update error for pkg-config-0.28.tar.gz

[junchend]

Hi Brad,

Recently, I used:

bcbio_nextgen.py upgrade -u development --data --tools

to update bcbio_nextgen

However, an error was occurred for pkg-config-0.28.tar.gz, the info was:

[localhost] local: /data1/bcbio_tools/bin/brew tap --repair
[localhost] local: /data1/bcbio_tools/bin/brew outdated
[localhost] local: /data1/bcbio_tools/bin/brew info expat
[localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export SHELL=${SHELL:-/bin/bash} && export PERL5LIB=/data1/bcbio_tools/lib/perl5:${PERL5LIB} && /data1/bcbio_tools/bin/brew install --env=inherit   pkg-config

Warning: local() encountered an error (return code 1) while executing 'export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export SHELL=${SHELL:-/bin/bash} && export PERL5LIB=/data1/bcbio_tools/lib/perl5:${PERL5LIB} && /data1/bcbio_tools/bin/brew install --env=inherit   pkg-config'

Traceback (most recent call last):
  File "/data1/tmpbcbio-install/cloudbiolinux/cloudbio/package/brew.py", line 271, in _install_pkg_latest
    cmd.replace("brew install", "brew install -v"))
    cmd.replace("brew install", "brew install -v"))
ValueError: Failed to install brew formula: pkg-config
To debug, please try re-running the install command with verbose output:
export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export SHELL=${SHELL:-/bin/bash} && export PERL5LIB=/data1/bcbio_tools/lib/perl5:${PERL5LIB} && /data1/bcbio_tools/bin/brew install -v --env=inherit   pkg-config

[root@I950 data1]# export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export SHELL=${SHELL:-/bin/bash} && export PERL5LIB=/data1/bcbio_tools/lib/perl5:${PERL5LIB} && /data1/bcbio_tools/bin/brew install --env=inherit   pkg-config
==> Downloading http://pkgconfig.freedesktop.org/releases/pkg-config-0.28.tar.gz
Already downloaded: /root/.cache/Homebrew/pkg-config-0.28.tar.gz
==> ./configure --prefix=/data1/bcbio_tools/Cellar/pkg-config/0.28 --disable-host-tool --with-internal-glib --with
==> make
make[2]: *** [all] Error 2
make[2]: Leaving directory `/tmp/pkg-config20150805-32797-4pheeh/pkg-config-0.28/glib'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/tmp/pkg-config20150805-32797-4pheeh/pkg-config-0.28'
make: *** [all] Error 2

READ THIS: https://github.com/Homebrew/linuxbrew/blob/master/share/doc/homebrew/Troubleshooting.md#troubleshooting

These open issues may also help:
document pkg-config configuration  https://github.com/Homebrew/homebrew/issues/21129

Could you please tell me how to fix it?

Thanks so much！

[chapmanb]

Sorry about the issue, it's failing to compile for some reason but it's not totally clear why from the output you posted. Would it be possible to re-run the command you did by hand but add the verbose flag (-v) after install. It looks like in your re-run you left this out and brew doesn't print much useful debug information without it. Hope this will give us more to go on. Thanks much.

[junchend]

Hi Brad,

Thanks for the response, I post the error message again:

[localhost] local: ls /data1/bcbio_tools/share/java/varscan-2.3.7
INFO: Custom install for 'varscan' end time: 2015-08-08 04:48:52.792900; duration: 0:00:01.325638
DBG [config.py]: Using config file /data1/tmpbcbio-install/cloudbiolinux/cloudbio/../config/chef_recipes.yaml
INFO: Reading /data1/tmpbcbio-install/cloudbiolinux/cloudbio/../config/chef_recipes.yaml
DBG [shared.py]: Packages to install: 
DBG [config.py]: Using config file /data1/tmpbcbio-install/cloudbiolinux/cloudbio/../config/puppet_classes.yaml
INFO: Reading /data1/tmpbcbio-install/cloudbiolinux/cloudbio/../config/puppet_classes.yaml
DBG [shared.py]: Packages to install: 
DBG [config.py]: Using config file /data1/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/main.yaml
INFO: Meta-package information from /data1/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/main.yaml
- Packages: minimal,libraries,perl,python,java,r,ruby,bio_nextgen
- Libraries: r-libs
DBG [config.py]: Using config file /data1/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/packages-homebrew.yaml
INFO: Reading /data1/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/packages-homebrew.yaml
DBG [shared.py]: Packages to install: bcftools,cufflinks-binary,htslib,samtools-library-0.1,samtools;--without-curses,bamtools,bedtools,biobambam,cramtools,express-binary,fastqc,grabix,kraken,oncofuse,picard-tools,qualimap,sambamba-binary,samblaster,seqtk,sickle,speedseq,staden_io_lib,bcbio-variation-recall,cancerit-allelecount,delly;--with-binary,freebayes,gatk-framework,hall-lab-sv-tools,impute2,lofreq,lumpy-sv,manta,pindel,platypus-variant,qsignature,rtg-tools,scalpel,snpeff,theta2,vardict,vardict-java,vcflib,vep,vt;--with-binary,wham;--with-binary,bowtie2;--without-tbb,bwa,bwakit,novoalign,rna-star,tophat-binary,cmake,p7zip,pkg-config,s3gof3r,cpanminus
[localhost] local: /data1/bcbio_tools/bin/brew tap
[localhost] local: /data1/bcbio_tools/bin/brew --prefix
[localhost] local: /data1/bcbio_tools/bin/brew untap homebrew/science
Untapping homebrew/science... (572 files, 3.6M)
Untapped 545 formulae
[localhost] local: /data1/bcbio_tools/bin/brew untap chapmanb/cbl
Untapping chapmanb/cbl... (117 files, 712K)
Untapped 46 formulae
[localhost] local: /data1/bcbio_tools/bin/brew update
error: unknown option `short'
usage: git symbolic-ref [options] name [ref]

    -q, --quiet           be quiet
    -m <reason>           reason of the update

Error: Failure while executing: git symbolic-ref --short HEAD 

Warning: local() encountered an error (return code 1) while executing '/data1/bcbio_tools/bin/brew update'



Homebrew update failed.
You might need to upgrade git by installing inside bcbio with:
'brew install git --env=inherit --ignore-dependences'


[localhost] local: /data1/bcbio_tools/bin/brew tap
[localhost] local: /data1/bcbio_tools/bin/brew tap homebrew/science
==> Tapping homebrew/science
Initialized empty Git repository in /data1/bcbio_tools/Library/Taps/homebrew/homebrew-science/.git/
remote: Counting objects: 2190, done.
remote: Compressing objects: 100% (1318/1318), done.
remote: Total 2190 (delta 1314), reused 1438 (delta 869), pack-reused 0
Receiving objects: 100% (2190/2190), 926.95 KiB | 336 KiB/s, done.
Resolving deltas: 100% (1314/1314), done.
Tapped 545 formulae (572 files, 3.6M)
[localhost] local: /data1/bcbio_tools/bin/brew tap chapmanb/cbl
==> Tapping chapmanb/cbl
Initialized empty Git repository in /data1/bcbio_tools/Library/Taps/chapmanb/homebrew-cbl/.git/
remote: Counting objects: 49, done.
remote: Compressing objects: 100% (48/48), done.
remote: Total 49 (delta 3), reused 19 (delta 1), pack-reused 0
Unpacking objects: 100% (49/49), done.
Tapped 46 formulae (117 files, 712K)
[localhost] local: /data1/bcbio_tools/bin/brew tap --repair
[localhost] local: /data1/bcbio_tools/bin/brew outdated
[localhost] local: /data1/bcbio_tools/bin/brew info expat
[localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export SHELL=${SHELL:-/bin/bash} && export PERL5LIB=/data1/bcbio_tools/lib/perl5:${PERL5LIB} && /data1/bcbio_tools/bin/brew install --env=inherit   pkg-config

Warning: local() encountered an error (return code 1) while executing 'export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export SHELL=${SHELL:-/bin/bash} && export PERL5LIB=/data1/bcbio_tools/lib/perl5:${PERL5LIB} && /data1/bcbio_tools/bin/brew install --env=inherit   pkg-config'

Traceback (most recent call last):
  File "/data1/tmpbcbio-install/cloudbiolinux/cloudbio/package/brew.py", line 271, in _install_pkg_latest
    cmd.replace("brew install", "brew install -v"))
ValueError: Failed to install brew formula: pkg-config
To debug, please try re-running the install command with verbose output:
export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export SHELL=${SHELL:-/bin/bash} && export PERL5LIB=/data1/bcbio_tools/lib/perl5:${PERL5LIB} && /data1/bcbio_tools/bin/brew install -v --env=inherit   pkg-config

It looks brew update error fist, could you pls check it?

[chapmanb]

Thanks for the additional information. The git error is expected since brew requires a recent git version to work. Once we fix the pkg-config issue bcbio will install an updated version of git as well to avoid it on your system going forward.

To try and fix this issue I'd need to know the output of the last command that error messages asks you to run:

export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export SHELL=${SHELL:-/bin/bash} && export PERL5LIB=/data1/bcbio_tools/lib/perl5:${PERL5LIB} && /data1/bcbio_tools/bin/brew install -v --env=inherit   pkg-config

which can hopefully help us figure out why it is not building. Thanks again.

[junchend]

Thanks Brad, the new error info is:

export CC=${CC:-which gcc} && export CXX=${CXX:-which g++} && export SHELL=${SHELL:-/bin/bash} && export PERL5LIB=/data1/bcbio_tools/lib/perl5:${PERL5LIB} && /data1/bcbio_tools/bin/brew install -v --env=inherit pkg-config
==> Downloading http://pkgconfig.freedesktop.org/releases/pkg-config-0.28.tar.gz
Already downloaded: /root/.cache/Homebrew/pkg-config-0.28.tar.gz
==> Verifying pkg-config-0.28.tar.gz checksum
tar xf /root/.cache/Homebrew/pkg-config-0.28.tar.gz
==> ./configure --disable-debug --prefix=/data1/bcbio_tools/Cellar/pkg-config/0.28 --disable-host-tool --with-internal-glib --with-pc-path=/data1/bcbio_tools/lib/pkgconfig:/data1/bcbio_tools/share/pkgconfig:/usr/local/lib/pkgconfig:/usr/lib/pkgconfig:/data1/bcbio_tools/Library/ENV/pkgconfig/0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking how to print strings... printf
checking for style of include used by make... GNU
checking for gcc... /usr/bin/gcc
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 /usr/bin/gcc accepts -g... yes
checking for /usr/bin/gcc option to accept ISO C89... none needed
checking dependency style of /usr/bin/gcc... gcc3
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by /usr/bin/gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 3458764513820540925
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @file support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from /usr/bin/gcc object... ok
checking for sysroot... no
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... /usr/bin/gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if /usr/bin/gcc supports -fno-rtti -fno-exceptions... yes
checking for /usr/bin/gcc option to produce PIC... -fPIC -DPIC
checking if /usr/bin/gcc PIC flag -fPIC -DPIC works... yes
checking if /usr/bin/gcc static flag -static works... no
checking if /usr/bin/gcc supports -c -o file.o... yes
checking if /usr/bin/gcc supports -c -o file.o... (cached) yes
checking whether the /usr/bin/gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking whether make supports nested variables... yes
checking for gcc... (cached) /usr/bin/gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether /usr/bin/gcc accepts -g... (cached) yes
checking for /usr/bin/gcc option to accept ISO C89... (cached) none needed
checking dependency style of /usr/bin/gcc... (cached) gcc3
checking for ln... ln
checking dirent.h usability... yes
checking dirent.h presence... yes
checking for dirent.h... yes
checking for unistd.h... (cached) yes
checking sys/wait.h usability... yes
checking sys/wait.h presence... yes
checking for sys/wait.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking for bash... /bin/bash
checking for default search path for .pc files... /data1/bcbio_tools/lib/pkgconfig:/data1/bcbio_tools/share/pkgconfig:/usr/local/lib/pkgconfig:/usr/lib/pkgconfig:/data1/bcbio_tools/Library/ENV/pkgconfig/0
checking for system include path to avoid -I flags... /usr/include
checking for system library path to avoid -L flags... /usr/lib:/lib
configure: creating ./config.lt
config.lt: creating libtool
checking whether to list both direct and indirect dependencies... no
checking for Win32... no
checking if internal glib should be used... yes
checking if host- prefixed tool should be installed... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating check/Makefile
config.status: creating check/config.sh
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in glib (/tmp/pkg-config20150808-18323-1oowm1u/pkg-config-0.28/glib)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/data1/bcbio_tools/Cellar/pkg-config/0.28' '--disable-debug' '--disable-host-tool' '--with-internal-glib' '--with-pc-path=/data1/bcbio_tools/lib/pkgconfig:/data1/bcbio_tools/share/pkgconfig:/usr/local/lib/pkgconfig:/usr/lib/pkgconfig:/data1/bcbio_tools/Library/ENV/pkgconfig/0' 'CC=/usr/bin/gcc' 'CFLAGS=-Os -w -pipe' 'LDFLAGS=-L/data1/bcbio_tools/lib -Wl,-rpath,/data1/bcbio_tools/lib' 'CPPFLAGS=-isystem/data1/bcbio_tools/include' 'PKG_CONFIG_PATH=:/usr/lib/pkgconfig' 'PKG_CONFIG_LIBDIR=/data1/bcbio_tools/lib/pkgconfig' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking whether to enable maintainer-specific portions of Makefiles... yes
checking whether make supports nested variables... yes
checking for gcc... /usr/bin/gcc
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 /usr/bin/gcc accepts -g... yes
checking for /usr/bin/gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of /usr/bin/gcc... gcc3
checking how to run the C preprocessor... /usr/bin/gcc -E
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for the BeOS... no
checking for Win32... no
checking for Mac OS X Carbon support... no
checking for Mac OS X Cocoa support... no
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether we are using the GNU C Library 2.1 or newer... yes
checking whether to enable garbage collector friendliness... no
checking whether to disable memory pools... no
checking whether we are using the GNU C++ compiler... yes
checking whether /usr/bin/g++ accepts -g... yes
checking dependency style of /usr/bin/g++... gcc3
checking for gcc... (cached) /usr/bin/gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether /usr/bin/gcc accepts -g... (cached) yes
checking for /usr/bin/gcc option to accept ISO C89... (cached) none needed
checking dependency style of /usr/bin/gcc... (cached) gcc3
checking whether /usr/bin/gcc and cc understand -c and -o together... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for gawk... (cached) gawk
checking for perl5... no
checking for perl... perl
checking for indent... indent
checking for perl... /usr/bin/perl
checking for a Python interpreter with version >= 2.5... python
checking for python... /usr/local/share/bcbio-nextgen/anaconda/bin/python
checking for python version... 2.7
checking for python platform... linux2
checking for python script directory... ${prefix}/lib/python2.7/site-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.7/site-packages
checking for iconv_open... yes
checking whether to cache iconv descriptors... no
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by /usr/bin/gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 3458764513820540925
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @file support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from /usr/bin/gcc object... ok
checking for sysroot... no
checking for mt... mt
checking if mt is a manifest tool... no
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if /usr/bin/gcc supports -fno-rtti -fno-exceptions... yes
checking for /usr/bin/gcc option to produce PIC... -fPIC -DPIC
checking if /usr/bin/gcc PIC flag -fPIC -DPIC works... yes
checking if /usr/bin/gcc static flag -static works... no
checking if /usr/bin/gcc supports -c -o file.o... yes
checking if /usr/bin/gcc supports -c -o file.o... (cached) yes
checking whether the /usr/bin/gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... /usr/bin/g++ -E
checking for ld used by /usr/bin/g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the /usr/bin/g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for /usr/bin/g++ option to produce PIC... -fPIC -DPIC
checking if /usr/bin/g++ PIC flag -fPIC -DPIC works... yes
checking if /usr/bin/g++ static flag -static works... no
checking if /usr/bin/g++ supports -c -o file.o... yes
checking if /usr/bin/g++ supports -c -o file.o... (cached) yes
checking whether the /usr/bin/g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
configure: creating ./config.lt
config.lt: creating libtool
checking for extra flags to get ANSI library prototypes... none needed
checking for extra flags for POSIX compliance... none needed
checking for vprintf... yes
checking for _doprnt... no
checking for size_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking for mmap... yes
checking for posix_memalign... yes
checking for memalign... yes
checking for valloc... yes
checking for fsync... yes
checking for pipe2... yes
checking for atexit... yes
checking for on_exit... yes
checking for timegm... yes
checking for gmtime_r... yes
checking size of char... 1
checking size of short... 2
checking size of long... 8
checking size of int... 4
checking size of void *... 8
checking size of long long... 8
checking size of __int64... 0
checking for sig_atomic_t... yes
checking for format to printf and scanf a guint64... %llu
checking for an ANSI C-conforming const... yes
checking if malloc() and friends prototypes are gmem.h compatible... yes
checking for growing stack pointer... no
checking for __inline... yes
checking for inline... yes
checking for inline... yes
checking if inline functions in headers work... yes
checking for working do while(0) macros... yes
checking for ISO C99 varargs macros in C... yes
checking for ISO C99 varargs macros in C++... yes
checking for GNUC varargs macros... yes
checking for GNUC visibility attribute... yes
checking whether using Sun Studio C compiler... no
checking whether byte ordering is bigendian... no
checking dirent.h usability... yes
checking dirent.h presence... yes
checking for dirent.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking pwd.h usability... yes
checking pwd.h presence... yes
checking for pwd.h... yes
checking grp.h usability... yes
checking grp.h presence... yes
checking for grp.h... yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking sys/poll.h usability... yes
checking sys/poll.h presence... yes
checking for sys/poll.h... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
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 sys/wait.h usability... yes
checking sys/wait.h presence... yes
checking for sys/wait.h... yes
checking for unistd.h... (cached) yes
checking values.h usability... yes
checking values.h presence... yes
checking for values.h... yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking for sys/types.h... (cached) yes
checking for stdint.h... (cached) yes
checking for inttypes.h... (cached) yes
checking sched.h usability... yes
checking sched.h presence... yes
checking for sched.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking sys/vfs.h usability... yes
checking sys/vfs.h presence... yes
checking for sys/vfs.h... yes
checking sys/vmount.h usability... no
checking sys/vmount.h presence... no
checking for sys/vmount.h... no
checking sys/statfs.h usability... yes
checking sys/statfs.h presence... yes
checking for sys/statfs.h... yes
checking sys/statvfs.h usability... yes
checking sys/statvfs.h presence... yes
checking for sys/statvfs.h... yes
checking mntent.h usability... yes
checking mntent.h presence... yes
checking for mntent.h... yes
checking sys/mnttab.h usability... no
checking sys/mnttab.h presence... no
checking for sys/mnttab.h... no
checking sys/vfstab.h usability... no
checking sys/vfstab.h presence... no
checking for sys/vfstab.h... no
checking sys/mntctl.h usability... no
checking sys/mntctl.h presence... no
checking for sys/mntctl.h... no
checking fstab.h usability... yes
checking fstab.h presence... yes
checking for fstab.h... yes
checking sys/uio.h usability... yes
checking sys/uio.h presence... yes
checking for sys/uio.h... yes
checking sys/mkdev.h usability... no
checking sys/mkdev.h presence... no
checking for sys/mkdev.h... no
checking linux/magic.h usability... yes
checking linux/magic.h presence... yes
checking for linux/magic.h... yes
checking sys/prctl.h usability... yes
checking sys/prctl.h presence... yes
checking for sys/prctl.h... yes
checking for sys/mount.h... yes
checking for sys/sysctl.h... yes
checking xlocale.h usability... yes
checking xlocale.h presence... yes
checking for xlocale.h... yes
checking for struct stat.st_mtimensec... no
checking for struct stat.st_mtim.tv_nsec... yes
checking for struct stat.st_atimensec... no
checking for struct stat.st_atim.tv_nsec... yes
checking for struct stat.st_ctimensec... no
checking for struct stat.st_ctim.tv_nsec... yes
checking for struct stat.st_blksize... yes
checking for struct stat.st_blocks... yes
checking for struct statfs.f_fstypename... no
checking for struct statfs.f_bavail... yes
checking for struct statvfs.f_basetype... no
checking for struct statvfs.f_fstypename... no
checking for struct tm.tm_gmtoff... yes
checking for struct tm.__tm_gmtoff... no
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for struct dirent.d_type... yes
checking for nl_langinfo and CODESET... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for setlocale... yes
checking size of size_t... 8
checking for the appropriate definition for size_t... unsigned long
checking for lstat... yes
checking for strerror... yes
checking for strsignal... yes
checking for memmove... yes
checking for vsnprintf... yes
checking for stpcpy... yes
checking for strcasecmp... yes
checking for strncasecmp... yes
checking for poll... yes
checking for getcwd... yes
checking for vasprintf... yes
checking for setenv... yes
checking for unsetenv... yes
checking for getc_unlocked... yes
checking for readlink... yes
checking for symlink... yes
checking for fdwalk... no
checking for memmem... yes
checking for chown... yes
checking for lchmod... no
checking for lchown... yes
checking for fchmod... yes
checking for fchown... yes
checking for link... yes
checking for utimes... yes
checking for getgrgid... yes
checking for getpwuid... yes
checking for getmntent_r... yes
checking for setmntent... yes
checking for endmntent... yes
checking for hasmntopt... yes
checking for getfsstat... no
checking for getvfsstat... no
checking for splice... yes
checking for prlimit... no
checking for statvfs... yes
checking for statfs... yes
checking whether to use statfs or statvfs... statfs
checking crt_externs.h usability... no
checking crt_externs.h presence... no
checking for crt_externs.h... no
checking for _NSGetEnviron... no
checking for newlocale... yes
checking for uselocale... yes
checking for strtod_l... yes
checking for strtoll_l... yes
checking for strtoull_l... yes
checking for C99 vsnprintf... yes
checking whether printf supports positional parameters... yes
checking value of AF_INET... 2
checking value of AF_INET6... 10
checking value of AF_UNIX... 1
checking value of MSG_PEEK... 2
checking value of MSG_OOB... 1
checking value of MSG_DONTROUTE... 4
checking for getprotobyname_r... yes
checking for endservent... yes
checking for if_nametoindex... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking wspiapi.h usability... no
checking wspiapi.h presence... no
checking for wspiapi.h... no
checking arpa/nameser_compat.h usability... yes
checking arpa/nameser_compat.h presence... yes
checking for arpa/nameser_compat.h... yes
checking for res_query... in -lresolv
checking for socket... yes
checking for linux/netlink.h... yes
checking for struct ip_mreqn... yes
checking number of arguments to statfs()... 2
checking for signed... yes
checking for long long... yes
checking for long double... yes
checking for wchar_t... yes
checking for wint_t... yes
checking for size_t... (cached) yes
checking for ptrdiff_t... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for snprintf... yes
checking for wcslen... yes
checking for C99 snprintf... yes
checking for fd_set... yes, found in sys/types.h
checking whether realloc (NULL,) will work... yes
checking for nl_langinfo (CODESET)... yes
checking for nl_langinfo (PM_STR)... yes
checking for nl_langinfo (_NL_CTYPE_OUTDIGITn_MB)... yes
checking for a compliant posix_memalign() implementation... yes
checking for OpenBSD strlcpy/strlcat... no
checking for an implementation of va_copy()... yes
checking for an implementation of __va_copy()... yes
checking whether va_lists can be copied by value... no
checking for dlopen... no
checking for NSLinkModule... no
checking for dlopen in -ldl... yes
checking for dlsym in -ldl... yes
checking for RTLD_GLOBAL brokenness... no
checking for preceeding underscore in symbols... no
checking for dlerror... yes
checking for the suffix of module shared libraries... .so
checking for gspawn implementation... gspawn.lo
checking for GIOChannel implementation... giounix.lo
checking for is_selinux_enabled in -lselinux... yes
checking selinux/selinux.h usability... yes
checking selinux/selinux.h presence... yes
checking for selinux/selinux.h... yes
checking for lgetfilecon_raw in -lselinux... yes
checking sys/inotify.h usability... yes
checking sys/inotify.h presence... yes
checking for sys/inotify.h... yes
checking for inotify_init1... yes
checking for getxattr in -lc... yes
checking sys/xattr.h usability... yes
checking sys/xattr.h presence... yes
checking for sys/xattr.h... yes
checking for XATTR_NOFOLLOW... no
checking for platform-dependent source...
checking whether to compile timeloop... yes
checking if building for some Win32 platform... no
checking for thread implementation... posix
checking thread related cflags... -pthread
checking thread related libraries... -pthread
checking for localtime_r... yes
checking for gmtime_r... (cached) yes
checking for posix getpwuid_r... yes
checking for posix getgrgid_r... yes
checking for pthread_attr_setstacksize... yes
checking for pthread_condattr_setclock... yes
checking for clock_gettime... no
checking for clock_gettime in -lrt... yes
checking for lock-free atomic intrinsics... yes
checking for futex(2) system call... yes
checking for eventfd(2) system call... yes
checking value of POLLIN... 1
checking value of POLLOUT... 4
checking value of POLLPRI... 2
checking value of POLLERR... 8
checking value of POLLHUP... 16
checking value of POLLNVAL... 32
checking for broken poll... no
checking for EILSEQ... yes
checking for guint32... yes
checking alignment of guint32... 4
checking for guint64... yes
checking alignment of guint64... 8
checking for unsigned long... yes
checking alignment of unsigned long... 8
checking for -Bsymbolic-functions linker flag... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating glib/Makefile
config.status: creating glib/libcharset/Makefile
config.status: creating glib/gnulib/Makefile
config.status: creating m4macros/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing glib/glibconfig.h commands
==> make
make all-recursive
make[1]: Entering directory /tmp/pkg-config20150808-18323-1oowm1u/pkg-config-0.28' Making all in glib make[2]: Entering directory/tmp/pkg-config20150808-18323-1oowm1u/pkg-config-0.28/glib'
make all-recursive
make[3]: Entering directory /tmp/pkg-config20150808-18323-1oowm1u/pkg-config-0.28/glib' Making all in . make[4]: Entering directory/tmp/pkg-config20150808-18323-1oowm1u/pkg-config-0.28/glib'
make[4]: Nothing to be done for all-am'. make[4]: Leaving directory/tmp/pkg-config20150808-18323-1oowm1u/pkg-config-0.28/glib'
Making all in m4macros
make[4]: Entering directory /tmp/pkg-config20150808-18323-1oowm1u/pkg-config-0.28/glib/m4macros' make[4]: Nothing to be done forall'.
make[4]: Leaving directory /tmp/pkg-config20150808-18323-1oowm1u/pkg-config-0.28/glib/m4macros' Making all in glib make[4]: Entering directory/tmp/pkg-config20150808-18323-1oowm1u/pkg-config-0.28/glib/glib'
GEN glibconfig-stamp
config.status: executing glib/glibconfig.h commands
config.status: glib/glibconfig.h is unchanged
make all-recursive
make[5]: Entering directory /tmp/pkg-config20150808-18323-1oowm1u/pkg-config-0.28/glib/glib' Making all in libcharset make[6]: Entering directory/tmp/pkg-config20150808-18323-1oowm1u/pkg-config-0.28/glib/glib/libcharset'
GEN ref-add.sed
CC localcharset.lo
GEN ref-del.sed
GEN charset.alias
CCLD libcharset.la
make[6]: Leaving directory /tmp/pkg-config20150808-18323-1oowm1u/pkg-config-0.28/glib/glib/libcharset' Making all in . make[6]: Entering directory/tmp/pkg-config20150808-18323-1oowm1u/pkg-config-0.28/glib/glib'
CC gcache.lo
CC gallocator.lo
CC gcompletion.lo
CC gthread-deprecated.lo
CC grel.lo
CC garray.lo
CC gasyncqueue.lo
CC gatomic.lo
CC gbacktrace.lo
CC gbase64.lo
CC gbitlock.lo
CC gbookmarkfile.lo
CC gbytes.lo
CC gcharset.lo
CC gchecksum.lo
CC gconvert.lo
CC gdataset.lo
CC gdate.lo
CC gdatetime.lo
CC gdir.lo
CC genviron.lo
CC gerror.lo
CC gfileutils.lo
CC ggettext.lo
CC ghash.lo
gconvert.c:66:2: error: #error GNU libiconv not in use but included iconv.h is from libiconv
make[6]: *** [gconvert.lo] Error 1
make[6]: *** Waiting for unfinished jobs....
make[6]: Leaving directory /tmp/pkg-config20150808-18323-1oowm1u/pkg-config-0.28/glib/glib' make[5]: *** [all-recursive] Error 1 make[5]: Leaving directory/tmp/pkg-config20150808-18323-1oowm1u/pkg-config-0.28/glib/glib'
make[4]: *** [all] Error 2
make[4]: Leaving directory /tmp/pkg-config20150808-18323-1oowm1u/pkg-config-0.28/glib/glib' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory/tmp/pkg-config20150808-18323-1oowm1u/pkg-config-0.28/glib'
make[2]: *** [all] Error 2
make[2]: Leaving directory /tmp/pkg-config20150808-18323-1oowm1u/pkg-config-0.28/glib' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory/tmp/pkg-config20150808-18323-1oowm1u/pkg-config-0.28'
make: *** [all] Error 2
==> Formula
Path: /data1/bcbio_tools/Library/Formula/pkg-config.rb
==> Configuration
HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/linuxbrew.git
HEAD: 16c51b5b4d0d987cddfbb153198fe25eef2930a6
Last commit: 5 days ago
HOMEBREW_PREFIX: /data1/bcbio_tools
HOMEBREW_CELLAR: /data1/bcbio_tools/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://linuxbrew.bintray.com
CPU: 64-core 64-bit 6
OS X: 0-x86_64
Xcode: N/A
CLT: N/A
Clang: N/A
X11: N/A
System Ruby: 1.8.7-p374 => /usr/bin/ruby
Perl: /usr/bin/perl
Python: /usr/local/share/bcbio-nextgen/anaconda/bin/python => /usr/local/share/bcbio-nextgen/anaconda/bin/python2.7
Ruby: /usr/bin/ruby
Java: 1.7.0_75
==> ENV
CC: /usr/bin/gcc
CXX: /usr/bin/g++
CFLAGS: -Os -w -pipe
CXXFLAGS: -Os -w -pipe
CPPFLAGS: -isystem/data1/bcbio_tools/include
LDFLAGS: -L/data1/bcbio_tools/lib -Wl,-rpath,/data1/bcbio_tools/lib
MAKEFLAGS: -j64
CMAKE_PREFIX_PATH: /data1/bcbio_tools
PKG_CONFIG_PATH: :/usr/lib/pkgconfig
PKG_CONFIG_LIBDIR: /data1/bcbio_tools/lib/pkgconfig
PATH: /data1/bcbio_tools/bin:/usr/local/share/bcbio-nextgen/anaconda/bin:/public/seq/software/cmake-2.8.12.2/bin:/usr/lib64/qt-3.3/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/public/seq/software/EXCAVATOR_Package_v2.2/EXCAVATOR:/public/software/glu-genetics/glu/:/root/bin:/data1/bcbio_tools/Library/ENV/scm

Error: pkg-config 0.28 did not build
Logs:
/root/.cache/Homebrew/Logs/pkg-config/01.configure
/root/.cache/Homebrew/Logs/pkg-config/02.make
/root/.cache/Homebrew/Logs/pkg-config/config.log

These open issues may also help:
document pkg-config configuration Homebrew/legacy-homebrew#21129

Could you pls help me ? thanks !

[chapmanb]

Thanks for posting the full error message. It looks like the relevant line is:

error: #error GNU libiconv not in use but included iconv.h is from libiconv

indicating there is something broken with your system glibc. Googling the error indicates the most common issue is due to multiple installations of libiconv on the system. You might have to dig around a bit to see if there are incompatible versions of libiconv installed in /usr and /usr/local. Most tools depend on glibc so this should be a general issue you need to fix to allow things to compile.

Hope this helps with identifying the issue. If not, it would be helpful to know more about your system to see if we can reproduce or otherwise help provide more specific ideas. Thanks.

[lpantano]

Hi,

I will close this since we use now bioconda, and hopefully this is better now.Thanks!