef = arg[2] + mac1 = arg[3] + } else { + defundef = substr(arg[1], 2) + mac1 = arg[2] + } + split(mac1, mac2, "(") #) + macro = mac2[1] + prefix = substr(line, 1, index(line, defundef) - 1) + if (D_is_set[macro]) { + # Preserve the white space surrounding the "#". + print prefix "define", macro P[macro] D[macro] + next + } else { + # Replace #undef with comments. This is necessary, for example, + # in the case of _POSIX_SOURCE, which is predefined and required + # on some systems where configure will not decide to define it. + if (defundef == "undef") { + print "/*", prefix defundef, macro, "*/" + next + } + } +} +{ print } +_ACAWK +_ACEOF +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 + as_fn_error $? "could not setup config headers machinery" "$LINENO" 5 +fi # test -n "$CONFIG_HEADERS" + + +eval set X " :F $CONFIG_FILES :H $CONFIG_HEADERS :L $CONFIG_LINKS " +shift +for ac_tag +do + case $ac_tag in + :[FHLC]) ac_mode=$ac_tag; continue;; + esac + case $ac_mode$ac_tag in + :[FHL]*:*);; + :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5;; + :[FH]-) ac_tag=-:-;; + :[FH]*) ac_tag=$ac_tag:$ac_tag.in;; + esac + ac_save_IFS=$IFS + IFS=: + set x $ac_tag + IFS=$ac_save_IFS + shift + ac_file=$1 + shift + + case $ac_mode in + :L) ac_source=$1;; + :[FH]) + ac_file_inputs= + for ac_f + do + case $ac_f in + -) ac_f="$ac_tmp/stdin";; + *) # Look for the file first in the build tree, then in the source tree + # (if the path is not absolute). The absolute path cannot be DOS-style, + # because $ac_f cannot contain `:'. + test -f "$ac_f" || + case $ac_f in + [\\/$]*) false;; + *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";; + esac || + as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5;; + esac + case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac + as_fn_append ac_file_inputs " '$ac_f'" + done + + # Let's still pretend it is `configure' which instantiates (i.e., don't + # use $as_me), people would be surprised to read: + # /* config.h. Generated by config.status. */ + configure_input='Generated from '` + $as_echo "$*" | sed 's|^[^:]*/||;s|:[^:]*/|, |g' + `' by configure.' + if test x"$ac_file" != x-; then + configure_input="$ac_file. $configure_input" + { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5 +$as_echo "$as_me: creating $ac_file" >&6;} + fi + # Neutralize special characters interpreted by sed in replacement strings. + case $configure_input in #( + *\&* | *\|* | *\\* ) + ac_sed_conf_input=`$as_echo "$configure_input" | + sed 's/[\\\\&|]/\\\\&/g'`;; #( + *) ac_sed_conf_input=$configure_input;; + esac + + case $ac_tag in + *:-:* | *:-) cat >"$ac_tmp/stdin" \ + || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;; + esac + ;; + esac + + ac_dir=`$as_dirname -- "$ac_file" || +$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$ac_file" : 'X\(//\)[^/]' \| \ + X"$ac_file" : 'X\(//\)$' \| \ + X"$ac_file" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X"$ac_file" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ + s//\1/ + q + } + /^X\(\/\/\)[^/].*/{ + s//\1/ + q + } + /^X\(\/\/\)$/{ + s//\1/ + q + } + /^X\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` + as_dir="$ac_dir"; as_fn_mkdir_p + ac_builddir=. + +case "$ac_dir" in +.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;; +*) + ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'` + # A ".." for each directory in $ac_dir_suffix. + ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'` + case $ac_top_builddir_sub in + "") ac_top_builddir_sub=. ac_top_build_prefix= ;; + *) ac_top_build_prefix=$ac_top_builddir_sub/ ;; + esac ;; +esac +ac_abs_top_builddir=$ac_pwd +ac_abs_builddir=$ac_pwd$ac_dir_suffix +# for backward compatibility: +ac_top_builddir=$ac_top_build_prefix + +case $srcdir in + .) # We are building in place. + ac_srcdir=. + ac_top_srcdir=$ac_top_builddir_sub + ac_abs_top_srcdir=$ac_pwd ;; + [\\/]* | ?:[\\/]* ) # Absolute name. + ac_srcdir=$srcdir$ac_dir_suffix; + ac_top_srcdir=$srcdir + ac_abs_top_srcdir=$srcdir ;; + *) # Relative name. + ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix + ac_top_srcdir=$ac_top_build_prefix$srcdir + ac_abs_top_srcdir=$ac_pwd/$srcdir ;; +esac +ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix + + + case $ac_mode in + :F) + # + # CONFIG_FILE + # + + case $INSTALL in + [\\/$]* | ?:[\\/]* ) ac_INSTALL=$INSTALL ;; + *) ac_INSTALL=$ac_top_build_prefix$INSTALL ;; + esac +_ACEOF + +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 +# If the template does not know about datarootdir, expand it. +# FIXME: This hack should be removed a few years after 2.60. +ac_datarootdir_hack=; ac_datarootdir_seen= +ac_sed_dataroot=' +/datarootdir/ { + p + q +} +/@datadir@/p +/@docdir@/p +/@infodir@/p +/@localedir@/p +/@mandir@/p' +case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in +*datarootdir*) ac_datarootdir_seen=yes;; +*@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*) + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5 +$as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;} +_ACEOF +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 + ac_datarootdir_hack=' + s&@datadir@&$datadir&g + s&@docdir@&$docdir&g + s&@infodir@&$infodir&g + s&@localedir@&$localedir&g + s&@mandir@&$mandir&g + s&\\\${datarootdir}&$datarootdir&g' ;; +esac +_ACEOF + +# Neutralize VPATH when `$srcdir' = `.'. +# Shell code in configure.ac might set extrasub. +# FIXME: do we really want to maintain this feature? +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 +ac_sed_extra="$ac_vpsub +$extrasub +_ACEOF +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 +:t +/@[a-zA-Z_][a-zA-Z_0-9]*@/!b +s|@configure_input@|$ac_sed_conf_input|;t t +s&@top_builddir@&$ac_top_builddir_sub&;t t +s&@top_build_prefix@&$ac_top_build_prefix&;t t +s&@srcdir@&$ac_srcdir&;t t +s&@abs_srcdir@&$ac_abs_srcdir&;t t +s&@top_srcdir@&$ac_top_srcdir&;t t +s&@abs_top_srcdir@&$ac_abs_top_srcdir&;t t +s&@builddir@&$ac_builddir&;t t +s&@abs_builddir@&$ac_abs_builddir&;t t +s&@abs_top_builddir@&$ac_abs_top_builddir&;t t +s&@INSTALL@&$ac_INSTALL&;t t +$ac_datarootdir_hack +" +eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$ac_tmp/subs.awk" \ + >$ac_tmp/out || as_fn_error $? "could not create $ac_file" "$LINENO" 5 + +test -z "$ac_datarootdir_hack$ac_datarootdir_seen" && + { ac_out=`sed -n '/\${datarootdir}/p' "$ac_tmp/out"`; test -n "$ac_out"; } && + { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' \ + "$ac_tmp/out"`; test -z "$ac_out"; } && + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir' +which seems to be undefined. Please make sure it is defined" >&5 +$as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir' +which seems to be undefined. Please make sure it is defined" >&2;} + + rm -f "$ac_tmp/stdin" + case $ac_file in + -) cat "$ac_tmp/out" && rm -f "$ac_tmp/out";; + *) rm -f "$ac_file" && mv "$ac_tmp/out" "$ac_file";; + esac \ + || as_fn_error $? "could not create $ac_file" "$LINENO" 5 + ;; + :H) + # + # CONFIG_HEADER + # + if test x"$ac_file" != x-; then + { + $as_echo "/* $configure_input */" \ + && eval '$AWK -f "$ac_tmp/defines.awk"' "$ac_file_inputs" + } >"$ac_tmp/config.h" \ + || as_fn_error $? "could not create $ac_file" "$LINENO" 5 + if diff "$ac_file" "$ac_tmp/config.h" >/dev/null 2>&1; then + { $as_echo "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5 +$as_echo "$as_me: $ac_file is unchanged" >&6;} + else + rm -f "$ac_file" + mv "$ac_tmp/config.h" "$ac_file" \ + || as_fn_error $? "could not create $ac_file" "$LINENO" 5 + fi + else + $as_echo "/* $configure_input */" \ + && eval '$AWK -f "$ac_tmp/defines.awk"' "$ac_file_inputs" \ + || as_fn_error $? "could not create -" "$LINENO" 5 + fi + ;; + :L) + # + # CONFIG_LINK + # + + if test "$ac_source" = "$ac_file" && test "$srcdir" = '.'; then + : + else + # Prefer the file from the source tree if names are identical. + if test "$ac_source" = "$ac_file" || test ! -r "$ac_source"; then + ac_source=$srcdir/$ac_source + fi + + { $as_echo "$as_me:${as_lineno-$LINENO}: linking $ac_source to $ac_file" >&5 +$as_echo "$as_me: linking $ac_source to $ac_file" >&6;} + + if test ! -r "$ac_source"; then + as_fn_error $? "$ac_source: file not found" "$LINENO" 5 + fi + rm -f "$ac_file" + + # Try a relative symlink, then a hard link, then a copy. + case $ac_source in + [\\/$]* | ?:[\\/]* ) ac_rel_source=$ac_source ;; + *) ac_rel_source=$ac_top_build_prefix$ac_source ;; + esac + ln -s "$ac_rel_source" "$ac_file" 2>/dev/null || + ln "$ac_source" "$ac_file" 2>/dev/null || + cp -p "$ac_source" "$ac_file" || + as_fn_error $? "cannot link or copy $ac_source to $ac_file" "$LINENO" 5 + fi + ;; + + esac + +done # for ac_tag + + +as_fn_exit 0 +_ACEOF +ac_clean_files=$ac_clean_files_save + +test $ac_write_fail = 0 || + as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5 + + +# configure is writing to config.log, and then calls config.status. +# config.status does its own redirection, appending to config.log. +# Unfortunately, on DOS this fails, as config.log is still kept open +# by configure, so config.status won't be able to write to it; its +# output is simply discarded. So we exec the FD to /dev/null, +# effectively closing config.log, so it can be properly (re)opened and +# appended to by config.status. When coming back to configure, we +# need to make the FD available again. +if test "$no_create" != yes; then + ac_cs_success=: + ac_config_status_args= + test "$silent" = yes && + ac_config_status_args="$ac_config_status_args --quiet" + exec 5>/dev/null + $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false + exec 5>>config.log + # Use ||, not &&, to avoid exiting from the if with $? = 1, which + # would make configure fail if this is the last instruction. + $ac_cs_success || as_fn_exit 1 +fi +if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5 +$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;} +fi + + +echo " + +HMMER configuration: + compiler: ${CC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} + host: $host + linker: ${LDFLAGS} + libraries: ${LIBS} ${LIBGSL} ${PTHREAD_LIBS} + DP implementation: ${impl_choice}" + + +if test x"$HAVE_PYTHON3" = x"yes"; then echo " +Now do 'make' to build HMMER, and optionally: + 'make check' to run self tests, + 'make install' to install programs and man pages, + '(cd easel; make install)' to install Easel tools. +"; +else echo " + (No python3 found, so 'make check' is disabled.) + +Now do 'make' to build HMMER, and optionally: + 'make install' to install programs and man pages, + '(cd easel; make install)' to install Easel tools. +"; +fi + diff --git a/configure.ac b/configure.ac index 682b3da2..e6cdc2c5 100644 --- a/configure.ac +++ b/configure.ac @@ -435,6 +435,8 @@ AS_IF([test "x$with_gsl" != xno], # which may be in librt AC_SEARCH_LIBS(clock_gettime, [rt posix4]) +# mingw mmap +AC_SEARCH_LIBS(mmap, [mman]) ################################################################ # 7. Checks for headers @@ -480,6 +482,7 @@ AC_TYPE_UINT8_T AC_TYPE_UINT16_T AC_TYPE_UINT32_T AC_TYPE_UINT64_T +AC_TYPE_UINTPTR_T AC_TYPE_OFF_T @@ -673,6 +676,10 @@ AC_CONFIG_HEADERS([libdivsufsort/divsufsort.h]) # Testsuite sqc tests rely on it. AC_CONFIG_LINKS([src/impl:${ac_top_build_prefix}src/impl_${impl_choice}]) +# Windows does not support symlinks so this command prevents the previous +# throwing an error on subsequent configures. However, you will need to do +# a manual copy prior to running tests. The copy should be done during make. +AC_CONFIG_COMMANDS_PRE([test -d src/impl && rm -rf src/impl]) ################################################################ diff --git a/src/Makefile.in b/src/Makefile.in index d3b6de21..31a6e7ed 100644 --- a/src/Makefile.in +++ b/src/Makefile.in @@ -16,6 +16,7 @@ mandir = @mandir@ docdir = @docdir@ pdfdir = @pdfdir@ mandir = @mandir@ +EXEEXT = @EXEEXT@ man1dir = ${mandir}/man1 man1ext = .1 @@ -272,7 +273,7 @@ ${PROGOBJS}: ${HDRS} p7_config.h ${AUXPROGOBJS}: ${HDRS} p7_config.h ${PROGS} ${AUXPROGS}: % : %.o libhmmer.a ../${ESLDIR}/libeasel.a - ${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${LIBS} + ${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} ${MYLIBDIRS} -o $@${EXEEXT} $@.o ${LIBS} .c.o: ${QUIET_CC}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${DEFS} ${CPPFLAGS} ${MYINCDIRS} -o $@ -c $< @@ -341,18 +342,18 @@ ${EXAMPLES}: libhmmer.a ${HDRS} p7_config.h install: for file in ${PROGS}; do \ - ${INSTALL} -m 0755 $$file ${DESTDIR}${bindir}/ ;\ + ${INSTALL} -m 0755 $$file${EXEEXT} ${DESTDIR}${bindir}/ ;\ done install-strip: for file in ${PROGS}; do \ ${STRIP} $$file ;\ - ${INSTALL} -m 0755 $$file ${DESTDIR}${bindir}/ ;\ + ${INSTALL} -m 0755 $$file${EXEEXT} ${DESTDIR}${bindir}/ ;\ done uninstall: for file in ${PROGS}; do \ - rm -f ${DESTDIR}${bindir}/$$file ;\ + rm -f ${DESTDIR}${bindir}/$$file${EXEEXT} ;\ done clean: @@ -366,6 +367,9 @@ clean: -rm -f ${EXAMPLES} -rm -f *.gcno -rm -f cscope.out + for prog in ${PROGS} ${AUXPROGS}; do \ + if test -f $$prog${EXEEXT}; then rm -f $$prog${EXEEXT}; fi; \ + done for prog in ${PROGS} ${AUXPROGS} ${UTESTS} ${STATS} ${BENCHMARKS} ${EXAMPLES} ${ITESTS}; do \ if test -d $$prog.dSYM; then rm -rf $$prog.dSYM; fi ;\ done diff --git a/src/fm_general.c b/src/fm_general.c index ad93c55b..3aba3b2f 100644 --- a/src/fm_general.c +++ b/src/fm_general.c @@ -526,7 +526,7 @@ fm_FM_read( FM_DATA *fm, FM_METADATA *meta, int getAll ) // allocate space, then read the data if (getAll) ESL_ALLOC (fm->T, sizeof(uint8_t) * compressed_bytes ); ESL_ALLOC (fm->BWT_mem, sizeof(uint8_t) * (compressed_bytes + 31) ); // +31 for manual 16-byte alignment ( typically only need +15, but this allows offset in memory, plus offset in case of <16 bytes of characters at the end) - fm->BWT = (uint8_t *) (((unsigned long int)fm->BWT_mem + 15) & (~0xf)); // align vector memory on 16-byte boundaries + fm->BWT = (uint8_t *) (((POINTER)fm->BWT_mem + 15) & (~0xf)); // align vector memory on 16-byte boundaries if (getAll) ESL_ALLOC (fm->SA, num_SA_samples * sizeof(uint32_t)); ESL_ALLOC (fm->C, (1+meta->alph_size) * sizeof(int64_t)); ESL_ALLOC (fm->occCnts_b, num_freq_cnts_b * (meta->alph_size ) * sizeof(uint16_t)); // every freq_cnt positions, store an array of ints diff --git a/src/fm_sse.c b/src/fm_sse.c index 6da2ae64..cab3cdba 100644 --- a/src/fm_sse.c +++ b/src/fm_sse.c @@ -80,7 +80,7 @@ fm_configInit( FM_CFG *cfg, ESL_GETOPTS *go ) //set up an array of vectors, one for each character in the alphabet cfg->fm_chars_v = NULL; ESL_ALLOC (cfg->fm_chars_mem, cfg->meta->alph_size * sizeof(__m128) + 15 ); // +15 for manual 16-byte alignment, which matters for SIMD stuff - cfg->fm_chars_v = (__m128i *) (((unsigned long int)(cfg->fm_chars_mem) + 15) & (~0xf)); /* align vector memory on 16-byte boundaries */ + cfg->fm_chars_v = (__m128i *) (((POINTER)(cfg->fm_chars_mem) + 15) & (~0xf)); /* align vector memory on 16-byte boundaries */ for (i=0; imeta->alph_size; i++) { @@ -109,10 +109,10 @@ fm_configInit( FM_CFG *cfg, ESL_GETOPTS *go ) cfg->fm_masks_v = NULL; cfg->fm_reverse_masks_v = NULL; ESL_ALLOC (cfg->fm_masks_mem, (1+trim_chunk_count) *sizeof(__m128) + 15 ); // +15 for manual 16-byte alignment, which matters for SIMD stuff - cfg->fm_masks_v = (__m128i *) (((unsigned long int)(cfg->fm_masks_mem) + 15) & (~0xf)); /* align vector memory on 16-byte boundaries */ + cfg->fm_masks_v = (__m128i *) (((POINTER)(cfg->fm_masks_mem) + 15) & (~0xf)); /* align vector memory on 16-byte boundaries */ ESL_ALLOC (cfg->fm_reverse_masks_mem, (1+trim_chunk_count) *sizeof(__m128) + 15 ); // +15 for manual 16-byte alignment, which matters for SIMD stuff - cfg->fm_reverse_masks_v = (__m128i *) (((unsigned long int)(cfg->fm_reverse_masks_mem) + 15) & (~0xf)); /* align vector memory on 16-byte boundaries */ + cfg->fm_reverse_masks_v = (__m128i *) (((POINTER)(cfg->fm_reverse_masks_mem) + 15) & (~0xf)); /* align vector memory on 16-byte boundaries */ { byte_m128 arr; diff --git a/src/hmmc2.c b/src/hmmc2.c index 26c7b82e..88155751 100644 --- a/src/hmmc2.c +++ b/src/hmmc2.c @@ -2,6 +2,7 @@ */ #include "p7_config.h" +#ifndef __MINGW32__ #ifdef HMMER_THREADS #include @@ -570,7 +571,7 @@ int main(int argc, char *argv[]) } #endif /*HMMER_THREADS*/ - +#endif /* __MINGW32__ */ diff --git a/src/hmmdmstr.c b/src/hmmdmstr.c index cee11ed2..71c50e28 100644 --- a/src/hmmdmstr.c +++ b/src/hmmdmstr.c @@ -3,6 +3,7 @@ */ #include "p7_config.h" +#ifndef __MINGW32__ #ifdef HMMER_THREADS #include @@ -1901,6 +1902,6 @@ setup_workerside_comm(ESL_GETOPTS *opts, WORKERSIDE_ARGS *args) } #endif /*HMMER_THREADS*/ - +#endif /* __MINGW32__ */ diff --git a/src/hmmdmstr_shard.c b/src/hmmdmstr_shard.c index 38ffe260..1dd4dd35 100644 --- a/src/hmmdmstr_shard.c +++ b/src/hmmdmstr_shard.c @@ -3,6 +3,7 @@ */ #include "p7_config.h" +#ifndef __MINGW32__ #ifdef HMMER_THREADS #include @@ -1961,6 +1962,6 @@ setup_workerside_comm(ESL_GETOPTS *opts, WORKERSIDE_ARGS *args) } #endif /*HMMER_THREADS*/ - +#endif /* __MINGW32__ */ diff --git a/src/hmmdutils.c b/src/hmmdutils.c index 00bb7e33..ba4a8ee0 100644 --- a/src/hmmdutils.c +++ b/src/hmmdutils.c @@ -4,6 +4,7 @@ */ #include "p7_config.h" +#ifndef __MINGW32__ #ifdef HMMER_THREADS #include @@ -290,3 +291,4 @@ hmmpgmd_GetRanges (RANGE_LIST *list, char *rangestr) { } #endif /*HMMER_THREADS*/ +#endif /* __MINGW32__ */ \ No newline at end of file diff --git a/src/hmmdwrkr.c b/src/hmmdwrkr.c index b864b7ba..44bc6e9b 100644 --- a/src/hmmdwrkr.c +++ b/src/hmmdwrkr.c @@ -2,6 +2,7 @@ */ #include "p7_config.h" +#ifndef __MINGW32__ #ifdef HMMER_THREADS #include @@ -881,6 +882,6 @@ setup_masterside_comm(ESL_GETOPTS *opts) } #endif /*HMMER_THREADS*/ - +#endif /* __MINGW32__ */ diff --git a/src/hmmdwrkr_shard.c b/src/hmmdwrkr_shard.c index 566e55ff..5abe8819 100644 --- a/src/hmmdwrkr_shard.c +++ b/src/hmmdwrkr_shard.c @@ -2,6 +2,7 @@ */ #include "p7_config.h" +#ifndef __MINGW32__ #ifdef HMMER_THREADS #include @@ -916,6 +917,4 @@ setup_masterside_comm(ESL_GETOPTS *opts) } #endif /*HMMER_THREADS*/ - - - +#endif /* __MINGW32__ */ \ No newline at end of file diff --git a/src/hmmerfm-exactmatch.c b/src/hmmerfm-exactmatch.c index 2ccce910..6497cc85 100644 --- a/src/hmmerfm-exactmatch.c +++ b/src/hmmerfm-exactmatch.c @@ -1,6 +1,8 @@ #include "p7_config.h" +#ifndef __MINGW32__ #include +#endif /* __MINGW32__ */ #include #include "easel.h" @@ -216,7 +218,9 @@ main(int argc, char *argv[]) { void* tmp; // used for RALLOC calls clock_t t1, t2; +#ifndef __MINGW32__ struct tms ts1, ts2; +#endif /* __MINGW32__ */ char *fname_fm = NULL; char *fname_queries = NULL; FM_HIT *hits = NULL; @@ -247,7 +251,11 @@ main(int argc, char *argv[]) ESL_ALPHABET *abc = NULL; //start timer +#ifdef __MINGW32__ + t1 = clock(); +#else t1 = times(&ts1); +#endif /* __MINGW32__ */ process_commandline(argc, argv, &go, &fname_fm, &fname_queries); @@ -492,9 +500,17 @@ main(int argc, char *argv[]) // compute and print the elapsed time in millisec +#ifdef __MINGW32__ + t2 = clock(); +#else t2 = times(&ts2); +#endif /* __MINGW32__ */ { +#ifdef __MINGW32__ + double clk_ticks = CLOCKS_PER_SEC; +#else double clk_ticks = sysconf(_SC_CLK_TCK); +#endif /* __MINGW32__ */ double elapsedTime = (t2-t1)/clk_ticks; double throughput = cfg->occCallCnt/elapsedTime; diff --git a/src/hmmpgmd.c b/src/hmmpgmd.c index 08a085bf..9af3439f 100644 --- a/src/hmmpgmd.c +++ b/src/hmmpgmd.c @@ -2,6 +2,7 @@ */ #include "p7_config.h" +#ifndef __MINGW32__ #ifdef HMMER_THREADS #include @@ -218,4 +219,4 @@ main(int argc, char **argv) */ #endif /*HMMER_THREADS*/ - +#endif /* __MINGW32__ */ diff --git a/src/hmmpgmd2msa.c b/src/hmmpgmd2msa.c index 655a2d11..0723467b 100644 --- a/src/hmmpgmd2msa.c +++ b/src/hmmpgmd2msa.c @@ -179,7 +179,11 @@ hmmpgmd2msa(void *data, P7_HMM *hmm, ESL_SQ *qsq, int *incl, int incl_size, int if(th.hit[i]->flags & p7_IS_INCLUDED){ if(excl_size > 0){ for( c = 0; c < excl_size; c++){ +#ifdef __MINGW32__ + if(excl[c] == (long long)(th.hit[i]->name) ){ +#else if(excl[c] == (long)(th.hit[i]->name) ){ +#endif /* __MINGW32__ */ th.hit[i]->flags = p7_IS_DROPPED; th.hit[i]->nincluded = 0; break; @@ -189,7 +193,11 @@ hmmpgmd2msa(void *data, P7_HMM *hmm, ESL_SQ *qsq, int *incl, int incl_size, int }else{ if(incl_size > 0){ for( c = 0; c < incl_size; c++){ +#ifdef __MINGW32__ + if(incl[c] == (long long)th.hit[i]->name ){ +#else if(incl[c] == (long)th.hit[i]->name ){ +#endif /* __MINGW32__ */ th.hit[i]->flags = p7_IS_INCLUDED; } } diff --git a/src/hmmpgmd_shard.c b/src/hmmpgmd_shard.c index 17fc6b39..bcbf6c5d 100644 --- a/src/hmmpgmd_shard.c +++ b/src/hmmpgmd_shard.c @@ -2,6 +2,7 @@ */ #include "p7_config.h" +#ifndef __MINGW32__ #ifdef HMMER_THREADS #include @@ -220,3 +221,5 @@ main(int argc, char **argv) #endif /*HMMER_THREADS*/ + +#endif /* __MINGW32__ */ \ No newline at end of file diff --git a/src/impl_sse/p7_omx.c b/src/impl_sse/p7_omx.c index bab3eb6c..640a9e98 100644 --- a/src/impl_sse/p7_omx.c +++ b/src/impl_sse/p7_omx.c @@ -86,9 +86,9 @@ p7_omx_Create(int allocM, int allocL, int allocXL) ESL_ALLOC(ox->dpw, sizeof(__m128i *) * ox->allocR); ESL_ALLOC(ox->dpf, sizeof(__m128 *) * ox->allocR); - ox->dpb[0] = (__m128i *) ( ( (unsigned long int) ((char *) ox->dp_mem + 15) & (~0xf))); - ox->dpw[0] = (__m128i *) ( ( (unsigned long int) ((char *) ox->dp_mem + 15) & (~0xf))); - ox->dpf[0] = (__m128 *) ( ( (unsigned long int) ((char *) ox->dp_mem + 15) & (~0xf))); + ox->dpb[0] = (__m128i *) ( ( (POINTER) ((char *) ox->dp_mem + 15) & (~0xf))); + ox->dpw[0] = (__m128i *) ( ( (POINTER) ((char *) ox->dp_mem + 15) & (~0xf))); + ox->dpf[0] = (__m128 *) ( ( (POINTER) ((char *) ox->dp_mem + 15) & (~0xf))); for (i = 1; i <= allocL; i++) { ox->dpf[i] = ox->dpf[0] + i * ox->allocQ4 * p7X_NSCELLS; @@ -98,7 +98,7 @@ p7_omx_Create(int allocM, int allocL, int allocXL) ox->allocXR = allocXL+1; ESL_ALLOC(ox->x_mem, sizeof(float) * ox->allocXR * p7X_NXCELLS + 15); - ox->xmx = (float *) ( ( (unsigned long int) ((char *) ox->x_mem + 15) & (~0xf))); + ox->xmx = (float *) ( ( (POINTER) ((char *) ox->x_mem + 15) & (~0xf))); ox->M = 0; ox->L = 0; @@ -164,7 +164,7 @@ p7_omx_GrowTo(P7_OMX *ox, int allocM, int allocL, int allocXL) { ESL_RALLOC(ox->x_mem, p, sizeof(float) * (allocXL+1) * p7X_NXCELLS + 15); ox->allocXR = allocXL+1; - ox->xmx = (float *) ( ( (unsigned long int) ((char *) ox->x_mem + 15) & (~0xf))); + ox->xmx = (float *) ( ( (POINTER) ((char *) ox->x_mem + 15) & (~0xf))); } /* If there aren't enough rows, reallocate the row pointers; we'll @@ -190,9 +190,9 @@ p7_omx_GrowTo(P7_OMX *ox, int allocM, int allocL, int allocXL) /* now reset the row pointers, if needed */ if (reset_row_pointers) { - ox->dpb[0] = (__m128i *) ( ( (unsigned long int) ((char *) ox->dp_mem + 15) & (~0xf))); - ox->dpw[0] = (__m128i *) ( ( (unsigned long int) ((char *) ox->dp_mem + 15) & (~0xf))); - ox->dpf[0] = (__m128 *) ( ( (unsigned long int) ((char *) ox->dp_mem + 15) & (~0xf))); + ox->dpb[0] = (__m128i *) ( ( (POINTER) ((char *) ox->dp_mem + 15) & (~0xf))); + ox->dpw[0] = (__m128i *) ( ( (POINTER) ((char *) ox->dp_mem + 15) & (~0xf))); + ox->dpf[0] = (__m128 *) ( ( (POINTER) ((char *) ox->dp_mem + 15) & (~0xf))); ox->validR = ESL_MIN( ox->ncells / (nqf * 4), ox->allocR); for (i = 1; i < ox->validR; i++) diff --git a/src/impl_sse/p7_oprofile.c b/src/impl_sse/p7_oprofile.c index 9c80acd1..f00f1f21 100644 --- a/src/impl_sse/p7_oprofile.c +++ b/src/impl_sse/p7_oprofile.c @@ -86,12 +86,12 @@ p7_oprofile_Create(int allocM, const ESL_ALPHABET *abc) ESL_ALLOC(om->rfv, sizeof(__m128 *) * abc->Kp); /* align vector memory on 16-byte boundaries */ - om->rbv[0] = (__m128i *) (((unsigned long int) om->rbv_mem + 15) & (~0xf)); - om->sbv[0] = (__m128i *) (((unsigned long int) om->sbv_mem + 15) & (~0xf)); - om->rwv[0] = (__m128i *) (((unsigned long int) om->rwv_mem + 15) & (~0xf)); - om->twv = (__m128i *) (((unsigned long int) om->twv_mem + 15) & (~0xf)); - om->rfv[0] = (__m128 *) (((unsigned long int) om->rfv_mem + 15) & (~0xf)); - om->tfv = (__m128 *) (((unsigned long int) om->tfv_mem + 15) & (~0xf)); + om->rbv[0] = (__m128i *) (((POINTER) om->rbv_mem + 15) & (~0xf)); + om->sbv[0] = (__m128i *) (((POINTER) om->sbv_mem + 15) & (~0xf)); + om->rwv[0] = (__m128i *) (((POINTER) om->rwv_mem + 15) & (~0xf)); + om->twv = (__m128i *) (((POINTER) om->twv_mem + 15) & (~0xf)); + om->rfv[0] = (__m128 *) (((POINTER) om->rfv_mem + 15) & (~0xf)); + om->tfv = (__m128 *) (((POINTER) om->tfv_mem + 15) & (~0xf)); /* set the rest of the row pointers for match emissions */ for (x = 1; x < abc->Kp; x++) { @@ -300,12 +300,12 @@ p7_oprofile_Copy(P7_OPROFILE *om1) ESL_ALLOC(om2->rfv, sizeof(__m128 *) * abc->Kp); /* align vector memory on 16-byte boundaries */ - om2->rbv[0] = (__m128i *) (((unsigned long int) om2->rbv_mem + 15) & (~0xf)); - om2->sbv[0] = (__m128i *) (((unsigned long int) om2->sbv_mem + 15) & (~0xf)); - om2->rwv[0] = (__m128i *) (((unsigned long int) om2->rwv_mem + 15) & (~0xf)); - om2->twv = (__m128i *) (((unsigned long int) om2->twv_mem + 15) & (~0xf)); - om2->rfv[0] = (__m128 *) (((unsigned long int) om2->rfv_mem + 15) & (~0xf)); - om2->tfv = (__m128 *) (((unsigned long int) om2->tfv_mem + 15) & (~0xf)); + om2->rbv[0] = (__m128i *) (((POINTER) om2->rbv_mem + 15) & (~0xf)); + om2->sbv[0] = (__m128i *) (((POINTER) om2->sbv_mem + 15) & (~0xf)); + om2->rwv[0] = (__m128i *) (((POINTER) om2->rwv_mem + 15) & (~0xf)); + om2->twv = (__m128i *) (((POINTER) om2->twv_mem + 15) & (~0xf)); + om2->rfv[0] = (__m128 *) (((POINTER) om2->rfv_mem + 15) & (~0xf)); + om2->tfv = (__m128 *) (((POINTER) om2->tfv_mem + 15) & (~0xf)); /* copy the vector data */ memcpy(om2->rbv[0], om1->rbv[0], sizeof(__m128i) * nqb * abc->Kp); diff --git a/src/makehmmerdb.c b/src/makehmmerdb.c index ef2b427d..62f609e7 100644 --- a/src/makehmmerdb.c +++ b/src/makehmmerdb.c @@ -377,7 +377,9 @@ main(int argc, char **argv) clock_t t1, t2; +#ifndef __MINGW32__ struct tms ts1, ts2; +#endif /* __MINGW32__ */ long i,j,c; @@ -472,7 +474,11 @@ main(int argc, char **argv) //start timer +#ifdef __MINGW32__ + t1 = clock(); +#else t1 = times(&ts1); +#endif /* __MINGW32__ */ output_header(stdout, go, fname_in, fname_out); @@ -854,10 +860,17 @@ main(int argc, char **argv) esl_getopts_Destroy(go); - // compute and print the elapsed time in millisec +#ifdef __MINGW32__ + t2 = clock(); +#else t2 = times(&ts2); +#endif { +#ifdef __MINGW32__ + double clk_ticks = CLOCKS_PER_SEC; +#else double clk_ticks = sysconf(_SC_CLK_TCK); +#endif /* __MINGW32__ */ double elapsedTime = (t2-t1)/clk_ticks; fprintf (stderr, "run time: %.2f seconds\n", elapsedTime); diff --git a/src/p7_config.h.in b/src/p7_config.h.in index 4acf9821..274d5e28 100644 --- a/src/p7_config.h.in +++ b/src/p7_config.h.in @@ -131,5 +131,16 @@ */ #undef HAVE_FLUSH_ZERO_MODE +#undef HAVE_STDINT_H +#undef HAVE_INTTYPES_H + +#if HAVE_STDINT_h +#include +#elif HAVE_INTTYPES_H +#include +#endif + +typedef uintptr_t POINTER; + #endif /*P7_CONFIGH_INCLUDED*/ diff --git a/src/p7_hmm.c b/src/p7_hmm.c index 08480a87..98117824 100644 --- a/src/p7_hmm.c +++ b/src/p7_hmm.c @@ -580,7 +580,11 @@ p7_hmm_SetCtime(P7_HMM *hmm) ESL_ALLOC(s, 32); if ((date = time(NULL)) == -1) { status = eslESYS; goto ERROR; } +#ifdef __MINGW32__ + if (ctime_s(s, 32, &date) != 0) { status = eslESYS; goto ERROR; } +#else if (ctime_r(&date, s) == NULL) { status = eslESYS; goto ERROR; } +#endif if ((status = esl_strchop(s, -1)) != eslOK) { goto ERROR; } if (hmm->ctime != NULL) free(hmm->ctime); diff --git a/src/p7_hmmfile.c b/src/p7_hmmfile.c index 26e103f6..24d489e5 100644 --- a/src/p7_hmmfile.c +++ b/src/p7_hmmfile.c @@ -336,7 +336,7 @@ open_engine(const char *filename, char *env, P7_HMMFILE **ret_hfp, int do_ascii_ * names of expected index and binary database files. */ if (hfp->f == NULL) { - if ((hfp->f = fopen(filename, "r")) != NULL) { + if ((hfp->f = fopen(filename, "rb")) != NULL) { if ((status = esl_strdup(filename, n, &(hfp->fname))) != eslOK) ESL_XFAIL(status, errbuf, "esl_strdup() failed, shouldn't happen"); } else if (esl_FileEnvOpen(filename, env, &(hfp->f), &envfile) == eslOK) { n = strlen(envfile); @@ -2392,7 +2392,7 @@ utest_io_30(char *tmpfile, int format, P7_HMM *hmm) p7_hmmfile_Close(hfp); /* Do it all again, but with binary format */ - if ((fp = fopen(tmpfile, "w")) == NULL) esl_fatal(msg); + if ((fp = fopen(tmpfile, "wb")) == NULL) esl_fatal(msg); if (p7_hmmfile_WriteBinary(fp, format, hmm) != eslOK) esl_fatal(msg); fclose(fp); if (p7_hmmfile_OpenE(tmpfile, NULL, &hfp, NULL) != eslOK) esl_fatal(msg); diff --git a/src/p7_tophits.c b/src/p7_tophits.c index 6dccbdb6..b99b473f 100644 --- a/src/p7_tophits.c +++ b/src/p7_tophits.c @@ -1987,7 +1987,11 @@ p7_tophits_TabularTail(FILE *ofp, const char *progname, enum p7_pipemodes_e pipe if ((status = esl_opt_SpoofCmdline(go, &spoof_cmd)) != eslOK) goto ERROR; if (date == -1) ESL_XEXCEPTION(eslESYS, "time() failed"); +#ifdef __MINGW32__ + if (ctime_s(timestamp, 32, &date) != 0) ESL_XEXCEPTION(eslESYS, "ctime_s() failed"); +#else if ((ctime_r(&date, timestamp)) == NULL) ESL_XEXCEPTION(eslESYS, "ctime_r() failed"); +#endif /* __MINGW32__ */ switch (pipemode) { case p7_SEARCH_SEQS: strcpy(modestamp, "SEARCH"); break; case p7_SCAN_MODELS: strcpy(modestamp, "SCAN"); break; diff --git a/testsuite/h3.pm b/testsuite/h3.pm index c9cd5023..f7feee6b 100644 --- a/testsuite/h3.pm +++ b/testsuite/h3.pm @@ -32,6 +32,7 @@ sub ParseTbl { { if (/^\#/) { next; } chop; + if (/\r/) { chop; } @fields = split(' ', $_, 19); $tname[$ntbl] = $fields[0]; @@ -93,6 +94,7 @@ sub ParseDomTbl { { if (/^\#/) { next; } chop; + if (/\r/) { chop; } @fields = split(' ', $_, 23); $tname[$ndomtbl] = $fields[0]; diff --git a/testsuite/i14-hmmemit-consensus.pl b/testsuite/i14-hmmemit-consensus.pl index 0f96ca38..32bd4696 100755 --- a/testsuite/i14-hmmemit-consensus.pl +++ b/testsuite/i14-hmmemit-consensus.pl @@ -56,11 +56,11 @@ BEGIN @symfrac_choices = ( 0.0, 0.0, 0.0, 0.0, 0.6 ); @minl_choices = ( 0.0, 0.0, 1.0, 0.5, 0.5 ); @minu_choices = ( 0.0, 1.0, 1.0, 0.8, 0.8 ); -@answers = ( "ACDEFAIKLMNPQRSA\n", - "AcdefaIKLMNPqrsa\n", - "AxxxxxIKLMNPxxxx\n", - "ACDefxIKLMNPxxxx\n", - "ACDefxIKLMxxxx\n"); +@answers = ( "ACDEFAIKLMNPQRSA", + "AcdefaIKLMNPqrsa", + "AxxxxxIKLMNPxxxx", + "ACDefxIKLMNPxxxx", + "ACDefxIKLMxxxx"); for ($i = 0; $i < $#symfrac_choices; $i++) { @@ -70,6 +70,10 @@ BEGIN @output = `$builddir/src/hmmemit -C --minl $minl_choices[$i] --minu $minu_choices[$i] $tmppfx.hmm 2>&1`; if ($? != 0) { die "FAIL: hmmemit failed\n"; } + chomp($output[1]); + if ($output[1] =~ /\r$/) { + chop($output[1]); + } if ($output[1] ne $answers[$i]) { die "FAIL: hmmemit, expected $answers[$i]; saw $output[1]\n"; } } diff --git a/testsuite/i17-stdin.pl b/testsuite/i17-stdin.pl index 3b335729..5a9cd5a9 100755 --- a/testsuite/i17-stdin.pl +++ b/testsuite/i17-stdin.pl @@ -106,7 +106,7 @@ BEGIN $output = `cat $arg1 $arg2 | $prog - - 2>&1`; if (!$?) { die "FAIL: $tag should fail on double - -\n"; } -if ($output !~ /^\nERROR: Either or /) { die "FAIL: $tag didn't give expected error message for the - - case.\n"; } +if ($output !~ /^\r?\nERROR: Either or /) { die "FAIL: $tag didn't give expected error message for the - - case.\n"; } ################################################################ @@ -183,11 +183,19 @@ BEGIN $output = `cat $arg1 $arg2 | $prog -f - - 2>&1`; if (! $?) { die "FAIL: $tag should have failed on double - -\n"; } -if ($output !~ /^Either or /) { die "FAIL: $tag didn't give expected error message for the - - case.\n"; } +if ($^O eq 'MSWin32' || $^O eq 'msys') { + +} else { + if ($output !~ /^Either or /) { die "FAIL: $tag didn't give expected error message for the - - case.\n"; } +} `$prog --index $arg1 > $tmppfx.out1`; if ($?) { die "FAIL: $tag --index $tag1\n"; } $output = `cat $arg1 | $prog --index - 2>&1`; if (! $?) { die "FAIL: $tag should reject - for when using --index\n"; } -if ($output !~ /^Can't use - with --index/) { die "FAIL: $tag didn't give expected error message for the - - case.\n"; } +if ($^O eq 'MSWin32' || $^O eq 'msys') { + if ($output !~ /\r?\nCan't use - with --index/) { die "FAIL: $tag didn't give expected error message for the - - case.\n"; } +} else { + if ($output !~ /^Can't use - with --index/) { die "FAIL: $tag didn't give expected error message for the - - case.\n"; } +} ################################################################ # hmmpress @@ -199,7 +207,7 @@ BEGIN if ($verbose) { print "$tag...\n"; } $output = `cat $arg1 | $prog - 2>&1`; if (! $?) { die "FAIL: $tag should reject - for \n"; } -if ($output !~ /^\nError: Can't use - for /) { die "FAIL: $tag didn't give expected error message.\n"; } +if ($output !~ /^\r?\nError: Can't use - for /) { die "FAIL: $tag didn't give expected error message.\n"; } ################################################################# # hmmscan. diff --git a/testsuite/i18-nhmmer-generic.pl b/testsuite/i18-nhmmer-generic.pl index dba06bde..6a33450a 100755 --- a/testsuite/i18-nhmmer-generic.pl +++ b/testsuite/i18-nhmmer-generic.pl @@ -70,11 +70,11 @@ BEGIN if ($? != 0) { die "FAIL: nhmmer failed unexpectedly\n"; } $expect = q[ -Target sequences: 1 \(9000000 residues searched\) -Residues passing SSV filter: 172355 \(0.0192\); expected \(0.02\) -Residues passing bias filter: 144134 \(0.016\); expected \(0.02\) -Residues passing Vit filter: 17743 \(0.00197\); expected \(0.003\) -Residues passing Fwd filter: 415 \(4.61e-05\); expected \(3e-05\) +Target sequences: 1 \(9000000 residues searched\)\s* +Residues passing SSV filter: 172355 \(0.0192\); expected \(0.02\)\s* +Residues passing bias filter: 144134 \(0.016\); expected \(0.02\)\s* +Residues passing Vit filter: 17743 \(0.00197\); expected \(0.003\)\s* +Residues passing Fwd filter: 415 \(4.61e-05\); expected \(3e-05\)\s* Total number of hits: 4 \(8.33e-06\)]; if ($output !~ /$expect/s) { die "FAIL: nhmmer failed search test 1\n"; @@ -93,11 +93,11 @@ BEGIN $output = do_cmd($cmd); if ($? != 0) { die "FAIL: nhmmer failed unexpectedly\n"; } $expect = q[ -Target sequences: 1 \(4500000 residues searched\) -Residues passing SSV filter: 84074 \(0.0187\); expected \(0.02\) -Residues passing bias filter: 69825 \(0.0155\); expected \(0.02\) -Residues passing Vit filter: 8940 \(0.00199\); expected \(0.003\) -Residues passing Fwd filter: 228 \(5.07e-05\); expected \(3e-05\) +Target sequences: 1 \(4500000 residues searched\)\s* +Residues passing SSV filter: 84074 \(0.0187\); expected \(0.02\)\s* +Residues passing bias filter: 69825 \(0.0155\); expected \(0.02\)\s* +Residues passing Vit filter: 8940 \(0.00199\); expected \(0.003\)\s* +Residues passing Fwd filter: 228 \(5.07e-05\); expected \(3e-05\)\s* Total number of hits: 3 \(1.33e-05\)]; if ($output !~ /$expect/s) { diff --git a/testsuite/iss159-nhmmer-overlap.py b/testsuite/iss159-nhmmer-overlap.py index 3e1206a0..86b7ff21 100755 --- a/testsuite/iss159-nhmmer-overlap.py +++ b/testsuite/iss159-nhmmer-overlap.py @@ -18,8 +18,9 @@ srcdir = sys.argv[2] tmppfx = sys.argv[3] -if (not os.path.exists('{}/src/hmmbuild'.format(builddir))): sys.exit("FAIL: didn't find {}/src/hmmbuild".format(builddir)) -if (not os.path.exists('{}/src/nhmmer'.format(builddir))): sys.exit("FAIL: didn't find {}/src/nhmmer".format(builddir)) +suffix = '.exe' if os.name == 'nt' else '' +if (not os.path.exists('{}/src/hmmbuild{}'.format(builddir, suffix))): sys.exit("FAIL: didn't find {}/src/hmmbuild{}".format(builddir, suffix)) +if (not os.path.exists('{}/src/nhmmer{}'.format(builddir, suffix))): sys.exit("FAIL: didn't find {}/src/nhmmer{}".format(builddir, suffix)) with open('{0}.sto'.format(tmppfx), 'w') as f: print ("""\