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Pyenv Build Failed, trying to install 3.7.0, cannot compute sizeof (size_t) #1201

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Dotnaught opened this issue Aug 15, 2018 · 5 comments
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@Dotnaught
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@Dotnaught Dotnaught commented Aug 15, 2018

macOS 10.13.6 (High Sierra)

I've tried various steps with reinstalling openssl and xcode command line tools, but nothing has helped.

env PYENV_DEBUG=1 pyenv install -v 3.7.0

  • [pyenv:22] enable -f /usr/local/bin/../libexec/pyenv-realpath.dylib realpath

  • [pyenv:29] '[' -z '' ']'
    ++ [pyenv:31] type -p greadlink readlink
    ++ [pyenv:31] head -1

  • [pyenv:31] READLINK=/usr/bin/readlink

  • [pyenv:32] '[' -n /usr/bin/readlink ']'

  • [pyenv:54] '[' -z '' ']'

  • [pyenv:55] PYENV_ROOT=/Users/tk/.pyenv

  • [pyenv:59] export PYENV_ROOT

  • [pyenv:62] '[' -z '' ']'

  • [pyenv:63] '[' -n '' ']'

  • [pyenv:79] '[' -z '' ']'

  • [pyenv:80] PYENV_DIR=/Users/tk/code/python

  • [pyenv:83] '[' '!' -d /Users/tk/code/python ']'

  • [pyenv:83] '[' '!' -e /Users/tk/code/python ']'
    ++ [pyenv:87] cd /Users/tk/code/python
    ++ [pyenv:87] echo /Users/tk/code/python

  • [pyenv:87] PYENV_DIR=/Users/tk/code/python

  • [pyenv:88] export PYENV_DIR

  • [pyenv:91] shopt -s nullglob
    ++ [pyenv:93] abs_dirname /usr/local/bin/pyenv
    ++ [pyenv:39] local path=/usr/local/bin/pyenv
    ++ [pyenv:43] '[' -n /usr/local/bin/pyenv ']'
    ++ [pyenv:44] cd /usr/local/bin
    ++ [pyenv:45] local name=pyenv
    +++ [pyenv:46] resolve_link pyenv
    +++ [pyenv:35] /usr/bin/readlink pyenv
    ++ [pyenv:46] path=../Cellar/pyenv/1.2.7/bin/pyenv
    ++ [pyenv:43] '[' -n ../Cellar/pyenv/1.2.7/bin/pyenv ']'
    ++ [pyenv:44] cd ../Cellar/pyenv/1.2.7/bin
    ++ [pyenv:45] local name=pyenv
    +++ [pyenv:46] resolve_link pyenv
    +++ [pyenv:35] /usr/bin/readlink pyenv
    ++ [pyenv:46] path=../libexec/pyenv
    ++ [pyenv:43] '[' -n ../libexec/pyenv ']'
    ++ [pyenv:44] cd ../libexec
    ++ [pyenv:45] local name=pyenv
    +++ [pyenv:46] resolve_link pyenv
    +++ [pyenv:35] /usr/bin/readlink pyenv
    +++ [pyenv:46] true
    ++ [pyenv:46] path=
    ++ [pyenv:43] '[' -n '' ']'
    ++ [pyenv:49] pwd

  • [pyenv:93] bin_path=/usr/local/Cellar/pyenv/1.2.7/libexec

  • [pyenv:97] export PATH=/usr/local/Cellar/pyenv/1.2.7/libexec:/Users/tk/.pyenv/shims:/Users/tk/.pyenv:/Users/tk/google-cloud-sdk/bin:/Users/tomclaburn/Code/git/flutter/bin:/usr/local/sbin:/usr/local/heroku/bin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/Users/tk/.pyenv/shims:/Users/tk/.pyenv:/Users/tk/google-cloud-sdk/bin:/Users/tomclaburn/Code/git/flutter/bin:/usr/local/sbin:/usr/local/heroku/bin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/Users/tk/.pyenv:/Users/tk/google-cloud-sdk/bin:/Users/tk/.nvm/versions/node/v8.11.3/bin:/Users/tomclaburn/Code/git/flutter/bin:/usr/local/sbin:/usr/local/heroku/bin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Applications/Postgres.app/Contents/Versions/latest/bin:/usr/local/mongodb/bin:/usr/local/mongodb/bin:/usr/local/mongodb/bin

  • [pyenv:97] PATH=/usr/local/Cellar/pyenv/1.2.7/libexec:/Users/tk/.pyenv/shims:/Users/tk/.pyenv:/Users/tk/google-cloud-sdk/bin:/Users/tomclaburn/Code/git/flutter/bin:/usr/local/sbin:/usr/local/heroku/bin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/Users/tk/.pyenv/shims:/Users/tk/.pyenv:/Users/tk/google-cloud-sdk/bin:/Users/tomclaburn/Code/git/flutter/bin:/usr/local/sbin:/usr/local/heroku/bin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/Users/tk/.pyenv:/Users/tk/google-cloud-sdk/bin:/Users/tk/.nvm/versions/node/v8.11.3/bin:/Users/tomclaburn/Code/git/flutter/bin:/usr/local/sbin:/usr/local/heroku/bin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Applications/Postgres.app/Contents/Versions/latest/bin:/usr/local/mongodb/bin:/usr/local/mongodb/bin:/usr/local/mongodb/bin

  • [pyenv:99] PYENV_HOOK_PATH=:/Users/tk/.pyenv/pyenv.d

  • [pyenv:100] '[' /usr/local/Cellar/pyenv/1.2.7 '!=' /Users/tk/.pyenv ']'

  • [pyenv:102] PYENV_HOOK_PATH=:/Users/tk/.pyenv/pyenv.d:/usr/local/Cellar/pyenv/1.2.7/pyenv.d

  • [pyenv:104] PYENV_HOOK_PATH=:/Users/tk/.pyenv/pyenv.d:/usr/local/Cellar/pyenv/1.2.7/pyenv.d:/usr/local/etc/pyenv.d:/etc/pyenv.d:/usr/lib/pyenv/hooks

  • [pyenv:108] PYENV_HOOK_PATH=/Users/tk/.pyenv/pyenv.d:/usr/local/Cellar/pyenv/1.2.7/pyenv.d:/usr/local/etc/pyenv.d:/etc/pyenv.d:/usr/lib/pyenv/hooks

  • [pyenv:109] export PYENV_HOOK_PATH

  • [pyenv:111] shopt -u nullglob

  • [pyenv:114] command=install

  • [pyenv:115] case "$command" in
    ++ [pyenv:128] command -v pyenv-install

  • [pyenv:128] command_path=/usr/local/bin/pyenv-install

  • [pyenv:129] '[' -z /usr/local/bin/pyenv-install ']'

  • [pyenv:137] shift 1

  • [pyenv:138] '[' -v = --help ']'

  • [pyenv:145] exec /usr/local/bin/pyenv-install -v 3.7.0

  • [pyenv-install:32] shopt -s nullglob

  • [pyenv-install:36] export PYTHON_BUILD_DEFINITIONS

  • [pyenv-install:37] shopt -u nullglob

  • [pyenv-install:40] '[' -v = --complete ']'
    ++ [pyenv-install:53] python-build --lib

  • [pyenv-install:53] eval 'lib ()
    {
    function parse_options ()
    {
    OPTIONS=();
    ARGUMENTS=();
    local arg option index;
    for arg in "$@";
    do
    if [ "${arg:0:1}" = "-" ]; then
    if [ "${arg:1:1}" = "-" ]; then
    OPTIONS[${#OPTIONS[]}]="${arg:2}";
    else
    index=1;
    while option="${arg:$index:1}"; do
    [ -n "$option" ] || break;
    OPTIONS[${#OPTIONS[
    ]}]="$option";
    index=$(($index+1));
    done;
    fi;
    else
    ARGUMENTS[${#ARGUMENTS[*]}]="$arg";
    fi;
    done
    };
    if [ "$1" == "--$FUNCNAME" ]; then
    declare -f "$FUNCNAME";
    echo "$FUNCNAME "$1";";
    exit;
    fi
    }
    lib "$1";'
    ++ [pyenv-install:84] lib -v
    ++ [pyenv-install:78] '[' -v == --lib ']'

  • [pyenv-install:69] unset FORCE

  • [pyenv-install:70] unset SKIP_EXISTING

  • [pyenv-install:71] unset KEEP

  • [pyenv-install:72] unset VERBOSE

  • [pyenv-install:73] unset HAS_PATCH

  • [pyenv-install:74] unset DEBUG

  • [pyenv-install:76] parse_options -v 3.7.0

  • [pyenv-install:57] OPTIONS=()

  • [pyenv-install:58] ARGUMENTS=()

  • [pyenv-install:59] local arg option index

  • [pyenv-install:60] for arg in "$@"

  • [pyenv-install:62] '[' - = - ']'

  • [pyenv-install:63] '[' v = - ']'

  • [pyenv-install:66] index=1

  • [pyenv-install:67] option=v

  • [pyenv-install:68] '[' -n v ']'

  • [pyenv-install:69] OPTIONS[${#OPTIONS[*]}]=v

  • [pyenv-install:70] index=2

  • [pyenv-install:67] option=

  • [pyenv-install:68] '[' -n '' ']'

  • [pyenv-install:68] break

  • [pyenv-install:60] for arg in "$@"

  • [pyenv-install:62] '[' 3 = - ']'

  • [pyenv-install:74] ARGUMENTS[${#ARGUMENTS[*]}]=3.7.0

  • [pyenv-install:77] for option in "${OPTIONS[@]}"

  • [pyenv-install:78] case "$option" in

  • [pyenv-install:97] VERBOSE=-v

  • [pyenv-install:114] '[' 1 -le 1 ']'

  • [pyenv-install:116] unset VERSION_NAME

  • [pyenv-install:122] DEFINITION=3.7.0

  • [pyenv-install:123] '[' -n 3.7.0 ']'

  • [pyenv-install:124] '[' -n 3.7.0 ']'

  • [pyenv-install:129] declare -a before_hooks after_hooks

  • [pyenv-install:141] OLDIFS='
    '

  • [pyenv-install:142] IFS='
    '

  • [pyenv-install:142] scripts=(pyenv-hooks install)
    ++ [pyenv-install:142] pyenv-hooks install

  • [pyenv-hooks:9] '[' install = --complete ']'

  • [pyenv-hooks:18] PYENV_COMMAND=install

  • [pyenv-hooks:19] '[' -z install ']'

  • [pyenv-hooks:24] enable -f /usr/local/Cellar/pyenv/1.2.7/libexec/pyenv-realpath.dylib realpath

  • [pyenv-hooks:55] IFS=:

  • [pyenv-hooks:55] hook_paths=($PYENV_HOOK_PATH)

  • [pyenv-hooks:57] shopt -s nullglob

  • [pyenv-hooks:58] for path in "${hook_paths[@]}"

  • [pyenv-hooks:58] for path in "${hook_paths[@]}"

  • [pyenv-hooks:58] for path in "${hook_paths[@]}"

  • [pyenv-hooks:58] for path in "${hook_paths[@]}"

  • [pyenv-hooks:58] for path in "${hook_paths[@]}"

  • [pyenv-hooks:63] shopt -u nullglob

  • [pyenv-install:143] IFS='
    '

  • [pyenv-install:149] '[' -n '' ']'

  • [pyenv-install:149] VERSION_NAME=3.7.0

  • [pyenv-install:150] '[' -n '' ']'

  • [pyenv-install:151] PREFIX=/Users/tk/.pyenv/versions/3.7.0

  • [pyenv-install:153] '[' -d /Users/tk/.pyenv/versions/3.7.0 ']'

  • [pyenv-install:157] '[' -d /Users/tk/.pyenv/versions/3.7.0/bin ']'

  • [pyenv-install:175] '[' -n '' ']'

  • [pyenv-install:182] '[' -z '' ']'

  • [pyenv-install:182] '[' -d /Users/tk/.pyenv/cache ']'

  • [pyenv-install:186] '[' -z '' ']'

  • [pyenv-install:187] case "${VERSION_NAME}" in

  • [pyenv-install:193] for version_info in "${VERSION_NAME%-dev}" "${VERSION_NAME%.}" "${VERSION_NAME%%.}"
    ++ [pyenv-install:195] pyenv-whence python3.7.0
    ++ [pyenv-install:195] true

  • [pyenv-install:193] for version_info in "${VERSION_NAME%-dev}" "${VERSION_NAME%.}" "${VERSION_NAME%%.}"
    ++ [pyenv-install:195] pyenv-whence python3.7
    ++ [pyenv-install:195] true

  • [pyenv-install:193] for version_info in "${VERSION_NAME%-dev}" "${VERSION_NAME%.}" "${VERSION_NAME%%.}"
    ++ [pyenv-install:195] pyenv-whence python3
    ++ [pyenv-install:195] true

  • [pyenv-install:230] '[' -n '' ']'

  • [pyenv-install:242] trap cleanup SIGINT

  • [pyenv-install:245] STATUS=0

  • [pyenv-install:246] python-build -v 3.7.0 /Users/tk/.pyenv/versions/3.7.0
    python-build: use openssl from homebrew
    python-build: use readline from homebrew
    /var/folders/jb/h01vxbqs6z93h_238q61d48h0000gn/T/python-build.20180815083027.58071 ~/code/python
    Downloading Python-3.7.0.tar.xz...
    -> https://www.python.org/ftp/python/3.7.0/Python-3.7.0.tar.xz
    /var/folders/jb/h01vxbqs6z93h_238q61d48h0000gn/T/python-build.20180815083027.58071/Python-3.7.0 /var/folders/jb/h01vxbqs6z93h_238q61d48h0000gn/T/python-build.20180815083027.58071 ~/code/python
    Installing Python-3.7.0...
    python-build: use readline from homebrew
    checking build system type... x86_64-apple-darwin17.7.0
    checking host system type... x86_64-apple-darwin17.7.0
    checking for python3.7... python3.7
    checking for --enable-universalsdk... no
    checking for --with-universal-archs... no
    checking MACHDEP... checking for --without-gcc... no
    checking for --with-icc... no
    checking for gcc... clang
    checking whether the C compiler works... yes
    checking for C compiler default output file name... a.out
    checking for suffix of executables...
    checking whether we are cross compiling... no
    checking for suffix of object files... o
    checking whether we are using the GNU C compiler... yes
    checking whether clang accepts -g... yes
    checking for clang option to accept ISO C89... none needed
    checking how to run the C preprocessor... clang -E
    checking for grep that handles long lines and -e... /usr/bin/grep
    checking for a sed that does not truncate output... /usr/bin/sed
    checking for --with-cxx-main=... no
    checking for clang++... no
    configure:

    By default, distutils will build C++ extension modules with "clang++".
    If this is not intended, then set CXX on the configure command line.

checking for the platform triplet based on compiler characteristics... darwin
checking for -Wl,--no-as-needed... no
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... no
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... no
checking for string.h... no
checking for memory.h... no
checking for strings.h... no
checking for inttypes.h... no
checking for stdint.h... no
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define EXTENSIONS... yes
checking for the Android API level... not Android
checking for --with-suffix...
checking for case-insensitive build directory... yes
checking LIBRARY... libpython$(VERSION)$(ABIFLAGS).a
checking LINKCC... $(PURIFY) $(MAINCC)
checking for GNU ld... no
checking for --enable-shared... no
checking for --enable-profiling... no
checking LDLIBRARY... libpython$(VERSION)$(ABIFLAGS).a
checking for ar... ar
checking for readelf... no
checking for a BSD-compatible install... /usr/bin/install -c
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for --with-pydebug... no
checking for --with-assertions... no
checking for --enable-optimizations... no
checking for --with-lto... no
checking target system type... x86_64-apple-darwin17.7.0
checking for -llvm-profdata... no
checking for llvm-profdata... ''
configure: llvm-profdata found via xcrun: /usr/bin/xcrun llvm-profdata
checking for -Wextra... yes
checking whether clang accepts and needs -fno-strict-aliasing... no
checking if we can turn off clang unused result warning... yes
checking if we can turn off clang unused parameter warning... yes
checking if we can turn off clang missing field initializers warning... yes
checking if we can turn off clang invalid function cast warning... no
checking if we can turn on clang mixed sign comparison warning... yes
checking if we can turn on clang unreachable code warning... yes
checking if we can turn on clang strict-prototypes warning... yes
checking if we can make implicit function declaration an error in clang... yes
checking which MACOSX_DEPLOYMENT_TARGET to use... 10.13
checking whether pthreads are available without options... yes
checking whether clang++ also accepts flags for thread support... no
checking for ANSI C header files... (cached) no
checking asm/types.h usability... no
checking asm/types.h presence... no
checking for asm/types.h... no
checking crypt.h usability... no
checking crypt.h presence... no
checking for crypt.h... no
checking conio.h usability... no
checking conio.h presence... no
checking for conio.h... no
checking direct.h usability... no
checking direct.h presence... no
checking for direct.h... no
checking dlfcn.h usability... no
checking dlfcn.h presence... no
checking for dlfcn.h... no
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking grp.h usability... yes
checking grp.h presence... yes
checking for grp.h... yes
checking ieeefp.h usability... no
checking ieeefp.h presence... no
checking for ieeefp.h... no
checking io.h usability... no
checking io.h presence... no
checking for io.h... no
checking langinfo.h usability... yes
checking langinfo.h presence... yes
checking for langinfo.h... yes
checking libintl.h usability... no
checking libintl.h presence... no
checking for libintl.h... no
checking process.h usability... no
checking process.h presence... no
checking for process.h... no
checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
checking sched.h usability... yes
checking sched.h presence... yes
checking for sched.h... yes
checking shadow.h usability... no
checking shadow.h presence... no
checking for shadow.h... no
checking signal.h usability... yes
checking signal.h presence... yes
checking for signal.h... yes
checking stropts.h usability... no
checking stropts.h presence... no
checking for stropts.h... no
checking termios.h usability... yes
checking termios.h presence... yes
checking for termios.h... yes
checking for unistd.h... (cached) yes
checking utime.h usability... yes
checking utime.h presence... yes
checking for utime.h... yes
checking poll.h usability... yes
checking poll.h presence... yes
checking for poll.h... yes
checking sys/devpoll.h usability... no
checking sys/devpoll.h presence... no
checking for sys/devpoll.h... no
checking sys/epoll.h usability... no
checking sys/epoll.h presence... no
checking for sys/epoll.h... no
checking sys/poll.h usability... yes
checking sys/poll.h presence... yes
checking for sys/poll.h... yes
checking sys/audioio.h usability... no
checking sys/audioio.h presence... no
checking for sys/audioio.h... no
checking sys/xattr.h usability... yes
checking sys/xattr.h presence... yes
checking for sys/xattr.h... yes
checking sys/bsdtty.h usability... no
checking sys/bsdtty.h presence... no
checking for sys/bsdtty.h... no
checking sys/event.h usability... no
checking sys/event.h presence... no
checking for sys/event.h... no
checking sys/file.h usability... yes
checking sys/file.h presence... yes
checking for sys/file.h... yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking sys/kern_control.h usability... yes
checking sys/kern_control.h presence... yes
checking for sys/kern_control.h... yes
checking sys/loadavg.h usability... no
checking sys/loadavg.h presence... no
checking for sys/loadavg.h... no
checking sys/lock.h usability... yes
checking sys/lock.h presence... yes
checking for sys/lock.h... yes
checking sys/mkdev.h usability... no
checking sys/mkdev.h presence... no
checking for sys/mkdev.h... no
checking sys/modem.h usability... no
checking sys/modem.h presence... no
checking for sys/modem.h... no
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking sys/random.h usability... yes
checking sys/random.h presence... yes
checking for sys/random.h... yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking sys/sendfile.h usability... no
checking sys/sendfile.h presence... no
checking for sys/sendfile.h... no
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking sys/statvfs.h usability... yes
checking sys/statvfs.h presence... yes
checking for sys/statvfs.h... yes
checking for sys/stat.h... (cached) yes
checking sys/syscall.h usability... yes
checking sys/syscall.h presence... yes
checking for sys/syscall.h... yes
checking sys/sys_domain.h usability... yes
checking sys/sys_domain.h presence... yes
checking for sys/sys_domain.h... yes
checking sys/termio.h usability... no
checking sys/termio.h presence... no
checking for sys/termio.h... no
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/times.h usability... yes
checking sys/times.h presence... yes
checking for sys/times.h... yes
checking for sys/types.h... (cached) yes
checking sys/uio.h usability... yes
checking sys/uio.h presence... yes
checking for sys/uio.h... yes
checking sys/un.h usability... yes
checking sys/un.h presence... yes
checking for sys/un.h... yes
checking sys/utsname.h usability... yes
checking sys/utsname.h presence... yes
checking for sys/utsname.h... yes
checking sys/wait.h usability... no
checking sys/wait.h presence... no
checking for sys/wait.h... no
checking pty.h usability... no
checking pty.h presence... no
checking for pty.h... no
checking libutil.h usability... no
checking libutil.h presence... no
checking for libutil.h... no
checking sys/resource.h usability... no
checking sys/resource.h presence... no
checking for sys/resource.h... no
checking netpacket/packet.h usability... no
checking netpacket/packet.h presence... no
checking for netpacket/packet.h... no
checking sysexits.h usability... yes
checking sysexits.h presence... yes
checking for sysexits.h... yes
checking bluetooth.h usability... no
checking bluetooth.h presence... no
checking for bluetooth.h... no
checking linux/tipc.h usability... no
checking linux/tipc.h presence... no
checking for linux/tipc.h... no
checking linux/random.h usability... no
checking linux/random.h presence... no
checking for linux/random.h... no
checking spawn.h usability... no
checking spawn.h presence... no
checking for spawn.h... no
checking util.h usability... yes
checking util.h presence... yes
checking for util.h... yes
checking alloca.h usability... yes
checking alloca.h presence... yes
checking for alloca.h... yes
checking endian.h usability... no
checking endian.h presence... no
checking for endian.h... no
checking sys/endian.h usability... no
checking sys/endian.h presence... no
checking for sys/endian.h... no
checking sys/sysmacros.h usability... no
checking sys/sysmacros.h presence... no
checking for sys/sysmacros.h... no
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking whether sys/types.h defines makedev... yes
checking bluetooth/bluetooth.h usability... no
checking bluetooth/bluetooth.h presence... no
checking for bluetooth/bluetooth.h... no
checking for net/if.h... no
checking for linux/netlink.h... no
checking for linux/vm_sockets.h... no
checking for linux/can.h... no
checking for linux/can/raw.h... no
checking for linux/can/bcm.h... no
checking for clock_t in time.h... yes
checking for makedev... yes
checking for le64toh... no
checking for mode_t... yes
checking for off_t... yes
checking for pid_t... yes
checking for size_t... yes
checking for uid_t in sys/types.h... yes
checking for ssize_t... yes
checking for __uint128_t... yes
checking size of int... 0
checking size of long... 0
checking size of long long... 0
checking size of void *... 0
checking size of short... 0
checking size of float... 0
checking size of double... 0
checking size of fpos_t... 0
checking size of size_t... configure: error: in /var/folders/jb/h01vxbqs6z93h_238q61d48h0000gn/T/python-build.20180815083027.58071/Python-3.7.0': configure: error: cannot compute sizeof (size_t) See config.log' for more details

BUILD FAILED (OS X 10.13.6 using python-build 20180424)

Inspect or clean up the working tree at /var/folders/jb/h01vxbqs6z93h_238q61d48h0000gn/T/python-build.20180815083027.58071
Results logged to /var/folders/jb/h01vxbqs6z93h_238q61d48h0000gn/T/python-build.20180815083027.58071.log

Last 10 log lines:
checking size of long... 0
checking size of long long... 0
checking size of void *... 0
checking size of short... 0
checking size of float... 0
checking size of double... 0
checking size of fpos_t... 0
checking size of size_t... configure: error: in /var/folders/jb/h01vxbqs6z93h_238q61d48h0000gn/T/python-build.20180815083027.58071/Python-3.7.0': configure: error: cannot compute sizeof (size_t) See config.log' for more details

  • [pyenv-install:246] STATUS=1
  • [pyenv-install:249] '[' 1 == 2 ']'
  • [pyenv-install:277] '[' 1 == 0 ']'
  • [pyenv-install:280] cleanup
  • [pyenv-install:239] '[' -z '' ']'
  • [pyenv-install:239] rm -rf /Users/tk/.pyenv/versions/3.7.0
  • [pyenv-install:283] exit 1
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@Dotnaught Dotnaught commented Aug 15, 2018

Trying to install using:
CFLAGS="-I$(xcrun --show-sdk-path)/usr/include" pyenv install -v 3.7.0

generated a bunch of warnings...

In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk/usr/include/stdio.h:64:
/Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk/usr/include/_stdio.h:93:16: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness]
unsigned char *_base;
^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk/usr/include/_stdio.h:93:16: note: insert '_Nullable' if the pointer may be null
unsigned char *_base;

and ending with...

/Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk/usr/include/pthread.h:527:6: warning: macro expansion producing 'defined' has undefined behavior [-Wexpansion-to-defined]
/Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk/usr/include/pthread.h:194:34: note: expanded from macro '_PTHREAD_SWIFT_IMPORTER_NULLABILITY_COMPAT'
defined(SWIFT_CLASS_EXTRA) && (!defined(SWIFT_SDK_OVERLAY_PTHREAD_EPOCH) || (SWIFT_SDK_OVERLAY_PTHREAD_EPOCH < 1))

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@Dotnaught Dotnaught commented Aug 19, 2018

I've described the issue more fully in a Stack Overflow post. According to pyenv-doctor, the OpenSSL headers are missing and I've not found a way to resolve that.

https://stackoverflow.com/questions/51919720/pyenv-python-installation-failure-openssl-development-header-is-not-installed

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@kitsunde kitsunde commented Aug 23, 2018

I had the same issue and I'm not sure this happened because I used the migration assistant to transfer to a new mac (some things appeared to break) or because of the new high sierra release, but either way it seems like brew was messing with pyenv.

The solution is here SOHU-Co/kafka-node#881 but basically if you run brew doctor you'll see there's a bunch of headers that shouldn't be there, these cause some include statements to be recursive according to console.log. You can fix it with:

mkdir /tmp/includes
brew doctor 2>&1 | grep "/usr/local/include" | awk '{$1=$1;print}' | xargs -I _ mv _ /tmp/includes

These were causing some include directive to blow up. After this pyenv doctor will report everything is okay and you can run pyenv install 3.7.0 like normal.

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@Dotnaught Dotnaught commented Aug 24, 2018

Thanks, that seems to have done the trick.

@Dotnaught Dotnaught closed this Aug 24, 2018
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@VladKha VladKha commented Jan 18, 2019

@kitsunde you saved my day, thank you so much. I also had an issue after using the migration assistant to transfer to a new mac (Mojave mac os version)

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