brew install mumps
==> Installing mumps from brewsci/science
==> Downloading http://mumps.enseeiht.fr/MUMPS_5.1.1.tar.gz
Already downloaded: /Users/allamtb/Library/Caches/Homebrew/mumps-5.1.1.tar.gz
==> make alllib LIBEXT=.dylib AR= -dynamiclib -Wl,-install_name -Wl,/usr/local/Cellar/mumps/5.1.1_1/lib/$(notdir $@) -undefined dynamic_lookup -o  RANLIB=echo OPTF=-O CDEFS=-DAdd_ ORDERINGSF=-Dpord CC= -f
Last 15 lines from /Users/allamtb/Library/Logs/Homebrew/mumps/01.make:
make[2]: [sort.o] Error 1 (ignored)
fPIC -I../include -O  -c minpriority.c -o minpriority.o
make[2]: fPIC: No such file or directory
make[2]: [minpriority.o] Error 1 (ignored)
dynamiclib -Wl,-install_name -Wl,/usr/local/Cellar/mumps/5.1.1_1/lib/libpord.dylib -undefined dynamic_lookup -o libpord.dylib graph.o gbipart.o gbisect.o ddcreate.o ddbisect.o nestdiss.o multisector.o gelim.o bucket.o tree.o symbfac.o interface.o sort.o minpriority.o
make[2]: dynamiclib: No such file or directory
make[2]: [libpord.dylib] Error 1 (ignored)
echo libpord.dylib
libpord.dylib
if [ "./PORD/lib/" != "" ] ; then \
	  cp ./PORD/lib//libpord.dylib lib/libpord.dylib; \
	fi;
cp: ./PORD/lib//libpord.dylib: No such file or directory
make[1]: *** [lib/libpord.dylib] Error 1
make: *** [c] Error 2

here is the log gist : https://gist.github.com/allamtb/fa0863ef3fffed1e523d29d4197f768b

Last 15 lines from /Users/ferdinakusumah/Library/Logs/Homebrew/openalpr/02.make:
[ 29%] Building CXX object openalpr/support/CMakeFiles/support.dir/re2/util/stringprintf.cc.o
cd /tmp/openalpr-20190305-84389-1m61jzt/openalpr-2.3.0/src/build/openalpr/support && /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++ -DINSTALL_PREFIX="/usr/local/Cellar/openalpr/2.3.0_1" -DOPENALPR_MAJOR_VERSION=2 -DOPENALPR_MINOR_VERSION=3 -DOPENALPR_PATCH_VERSION=0 -DOPENCV_MAJOR_VERSION=2 -DSKIP_STATE_DETECTION=1 -I/usr/local/include -I/usr/local/include/tesseract -I/usr/local/Cellar/opencv@2/2.4.13.7_2/include/opencv -I/usr/local/Cellar/opencv@2/2.4.13.7_2/include -I/tmp/openalpr-20190305-84389-1m61jzt/openalpr-2.3.0/src/./openalpr -I/tmp/openalpr-20190305-84389-1m61jzt/openalpr-2.3.0/src/openalpr/support/. -I/Library/Java/JavaVirtualMachines/jdk-10.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk-10.0.2.jdk/Contents/Home/include/darwin -fPIC -o CMakeFiles/support.dir/re2/util/stringprintf.cc.o -c /tmp/openalpr-20190305-84389-1m61jzt/openalpr-2.3.0/src/openalpr/support/re2/util/stringprintf.cc
[ 30%] Building CXX object openalpr/support/CMakeFiles/support.dir/re2/util/rune.cc.o
cd /tmp/openalpr-20190305-84389-1m61jzt/openalpr-2.3.0/src/build/openalpr/support && /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++ -DINSTALL_PREFIX="/usr/local/Cellar/openalpr/2.3.0_1" -DOPENALPR_MAJOR_VERSION=2 -DOPENALPR_MINOR_VERSION=3 -DOPENALPR_PATCH_VERSION=0 -DOPENCV_MAJOR_VERSION=2 -DSKIP_STATE_DETECTION=1 -I/usr/local/include -I/usr/local/include/tesseract -I/usr/local/Cellar/opencv@2/2.4.13.7_2/include/opencv -I/usr/local/Cellar/opencv@2/2.4.13.7_2/include -I/tmp/openalpr-20190305-84389-1m61jzt/openalpr-2.3.0/src/./openalpr -I/tmp/openalpr-20190305-84389-1m61jzt/openalpr-2.3.0/src/openalpr/support/. -I/Library/Java/JavaVirtualMachines/jdk-10.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk-10.0.2.jdk/Contents/Home/include/darwin -fPIC -o CMakeFiles/support.dir/re2/util/rune.cc.o -c /tmp/openalpr-20190305-84389-1m61jzt/openalpr-2.3.0/src/openalpr/support/re2/util/rune.cc
[ 31%] Building CXX object openalpr/support/CMakeFiles/support.dir/re2/util/strutil.cc.o
cd /tmp/openalpr-20190305-84389-1m61jzt/openalpr-2.3.0/src/build/openalpr/support && /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++ -DINSTALL_PREFIX="/usr/local/Cellar/openalpr/2.3.0_1" -DOPENALPR_MAJOR_VERSION=2 -DOPENALPR_MINOR_VERSION=3 -DOPENALPR_PATCH_VERSION=0 -DOPENCV_MAJOR_VERSION=2 -DSKIP_STATE_DETECTION=1 -I/usr/local/include -I/usr/local/include/tesseract -I/usr/local/Cellar/opencv@2/2.4.13.7_2/include/opencv -I/usr/local/Cellar/opencv@2/2.4.13.7_2/include -I/tmp/openalpr-20190305-84389-1m61jzt/openalpr-2.3.0/src/./openalpr -I/tmp/openalpr-20190305-84389-1m61jzt/openalpr-2.3.0/src/openalpr/support/. -I/Library/Java/JavaVirtualMachines/jdk-10.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk-10.0.2.jdk/Contents/Home/include/darwin -fPIC -o CMakeFiles/support.dir/re2/util/strutil.cc.o -c /tmp/openalpr-20190305-84389-1m61jzt/openalpr-2.3.0/src/openalpr/support/re2/util/strutil.cc
[ 31%] Building CXX object openalpr/support/CMakeFiles/support.dir/re2/util/valgrind.cc.o
cd /tmp/openalpr-20190305-84389-1m61jzt/openalpr-2.3.0/src/build/openalpr/support && /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++ -DINSTALL_PREFIX="/usr/local/Cellar/openalpr/2.3.0_1" -DOPENALPR_MAJOR_VERSION=2 -DOPENALPR_MINOR_VERSION=3 -DOPENALPR_PATCH_VERSION=0 -DOPENCV_MAJOR_VERSION=2 -DSKIP_STATE_DETECTION=1 -I/usr/local/include -I/usr/local/include/tesseract -I/usr/local/Cellar/opencv@2/2.4.13.7_2/include/opencv -I/usr/local/Cellar/opencv@2/2.4.13.7_2/include -I/tmp/openalpr-20190305-84389-1m61jzt/openalpr-2.3.0/src/./openalpr -I/tmp/openalpr-20190305-84389-1m61jzt/openalpr-2.3.0/src/openalpr/support/. -I/Library/Java/JavaVirtualMachines/jdk-10.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk-10.0.2.jdk/Contents/Home/include/darwin -fPIC -o CMakeFiles/support.dir/re2/util/valgrind.cc.o -c /tmp/openalpr-20190305-84389-1m61jzt/openalpr-2.3.0/src/openalpr/support/re2/util/valgrind.cc
[ 32%] Linking CXX static library libsupport.a
cd /tmp/openalpr-20190305-84389-1m61jzt/openalpr-2.3.0/src/build/openalpr/support && /usr/local/Cellar/cmake/3.13.4/bin/cmake -P CMakeFiles/support.dir/cmake_clean_target.cmake
cd /tmp/openalpr-20190305-84389-1m61jzt/openalpr-2.3.0/src/build/openalpr/support && /usr/local/Cellar/cmake/3.13.4/bin/cmake -E cmake_link_script CMakeFiles/support.dir/link.txt --verbose=1
/usr/bin/ar qc libsupport.a CMakeFiles/support.dir/filesystem.cpp.o CMakeFiles/support.dir/timing.cpp.o CMakeFiles/support.dir/tinythread.cpp.o CMakeFiles/support.dir/platform.cpp.o CMakeFiles/support.dir/utf8.cpp.o CMakeFiles/support.dir/version.cpp.o CMakeFiles/support.dir/re2/bitstate.cc.o CMakeFiles/support.dir/re2/compile.cc.o CMakeFiles/support.dir/re2/dfa.cc.o CMakeFiles/support.dir/re2/filtered_re2.cc.o CMakeFiles/support.dir/re2/mimics_pcre.cc.o CMakeFiles/support.dir/re2/nfa.cc.o CMakeFiles/support.dir/re2/onepass.cc.o CMakeFiles/support.dir/re2/parse.cc.o CMakeFiles/support.dir/re2/perl_groups.cc.o CMakeFiles/support.dir/re2/prefilter.cc.o CMakeFiles/support.dir/re2/prefilter_tree.cc.o CMakeFiles/support.dir/re2/prog.cc.o CMakeFiles/support.dir/re2/re2.cc.o CMakeFiles/support.dir/re2/regexp.cc.o CMakeFiles/support.dir/re2/set.cc.o CMakeFiles/support.dir/re2/simplify.cc.o CMakeFiles/support.dir/re2/stringpiece.cc.o CMakeFiles/support.dir/re2/tostring.cc.o CMakeFiles/support.dir/re2/unicode_casefold.cc.o CMakeFiles/support.dir/re2/unicode_groups.cc.o CMakeFiles/support.dir/re2/util/hash.cc.o CMakeFiles/support.dir/re2/util/stringprintf.cc.o CMakeFiles/support.dir/re2/util/rune.cc.o CMakeFiles/support.dir/re2/util/strutil.cc.o CMakeFiles/support.dir/re2/util/valgrind.cc.o
/usr/bin/ranlib libsupport.a
[ 32%] Built target support
make: *** [all] Error 2

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/brewsci/homebrew-science/issues

OSX (Mojave)
8 Gb ram

Last 15 lines from /Users/rochakchandra/Library/Logs/Homebrew/openalpr/02.make:
make[1]: *** [CMakeFiles/alprd.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 80%] Linking CXX executable openalpr-utils-calibrate
cd /tmp/openalpr-20180517-25258-10f3ke6/openalpr-2.3.0/src/build/misc_utilities && /usr/local/Cellar/cmake/3.11.1/bin/cmake -E cmake_link_script CMakeFiles/openalpr-utils-calibrate.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/super/clang++ -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/openalpr-utils-calibrate.dir/calibrate.cpp.o -o openalpr-utils-calibrate -Wl,-rpath,/tmp/openalpr-20180517-25258-10f3ke6/openalpr-2.3.0/src/build/openalpr ../openalpr/libopenalpr.2.dylib ../openalpr/support/libsupport.a /usr/local/opt/opencv@2/lib/libopencv_videostab.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_ts.a /usr/local/opt/opencv@2/lib/libopencv_superres.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_stitching.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_contrib.2.4.13.dylib /usr/local/lib/libtesseract.dylib /usr/local/lib/liblept.dylib /usr/local/lib/libtesseract.dylib /usr/local/lib/liblept.dylib /usr/local/opt/opencv@2/lib/libopencv_nonfree.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_ocl.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_gpu.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_photo.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_objdetect.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_legacy.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_video.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_ml.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_calib3d.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_features2d.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_highgui.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_imgproc.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_flann.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_core.2.4.13.dylib
[ 80%] Built target openalpr-utils-calibrate
[ 81%] Linking CXX executable openalpr-utils-binarizefontsheet
cd /tmp/openalpr-20180517-25258-10f3ke6/openalpr-2.3.0/src/build/misc_utilities && /usr/local/Cellar/cmake/3.11.1/bin/cmake -E cmake_link_script CMakeFiles/openalpr-utils-binarizefontsheet.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/super/clang++ -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/openalpr-utils-binarizefontsheet.dir/binarizefontsheet.cpp.o -o openalpr-utils-binarizefontsheet -Wl,-rpath,/tmp/openalpr-20180517-25258-10f3ke6/openalpr-2.3.0/src/build/openalpr ../openalpr/libopenalpr.2.dylib ../openalpr/support/libsupport.a /usr/local/opt/opencv@2/lib/libopencv_videostab.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_ts.a /usr/local/opt/opencv@2/lib/libopencv_superres.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_stitching.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_contrib.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_nonfree.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_ocl.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_gpu.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_photo.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_objdetect.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_legacy.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_video.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_ml.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_calib3d.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_features2d.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_highgui.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_imgproc.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_flann.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_core.2.4.13.dylib /usr/local/lib/libtesseract.dylib /usr/local/lib/liblept.dylib /usr/local/lib/libtesseract.dylib /usr/local/lib/liblept.dylib
[ 82%] Linking CXX executable alpr
/usr/local/Cellar/cmake/3.11.1/bin/cmake -E cmake_link_script CMakeFiles/alpr.dir/link.txt --verbose=1
[ 82%] Built target openalpr-utils-binarizefontsheet
/usr/local/Homebrew/Library/Homebrew/shims/super/clang++ -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/alpr.dir/main.cpp.o -o alpr -Wl,-rpath,/tmp/openalpr-20180517-25258-10f3ke6/openalpr-2.3.0/src/build/openalpr openalpr/libopenalpr.2.dylib openalpr/support/libsupport.a video/libvideo.a /usr/local/opt/opencv@2/lib/libopencv_videostab.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_ts.a /usr/local/opt/opencv@2/lib/libopencv_superres.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_stitching.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_contrib.2.4.13.dylib /usr/local/lib/libtesseract.dylib /usr/local/lib/liblept.dylib /usr/local/lib/libtesseract.dylib /usr/local/lib/liblept.dylib -lpthread /usr/local/opt/opencv@2/lib/libopencv_nonfree.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_ocl.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_gpu.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_photo.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_objdetect.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_legacy.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_video.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_ml.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_calib3d.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_features2d.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_highgui.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_imgproc.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_flann.2.4.13.dylib /usr/local/opt/opencv@2/lib/libopencv_core.2.4.13.dylib openalpr/support/libsupport.a
[ 82%] Built target alpr
make: *** [all] Error 2

I got the following error when trying to install mumps:

brew install mumps
==> Installing mumps from brewsci/science
==> Downloading http://mumps.enseeiht.fr/MUMPS_5.1.1.tar.gz
Already downloaded: /Users/paufigueras/Library/Caches/Homebrew/mumps-5.1.1.tar.gz
==> make alllib LIBEXT=.dylib AR= -dynamiclib -Wl,-install_name -Wl,/usr/local/Cellar/mumps/5.1.1_1/lib/$(notdir $@) -u
Last 15 lines from /Users/paufigueras/Library/Logs/Homebrew/mumps/01.make:
make[2]: [sort.o] Error 1 (ignored)
fPIC -I../include -O  -c minpriority.c -o minpriority.o
make[2]: fPIC: No such file or directory
make[2]: [minpriority.o] Error 1 (ignored)
dynamiclib -Wl,-install_name -Wl,/usr/local/Cellar/mumps/5.1.1_1/lib/libpord.dylib -undefined dynamic_lookup -o libpord.dylib graph.o gbipart.o gbisect.o ddcreate.o ddbisect.o nestdiss.o multisector.o gelim.o bucket.o tree.o symbfac.o interface.o sort.o minpriority.o 
make[2]: dynamiclib: No such file or directory
make[2]: [libpord.dylib] Error 1 (ignored)
echo libpord.dylib
libpord.dylib
if [ "./PORD/lib/" != "" ] ; then \
	  cp ./PORD/lib//libpord.dylib lib/libpord.dylib; \
	fi;
cp: ./PORD/lib//libpord.dylib: No such file or directory
make[1]: *** [lib/libpord.dylib] Error 1
make: *** [c] Error 2

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/brewsci/homebrew-science/issues

This issue originated in bcgsc/orca#44 but this is not specific to orca or Singularity.

I installed all the perl dependencies with cpanm and can confirm they are to be found in: ~/.linuxbrew/Cellar/perl/5.26.1/lib/perl5/5.26.1/
export PERL_LOCAL_LIB_ROOT="~/.linuxbrew/Cellar/perl/5.26.1/lib/perl5/5.26.1"

brew update
Already up-to-date.

They are available, e.g.
perl -e 'use PerlIO::gzip'
(no error)

brew install brewsci/homebrew-science/maker

Warning: Calling 'depends_on :mpi' is deprecated!
Use 'depends_on "open-mpi"' instead.
/home/ckeeling/.linuxbrew/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/maker.rb:14:in `<class:Maker>'
Please report this to the brewsci/science tap!

Warning: Calling 'depends_on ... => :perl' is deprecated!
There is no replacement.
/home/ckeeling/.linuxbrew/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/maker.rb:23:in `<class:Maker>'
Please report this to the brewsci/science tap!

Warning: Calling 'depends_on ... => :perl' is deprecated!
There is no replacement.
/home/ckeeling/.linuxbrew/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/maker.rb:24:in `<class:Maker>'
Please report this to the brewsci/science tap!

Warning: Calling 'depends_on ... => :perl' is deprecated!
There is no replacement.
/home/ckeeling/.linuxbrew/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/maker.rb:25:in `<class:Maker>'
Please report this to the brewsci/science tap!

Warning: Calling 'depends_on ... => :perl' is deprecated!
There is no replacement.
/home/ckeeling/.linuxbrew/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/maker.rb:26:in `<class:Maker>'
Please report this to the brewsci/science tap!

Warning: Calling 'depends_on ... => :perl' is deprecated!
There is no replacement.
/home/ckeeling/.linuxbrew/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/maker.rb:27:in `<class:Maker>'
Please report this to the brewsci/science tap!

Warning: Calling 'depends_on ... => :perl' is deprecated!
There is no replacement.
/home/ckeeling/.linuxbrew/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/maker.rb:28:in `<class:Maker>'
Please report this to the brewsci/science tap!

Warning: Calling 'depends_on ... => :perl' is deprecated!
There is no replacement.
/home/ckeeling/.linuxbrew/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/maker.rb:29:in `<class:Maker>'
Please report this to the brewsci/science tap!

Warning: Calling 'depends_on ... => :perl' is deprecated!
There is no replacement.
/home/ckeeling/.linuxbrew/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/maker.rb:30:in `<class:Maker>'
Please report this to the brewsci/science tap!

Warning: Calling 'depends_on ... => :perl' is deprecated!
There is no replacement.
/home/ckeeling/.linuxbrew/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/maker.rb:32:in `<class:Maker>'
Please report this to the brewsci/science tap!

Warning: Calling 'depends_on ... => :perl' is deprecated!
There is no replacement.
/home/ckeeling/.linuxbrew/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/maker.rb:33:in `<class:Maker>'
Please report this to the brewsci/science tap!

Warning: Calling 'depends_on ... => :perl' is deprecated!
There is no replacement.
/home/ckeeling/.linuxbrew/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/maker.rb:34:in `<class:Maker>'
Please report this to the brewsci/science tap!

Warning: Calling 'depends_on ... => :perl' is deprecated!
There is no replacement.
/home/ckeeling/.linuxbrew/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/maker.rb:35:in `<class:Maker>'
Please report this to the brewsci/science tap!

==> Installing maker from brewsci/science
maker: Unsatisfied dependency: Bio::Perl
Homebrew does not provide special Perl dependencies; install with:
  `cpan -i Bio::Perl`
maker: Unsatisfied dependency: Bit::Vector
Homebrew does not provide special Perl dependencies; install with:
  `cpan -i Bit::Vector`
maker: Unsatisfied dependency: DBD::SQLite
Homebrew does not provide special Perl dependencies; install with:
  `cpan -i DBD::SQLite`
maker: Unsatisfied dependency: DBI
Homebrew does not provide special Perl dependencies; install with:
  `cpan -i DBI`
maker: Unsatisfied dependency: File::Which
Homebrew does not provide special Perl dependencies; install with:
  `cpan -i File::Which`
maker: Unsatisfied dependency: IO::All
Homebrew does not provide special Perl dependencies; install with:
  `cpan -i IO::All`
maker: Unsatisfied dependency: IO::Prompt
Homebrew does not provide special Perl dependencies; install with:
  `cpan -i IO::Prompt`
maker: Unsatisfied dependency: Inline::C
Homebrew does not provide special Perl dependencies; install with:
  `cpan -i Inline::C`
maker: Unsatisfied dependency: Perl::Unsafe::Signals
Homebrew does not provide special Perl dependencies; install with:
  `cpan -i Perl::Unsafe::Signals`
maker: Unsatisfied dependency: PerlIO::gzip
Homebrew does not provide special Perl dependencies; install with:
  `cpan -i PerlIO::gzip`
maker: Unsatisfied dependency: forks
Homebrew does not provide special Perl dependencies; install with:
  `cpan -i forks`
maker: Unsatisfied dependency: forks::shared
Homebrew does not provide special Perl dependencies; install with:
  `cpan -i forks::shared`
Error: Unsatisfied requirements failed this build.

I am trying to install gnudatalanguage in my 2017 macOS Mojave version 10.14
I already had Xcode, Xquartz, Anaconda and Astroconda installed

These were my installation steps i followed:

Assure home-brew is current
$ brew update

Assure that “node" is functioning properly
$ brew uninstall --force node
$ brew install node

$ brew tap brewsci/science
$ brew install -v gnudatalanguage

The error occurs on the last step so here is all the output and i also attached the logs that it mentions at the end of this output. Thank you for your help.

==> Installing gnudatalanguage from brewsci/science
/usr/bin/sandbox-exec -f /private/tmp/homebrew20190217-15680-2r21r5.sb nice /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby -W0 -I /usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/ruby-macho-2.1.0/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/rubocop-rspec-1.32.0/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/rubocop-0.63.1/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/unicode-display_width-1.4.1/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/ruby-progressbar-1.10.0/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/rainbow-3.0.0/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/powerpack-0.1.2/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/plist-3.5.0/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/parser-2.6.0.0/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/parallel-1.13.0/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/mechanize-2.7.6/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/webrobots-0.1.2/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/ntlm-http-0.1.1/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/nokogiri-1.10.1/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/extensions/universal-darwin-18/2.3.0/nokogiri-1.10.1:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/mini_portile2-2.4.0/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/net-http-persistent-3.0.0/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/net-http-digest_auth-1.4.1/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/mime-types-3.2.2/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/mime-types-data-3.2018.0812/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/jaro_winkler-1.5.2/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/extensions/universal-darwin-18/2.3.0/jaro_winkler-1.5.2:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/http-cookie-1.0.3/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/domain_name-0.5.20180417/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/unf-0.1.4/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/unf_ext-0.0.7.5/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/extensions/universal-darwin-18/2.3.0/unf_ext-0.0.7.5:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/connection_pool-2.2.2/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/backports-3.11.4/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/ast-2.4.0/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/activesupport-5.2.2/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/tzinfo-1.2.5/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/thread_safe-0.3.6/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/minitest-5.11.3/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/i18n-1.5.3/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/concurrent-ruby-1.1.4/lib:/Library/Ruby/Gems/2.3.0/gems/did_you_mean-1.0.0/lib:/Library/Ruby/Site/2.3.0:/Library/Ruby/Site/2.3.0/x86_64-darwin18:/Library/Ruby/Site/2.3.0/universal-darwin18:/Library/Ruby/Site:/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/vendor_ruby/2.3.0:/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/vendor_ruby/2.3.0/x86_64-darwin18:/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/vendor_ruby/2.3.0/universal-darwin18:/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/vendor_ruby:/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0:/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/x86_64-darwin18:/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/universal-darwin18:/usr/local/Homebrew/Library/Homebrew -- /usr/local/Homebrew/Library/Homebrew/build.rb /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/gnudatalanguage.rb --verbose
==> Downloading https://downloads.sourceforge.net/project/gnudatalanguage/gdl/0.9.7/gdl-0.9.7.tgz
Already downloaded: /Users/jtorresh/Library/Caches/Homebrew/downloads/c2d2624306a740e8cf1a81fedef81bc51f1a68f82ec1512a9366e4afcdafc36b--gdl-0.9.7.tgz
==> Verifying c2d2624306a740e8cf1a81fedef81bc51f1a68f82ec1512a9366e4afcdafc36b--gdl-0.9.7.tgz checksum
tar xf /Users/jtorresh/Library/Caches/Homebrew/downloads/c2d2624306a740e8cf1a81fedef81bc51f1a68f82ec1512a9366e4afcdafc36b--gdl-0.9.7.tgz -C /private/tmp/d20190217-15681-yyz58u
cp -pR /private/tmp/d20190217-15681-yyz58u/gdl-0.9.7/. /private/tmp/gnudatalanguage-20190217-15681-15ozq04/gdl-0.9.7
chmod -Rf +w /private/tmp/d20190217-15681-yyz58u
==> Downloading https://gist.githubusercontent.com/sjackman/00fb95e10b7775d16924efb6faf462f6/raw/71ed3e05138a20b824c9e68707e403afc0f92c98/gnudatalanguage-hdf5-1.10.patch
Already downloaded: /Users/jtorresh/Library/Caches/Homebrew/downloads/d9d78e4e87c5a1699eeebbc3b759e9751099c77ec278d19cdc98c3621175ef1d--gnudatalanguage-hdf5-1.10.patch
==> Verifying d9d78e4e87c5a1699eeebbc3b759e9751099c77ec278d19cdc98c3621175ef1d--gnudatalanguage-hdf5-1.10.patch checksum
==> Patching
cp -p /Users/jtorresh/Library/Caches/Homebrew/downloads/d9d78e4e87c5a1699eeebbc3b759e9751099c77ec278d19cdc98c3621175ef1d--gnudatalanguage-hdf5-1.10.patch /private/tmp/gnudatalanguage--patch-20190217-15681-x3fxnt/gnudatalanguage-hdf5-1.10.patch
==> Applying gnudatalanguage-hdf5-1.10.patch
patch -g 0 -f -p1 -i /private/tmp/gnudatalanguage--patch-20190217-15681-x3fxnt/gnudatalanguage-hdf5-1.10.patch
patching file src/hdf5_fun.cpp
==> Downloading https://downloads.sourceforge.net/project/plplot/plplot/5.12.0%20Source/plplot-5.12.0.tar.gz
Already downloaded: /Users/jtorresh/Library/Caches/Homebrew/downloads/981caf8d1af1aaeb3f23dc9f77ee3c4e442d93e1787cc6a56a932b19f8e4f80a--plplot-5.12.0.tar.gz
==> Verifying 981caf8d1af1aaeb3f23dc9f77ee3c4e442d93e1787cc6a56a932b19f8e4f80a--plplot-5.12.0.tar.gz checksum
tar xf /Users/jtorresh/Library/Caches/Homebrew/downloads/981caf8d1af1aaeb3f23dc9f77ee3c4e442d93e1787cc6a56a932b19f8e4f80a--plplot-5.12.0.tar.gz -C /private/tmp/d20190217-15681-17h86qw
cp -pR /private/tmp/d20190217-15681-17h86qw/plplot-5.12.0/. /private/tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0
chmod -Rf +w /private/tmp/d20190217-15681-17h86qw
==> cmake .. -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/gnudatalanguage/0.9.7_4 -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_VERBOSE_MAKEFILE=ON -Wno-dev -DPLD_xwin=ON -DENABLE_ada=OFF -DENABLE_d=OFF -DENABLE_qt=OFF -DENABLE_lua=OFF -DENABLE_tk=OFF -DENABLE_python=OFF -DENABLE_tcl=OFF -DPLD_xcairo=OFF -DPLD_wxwidgets=OFF -DENABLE_wxwidgets=OFF -DENABLE_java=OFF -DENABLE_f95=OFF
-- The C compiler identification is AppleClang 10.0.0.10001145
-- Check for working C compiler: /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang
-- Check for working C compiler: /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- CMake version = 3.13.4
-- CMAKE_SYSTEM_NAME = Darwin
-- SH_EXECUTABLE = /bin/bash
-- Checking whether system has ANSI C header files
-- Looking for 4 include files stdlib.h, ..., float.h
-- Looking for 4 include files stdlib.h, ..., float.h - found
-- Performing Test memchrExists
-- Performing Test memchrExists - Success
-- Performing Test freeExists
-- Performing Test freeExists - Success
-- Check for whether ctype.h macros work on characters with the
high bit set.
-- High-bit characters - work
-- ANSI C header files - found
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file termios.h
-- Looking for include file termios.h - found
-- Looking for include file stdint.h
-- Looking for include file stdint.h - found
-- Looking for crt_externs.h
-- Looking for crt_externs.h - found
-- Performing Test HAVE_SYS_WAIT_H
-- Performing Test HAVE_SYS_WAIT_H - Success
-- Looking for DIR symbol in sys/types.h;dirent.h
-- Looking for DIR symbol in sys/types.h;dirent.h - found
-- Check for signal return type in <signal.h>
-- Check for signal handler return type type void - found
-- Looking for popen
-- Looking for popen - found
-- Looking for usleep
-- Looking for usleep - found
-- Looking for nanosleep
-- Looking for nanosleep - found
-- Looking for mkstemp
-- Looking for mkstemp - found
-- Looking for mkdtemp
-- Looking for mkdtemp - found
-- Looking for mkfifo
-- Looking for mkfifo - found
-- Looking for unlink
-- Looking for unlink - found
-- Looking for _NSGetArgc
-- Looking for _NSGetArgc - found
-- Looking for isfinite
-- Looking for isfinite - found
-- Looking for finite
-- Looking for finite - found
-- Looking for isnan
-- Looking for isnan - found
-- Looking for isinf
-- Looking for isinf - found
-- Looking for snprintf
-- Looking for snprintf - found
-- SWIG_VERSION = 3.0.12
-- Found Perl: /usr/bin/perl (found version "5.18.2")
-- WARNING: Perl module XML::DOM not found
-- The CXX compiler identification is AppleClang 10.0.0.10001145
-- Check for working CXX compiler: /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++
-- Check for working CXX compiler: /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for using namespace support
-- Check for using namespace - found
-- Looking for C++ include cmath
-- Looking for C++ include cmath - found
-- Check for broken isnan support in
-- Check for isnan in - found
-- Check for using stdint.h with CXX compiler
-- Check for using stdint.h with CXX compiler - ok
-- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2")
-- Looking for pkg-config - found
-- cxx_compiler_library_pathname_list = /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/lib/libc++.tbd
-- Looking for XOpenDisplay in /opt/X11/lib/libX11.dylib;/opt/X11/lib/libXext.dylib
-- Looking for XOpenDisplay in /opt/X11/lib/libX11.dylib;/opt/X11/lib/libXext.dylib - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for IceConnectionNumber in ICE
-- Looking for IceConnectionNumber in ICE - found
-- Found X11: /opt/X11/lib/libX11.dylib
-- X11_FOUND = 1
-- X11_INCLUDE_DIR = /opt/X11/include
-- X11_COMPILE_FLAGS = -I/opt/X11/include
-- X11_LIBRARIES = /opt/X11/lib/libSM.dylib;/opt/X11/lib/libICE.dylib;/opt/X11/lib/libX11.dylib;/opt/X11/lib/libXext.dylib
-- WARNING: The octave command not found. Disabling Octave binding
-- WARNING: ENABLE_tcl is OFF so disabling everything else that is Tcl/Tk related
-- FindShapelib: Found shapelib header directory, /opt/local/include, and library, /opt/local/lib/libshp.dylib.
-- WARNING: the (rather ancient) version of shapelib that has been found does not
include the SAHooks type. Therefore, the misleading "Unable to open ..."
error messages that shapelib generates as PLplot checks several directories
for specified shapefiles will not be quieted.
-- Found Freetype: /usr/local/lib/libfreetype.dylib (found version "2.9.1")
-- FREETYPE_CFLAGS = -I/usr/local/include/freetype2
-- FREETYPE_LIBRARIES = /usr/local/lib/libfreetype.dylib
Fonts not found - disabling freetype
-- Check for NaN awareness in C compiler
-- Check for NaN awareness in C compiler - found
-- Found QHULL: /opt/local/include
-- QHULL_INCLUDE_DIRS = /opt/local/include
-- HAS_LIBQHULL_INCLUDE = OFF
-- QHULL_LIBRARIES = /opt/local/lib/libqhull.dylib
-- QHULL_RPATH = /opt/local/lib
-- Looking for qh_new_qhull
-- Looking for qh_new_qhull - found
-- Checking for modules ''
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
-- WARNING: pkg-config does not find pango.
-- Checking for modules ''
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
-- WARNING: pkg-config does not find pangoft2.
-- Found LTDL: /usr/local/lib/libltdl.dylib
-- LTDL_INCLUDE_DIR = /usr/local/include
-- LTDL_LIBRARY_DIR = /usr/local/lib
-- LTDL_LIBRARIES = /usr/local/lib/libltdl.dylib
-- Checking for modules ''
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
Must specify package names on the command line
includedir =
linkdir =
linkflags =
cflags =
-- WARNING: pango and/or cairo not found with pkg-config.
Disabling cairo drivers. To enable these drivers you must install
development versions of pango and cairo and/or set
the environment variable PKG_CONFIG_PATH appropriately.
-- WARNING: ENABLE_tk OFF. Therefore turning off tk, tkwin, and ntk devices
-- Checking for modules ''
Package LIBRARIES was not found in the pkg-config search path.
Perhaps you should add the directory containing LIBRARIES.pc' to the PKG_CONFIG_PATH environment variable No package 'LIBRARIES' found Package (^| was not found in the pkg-config search path. Perhaps you should add the directory containing (^|.pc'
to the PKG_CONFIG_PATH environment variable
No package '(^|' found
Package )-l was not found in the pkg-config search path.
Perhaps you should add the directory containing )-l.pc' to the PKG_CONFIG_PATH environment variable No package ')-l' found Package STATIC_LIBRARIES was not found in the pkg-config search path. Perhaps you should add the directory containing STATIC_LIBRARIES.pc'
to the PKG_CONFIG_PATH environment variable
No package 'STATIC_LIBRARIES' found
Package (^| was not found in the pkg-config search path.
Perhaps you should add the directory containing (^|.pc' to the PKG_CONFIG_PATH environment variable No package '(^|' found Package )-l was not found in the pkg-config search path. Perhaps you should add the directory containing )-l.pc'
to the PKG_CONFIG_PATH environment variable
No package ')-l' found
Package LIBRARY_DIRS was not found in the pkg-config search path.
Perhaps you should add the directory containing LIBRARY_DIRS.pc' to the PKG_CONFIG_PATH environment variable No package 'LIBRARY_DIRS' found Package (^| was not found in the pkg-config search path. Perhaps you should add the directory containing (^|.pc'
to the PKG_CONFIG_PATH environment variable
No package '(^|' found
Package )-L was not found in the pkg-config search path.
Perhaps you should add the directory containing )-L.pc' to the PKG_CONFIG_PATH environment variable No package ')-L' found Package STATIC_LIBRARY_DIRS was not found in the pkg-config search path. Perhaps you should add the directory containing STATIC_LIBRARY_DIRS.pc'
to the PKG_CONFIG_PATH environment variable
No package 'STATIC_LIBRARY_DIRS' found
Package (^| was not found in the pkg-config search path.
Perhaps you should add the directory containing (^|.pc' to the PKG_CONFIG_PATH environment variable No package '(^|' found Package )-L was not found in the pkg-config search path. Perhaps you should add the directory containing )-L.pc'
to the PKG_CONFIG_PATH environment variable
No package ')-L' found
Package LDFLAGS was not found in the pkg-config search path.
Perhaps you should add the directory containing LDFLAGS.pc' to the PKG_CONFIG_PATH environment variable No package 'LDFLAGS' found Package STATIC_LDFLAGS was not found in the pkg-config search path. Perhaps you should add the directory containing STATIC_LDFLAGS.pc'
to the PKG_CONFIG_PATH environment variable
No package 'STATIC_LDFLAGS' found
Package LDFLAGS_OTHER was not found in the pkg-config search path.
Perhaps you should add the directory containing LDFLAGS_OTHER.pc' to the PKG_CONFIG_PATH environment variable No package 'LDFLAGS_OTHER' found Package STATIC_LDFLAGS_OTHER was not found in the pkg-config search path. Perhaps you should add the directory containing STATIC_LDFLAGS_OTHER.pc'
to the PKG_CONFIG_PATH environment variable
No package 'STATIC_LDFLAGS_OTHER' found
Package INCLUDE_DIRS was not found in the pkg-config search path.
Perhaps you should add the directory containing INCLUDE_DIRS.pc' to the PKG_CONFIG_PATH environment variable No package 'INCLUDE_DIRS' found Package (^| was not found in the pkg-config search path. Perhaps you should add the directory containing (^|.pc'
to the PKG_CONFIG_PATH environment variable
No package '(^|' found
Package )-I was not found in the pkg-config search path.
Perhaps you should add the directory containing )-I.pc' to the PKG_CONFIG_PATH environment variable No package ')-I' found Package STATIC_INCLUDE_DIRS was not found in the pkg-config search path. Perhaps you should add the directory containing STATIC_INCLUDE_DIRS.pc'
to the PKG_CONFIG_PATH environment variable
No package 'STATIC_INCLUDE_DIRS' found
Package (^| was not found in the pkg-config search path.
Perhaps you should add the directory containing (^|.pc' to the PKG_CONFIG_PATH environment variable No package '(^|' found Package )-I was not found in the pkg-config search path. Perhaps you should add the directory containing )-I.pc'
to the PKG_CONFIG_PATH environment variable
No package ')-I' found
Package CFLAGS was not found in the pkg-config search path.
Perhaps you should add the directory containing CFLAGS.pc' to the PKG_CONFIG_PATH environment variable No package 'CFLAGS' found Package STATIC_CFLAGS was not found in the pkg-config search path. Perhaps you should add the directory containing STATIC_CFLAGS.pc'
to the PKG_CONFIG_PATH environment variable
No package 'STATIC_CFLAGS' found
Package CFLAGS_OTHER was not found in the pkg-config search path.
Perhaps you should add the directory containing CFLAGS_OTHER.pc' to the PKG_CONFIG_PATH environment variable No package 'CFLAGS_OTHER' found Package STATIC_CFLAGS_OTHER was not found in the pkg-config search path. Perhaps you should add the directory containing STATIC_CFLAGS_OTHER.pc'
to the PKG_CONFIG_PATH environment variable
No package 'STATIC_CFLAGS_OTHER' found
includedir =
libdir =
linkflags =
cflags =
-- WARNING: pango, pangoft2, or lasi not found with pkg-config.
Setting PLD_psttf to OFF. Please install all of these packages
and/or set the environment variable PKG_CONFIG_PATH appropriately.
-- WARNING: ENABLE_qt is OFF so setting all qt devices to OFF.
-- WARNING: PLPLOT_USE_QT5 is OFF so setting ENABLE_pyqt5 to OFF.
-- WARNING: ENABLE_python is OFF so setting ENABLE_pyqt4 to OFF.
-- WARNING: ENABLE_wxwidgets is OFF so setting all wxwidgets devices to OFF.
-- Looking for haru pdf header and library
-- Findhpdf: Found haru header directory, /opt/local/include, and library, /opt/local/lib/libhpdf.dylib.
-- Looking for haru pdf header and library - found
-- Checking whether libharu version >= 2.3.0
-- Performing Test LIBHARU_VERSION_LARGE_ENOUGH
-- Performing Test LIBHARU_VERSION_LARGE_ENOUGH - Failed
-- WARNING: libharu version is less than 2.3.0 (required for handling medium-large fonts and other fixes) so setting PLD_pdf to OFF.
-- WARNING: The ocamlc application not found. Disabling OCaml binding
-- WARNING: ENABLE_ocaml is OFF so disabling Plcairo module and lablgtk2 support
-- WARNING: validate target will not be available to check for syntax issues in the PLplot DocBook documentation because onsgmls (or env) was not found.
pc_libplplot_LINK_FLAGS = /usr/local/lib/libltdl.dylib;/usr/lib/libm.dylib;/opt/local/lib/libshp.dylib;-lcsirocsa;-lcsironn;-L/opt/local/lib;-lqhull;-lqsastime
-- WARNING: Perl modules XML::Parser and/or XML::DOM not available
so cannot check that swig_documentation.i is up to date.
-- TEST_ENVIRONMENT = EXAMPLES_DIR=/tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/examples SRC_EXAMPLES_DIR=/tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/examples OUTPUT_DIR=/tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/ctest_examples_output_dir VC_CTEST_DIRECTORY=

Summary of CMake build system results for PLplot

Install location variables which can be set by the user:
CMAKE_INSTALL_PREFIX: /usr/local/Cellar/gnudatalanguage/0.9.7_4
CMAKE_INSTALL_EXEC_PREFIX /usr/local/Cellar/gnudatalanguage/0.9.7_4
CMAKE_INSTALL_BINDIR /usr/local/Cellar/gnudatalanguage/0.9.7_4/bin
CMAKE_INSTALL_DATADIR /usr/local/Cellar/gnudatalanguage/0.9.7_4/share
CMAKE_INSTALL_LIBDIR /usr/local/Cellar/gnudatalanguage/0.9.7_4/lib
CMAKE_INSTALL_INCLUDEDIR /usr/local/Cellar/gnudatalanguage/0.9.7_4/include
CMAKE_INSTALL_INFODIR /usr/local/Cellar/gnudatalanguage/0.9.7_4/share/info
CMAKE_INSTALL_MANDIR /usr/local/Cellar/gnudatalanguage/0.9.7_4/share/man

Derived install location variables:
DATA_DIR /usr/local/Cellar/gnudatalanguage/0.9.7_4/share/plplot5.12.0
LIB_DIR /usr/local/Cellar/gnudatalanguage/0.9.7_4/lib
INCLUDE_DIR /usr/local/Cellar/gnudatalanguage/0.9.7_4/include/plplot
BIN_DIR /usr/local/Cellar/gnudatalanguage/0.9.7_4/bin
TCL_DIR /usr/local/Cellar/gnudatalanguage/0.9.7_4/share/plplot5.12.0/tcl
ADA_INCLUDE_DIR /usr/local/Cellar/gnudatalanguage/0.9.7_4/share/ada/adainclude/plplotada
ADA_LIB_DIR /usr/local/Cellar/gnudatalanguage/0.9.7_4/lib/ada/adalib/plplotada
PYTHON_INSTDIR
DRV_DIR /usr/local/Cellar/gnudatalanguage/0.9.7_4/lib/plplot5.12.0/drivers
DOC_DIR /usr/local/Cellar/gnudatalanguage/0.9.7_4/share/doc/plplot
MAN_DIR /usr/local/Cellar/gnudatalanguage/0.9.7_4/share/man
INFO_DIR /usr/local/Cellar/gnudatalanguage/0.9.7_4/share/info

Other important CMake variables:

CMAKE_SYSTEM_NAME: Darwin
UNIX: 1
WIN32:
APPLE: 1
MSVC: (MSVC_VERSION: )
MINGW:
MSYS:
CYGWIN:
BORLAND:
WATCOM:

SWIG_FOUND: 1
PERL_FOUND: TRUE
X11_FOUND: 1

CMAKE_BUILD_TYPE: Release
CMAKE_C_COMPILER CMAKE_C_FLAGS: /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang
CMAKE_CXX_COMPILER CMAKE_CXX_FLAGS: /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++

ENABLE_DYNDRIVERS: ON
DRIVERS_LIST: mem;null;ps;svg;xfig;xwin
DEVICES_LIST: mem;null;ps;svg;xfig;xwin

Library options:
BUILD_SHARED_LIBS: ON PL_DOUBLE: ON

Optional libraries:
PL_HAVE_QHULL: ON WITH_CSA: ON
PL_HAVE_FREETYPE: PL_HAVE_PTHREAD: OFF
HAVE_AGG: HAVE_SHAPELIB: ON

Language Bindings:
ENABLE_ada: OFF
ENABLE_cxx: ON
ENABLE_d: OFF
ENABLE_f95: OFF
ENABLE_java: OFF
ENABLE_lua: OFF
ENABLE_ocaml: OFF
ENABLE_octave: OFF
ENABLE_pdl: OFF
ENABLE_python: OFF
ENABLE_qt: OFF
ENABLE_pyqt4: OFF
ENABLE_pyqt5: OFF
ENABLE_tcl: OFF
ENABLE_itcl: OFF
ENABLE_tk: OFF
ENABLE_itk: OFF
ENABLE_wxwidgets: OFF

-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build
==> make
/usr/local/Cellar/cmake/3.13.4/bin/cmake -S/tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0 -B/tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/local/Cellar/cmake/3.13.4/bin/cmake -E cmake_progress_start /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/CMakeFiles /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/CMakeFiles/progress.marks
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/Makefile2 all
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f lib/csa/CMakeFiles/csirocsa.dir/build.make lib/csa/CMakeFiles/csirocsa.dir/depend
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f lib/nn/CMakeFiles/csironn.dir/build.make lib/nn/CMakeFiles/csironn.dir/depend
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f lib/qsastime/CMakeFiles/deltaT-gen.dir/build.make lib/qsastime/CMakeFiles/deltaT-gen.dir/depend
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f lib/qsastime/CMakeFiles/tai-utc-gen.dir/build.make lib/qsastime/CMakeFiles/tai-utc-gen.dir/depend
cd /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build && /usr/local/Cellar/cmake/3.13.4/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0 /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/lib/csa /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/lib/csa /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/lib/csa/CMakeFiles/csirocsa.dir/DependInfo.cmake --color=
cd /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build && /usr/local/Cellar/cmake/3.13.4/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0 /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/lib/nn /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/lib/nn /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/lib/nn/CMakeFiles/csironn.dir/DependInfo.cmake --color=
cd /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build && /usr/local/Cellar/cmake/3.13.4/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0 /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/lib/qsastime /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/lib/qsastime /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/lib/qsastime/CMakeFiles/deltaT-gen.dir/DependInfo.cmake --color=
cd /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build && /usr/local/Cellar/cmake/3.13.4/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0 /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/lib/qsastime /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/lib/qsastime /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/lib/qsastime/CMakeFiles/tai-utc-gen.dir/DependInfo.cmake --color=
Scanning dependencies of target deltaT-gen
Scanning dependencies of target tai-utc-gen
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f lib/qsastime/CMakeFiles/tai-utc-gen.dir/build.make lib/qsastime/CMakeFiles/tai-utc-gen.dir/build
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f lib/qsastime/CMakeFiles/deltaT-gen.dir/build.make lib/qsastime/CMakeFiles/deltaT-gen.dir/build
Scanning dependencies of target csirocsa
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f lib/csa/CMakeFiles/csirocsa.dir/build.make lib/csa/CMakeFiles/csirocsa.dir/build
Scanning dependencies of target csironn
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f lib/nn/CMakeFiles/csironn.dir/build.make lib/nn/CMakeFiles/csironn.dir/build
[ 1%] Building C object lib/qsastime/CMakeFiles/deltaT-gen.dir/deltaT-gen.c.o
cd /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/lib/qsastime && /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang -DPLPLOT_HAVE_CONFIG_H -I/tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/lib/qsastime -I/tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/lib/qsastime -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -o CMakeFiles/deltaT-gen.dir/deltaT-gen.c.o -c /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/lib/qsastime/deltaT-gen.c
[ 1%] Building C object lib/csa/CMakeFiles/csirocsa.dir/csa.c.o
cd /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/lib/csa && /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang -DPLPLOT_HAVE_CONFIG_H -DUSINGDLL -Dcsirocsa_EXPORTS -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -fPIC -o CMakeFiles/csirocsa.dir/csa.c.o -c /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/lib/csa/csa.c
[ 3%] Building C object lib/qsastime/CMakeFiles/tai-utc-gen.dir/tai-utc-gen.c.o
cd /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/lib/qsastime && /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang -DPLPLOT_HAVE_CONFIG_H -I/tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/lib/qsastime -I/tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/lib/qsastime -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -o CMakeFiles/tai-utc-gen.dir/tai-utc-gen.c.o -c /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/lib/qsastime/tai-utc-gen.c
[ 4%] Building C object lib/nn/CMakeFiles/csironn.dir/delaunay.c.o
cd /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/lib/nn && /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang -DPLPLOT_HAVE_CONFIG_H -DUSINGDLL -Dcsironn_EXPORTS -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -fPIC -I/opt/local/include -o CMakeFiles/csironn.dir/delaunay.c.o -c /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/lib/nn/delaunay.c
/tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/lib/nn/delaunay.c:40:10: fatal error: 'qhull/qhull_a.h' file not found
#include <qhull/qhull_a.h>
^~~~~~~~~~~~~~~~~
1 error generated.
make[2]: *** [lib/nn/CMakeFiles/csironn.dir/delaunay.c.o] Error 1
make[1]: *** [lib/nn/CMakeFiles/csironn.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 6%] Building C object lib/qsastime/CMakeFiles/deltaT-gen.dir/dspline.c.o
cd /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/lib/qsastime && /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang -DPLPLOT_HAVE_CONFIG_H -I/tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/lib/qsastime -I/tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/lib/qsastime -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -o CMakeFiles/deltaT-gen.dir/dspline.c.o -c /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/lib/qsastime/dspline.c
[ 6%] Linking C executable tai-utc-gen
cd /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/lib/qsastime && /usr/local/Cellar/cmake/3.13.4/bin/cmake -E cmake_link_script CMakeFiles/tai-utc-gen.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/tai-utc-gen.dir/tai-utc-gen.c.o -o tai-utc-gen /usr/lib/libm.dylib
[ 7%] Linking C executable deltaT-gen
cd /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/lib/qsastime && /usr/local/Cellar/cmake/3.13.4/bin/cmake -E cmake_link_script CMakeFiles/deltaT-gen.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/deltaT-gen.dir/deltaT-gen.c.o CMakeFiles/deltaT-gen.dir/dspline.c.o -o deltaT-gen
[ 7%] Built target tai-utc-gen
[ 7%] Built target deltaT-gen
[ 9%] Linking C shared library libcsirocsa.dylib
cd /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/lib/csa && /usr/local/Cellar/cmake/3.13.4/bin/cmake -E cmake_link_script CMakeFiles/csirocsa.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -dynamiclib -Wl,-headerpad_max_install_names -single_module -current_version 0.0.1 -o libcsirocsa.0.0.1.dylib -install_name @rpath/libcsirocsa.0.dylib CMakeFiles/csirocsa.dir/csa.c.o /usr/lib/libm.dylib
cd /tmp/gnudatalanguage--plplot-x11-20190217-15681-gmh1kt/plplot-5.12.0/plplot-build/lib/csa && /usr/local/Cellar/cmake/3.13.4/bin/cmake -E cmake_symlink_library libcsirocsa.0.0.1.dylib libcsirocsa.0.dylib libcsirocsa.dylib
[ 9%] Built target csirocsa
make: *** [all] Error 2

==> Formula
Tap: brewsci/science
Path: /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/gnudatalanguage.rb
==> Configuration
HOMEBREW_VERSION: 2.0.1
ORIGIN: https://github.com/Homebrew/brew
HEAD: e32c1515432a938093d5ef1d8c4b4408991873df
Last commit: 11 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 3475e13f84fd10e88e3f81bfa1b390f0f7794224
Core tap last commit: 3 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_ENABLE_AUTO_UPDATE_MIGRATION: 1
HOMEBREW_LOGS: /Users/jtorresh/Library/Logs/Homebrew
CPU: quad-core 64-bit kabylake
Homebrew Ruby: 2.3.7 => /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby
Clang: 10.0 build 1000
Git: 2.20.1 => /usr/local/bin/git
Curl: 7.54.0 => /usr/bin/curl
Java: 11.0.2, 1.8.0_202
macOS: 10.14-x86_64
CLT: 10.1.0.0.1.1539992718
Xcode: 10.1
XQuartz: 2.7.11 => /opt/X11
==> ENV
HOMEBREW_CC: clang
HOMEBREW_CXX: clang++
MAKEFLAGS: -j4
CMAKE_PREFIX_PATH: /usr/local/opt/readline:/usr/local/opt/openssl:/usr/local/opt/gettext:/usr/local/opt/libffi:/usr/local/opt/icu4c:/usr/local
CMAKE_INCLUDE_PATH: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/libxml2:/opt/X11/include:/opt/X11/include/freetype2:/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
CMAKE_LIBRARY_PATH: /opt/X11/lib:/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
PKG_CONFIG_PATH: /usr/local/opt/gsl/lib/pkgconfig:/usr/local/opt/readline/lib/pkgconfig:/usr/local/opt/libpng/lib/pkgconfig:/usr/local/opt/freetype/lib/pkgconfig:/usr/local/opt/jpeg/lib/pkgconfig:/usr/local/opt/jasper/lib/pkgconfig:/usr/local/opt/libtiff/lib/pkgconfig:/usr/local/opt/little-cms2/lib/pkgconfig:/usr/local/opt/webp/lib/pkgconfig:/usr/local/opt/graphicsmagick/lib/pkgconfig:/usr/local/opt/isl/lib/pkgconfig:/usr/local/opt/mpfr/lib/pkgconfig:/usr/local/opt/netcdf/lib/pkgconfig:/usr/local/opt/openssl/lib/pkgconfig:/usr/local/opt/libevent/lib/pkgconfig:/usr/local/opt/open-mpi/lib/pkgconfig:/usr/local/opt/fftw/lib/pkgconfig:/usr/local/opt/fontconfig/lib/pkgconfig:/usr/local/opt/libffi/lib/pkgconfig:/usr/local/opt/pcre/lib/pkgconfig:/usr/local/opt/glib/lib/pkgconfig:/usr/local/opt/pixman/lib/pkgconfig:/usr/local/opt/cairo/lib/pkgconfig:/usr/local/opt/fribidi/lib/pkgconfig:/usr/local/opt/graphite2/lib/pkgconfig:/usr/local/opt/icu4c/lib/pkgconfig:/usr/local/opt/harfbuzz/lib/pkgconfig:/usr/local/opt/pango/lib/pkgconfig:/usr/local/opt/eigen/share/pkgconfig
PKG_CONFIG_LIBDIR: /usr/lib/pkgconfig:/usr/local/Homebrew/Library/Homebrew/os/mac/pkgconfig/10.14:/opt/X11/lib/pkgconfig:/opt/X11/share/pkgconfig
HOMEBREW_GIT: git
HOMEBREW_SDKROOT: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ACLOCAL_PATH: /usr/local/opt/gettext/share/aclocal:/usr/local/share/aclocal:/opt/X11/share/aclocal
PATH: /usr/local/Homebrew/Library/Homebrew/shims/mac/super:/usr/local/opt/cmake/bin:/usr/local/opt/pkg-config/bin:/usr/local/opt/gsl/bin:/usr/local/opt/libpng/bin:/usr/local/opt/freetype/bin:/usr/local/opt/jpeg/bin:/usr/local/opt/jasper/bin:/usr/local/opt/libtiff/bin:/usr/local/opt/libtool/bin:/usr/local/opt/little-cms2/bin:/usr/local/opt/webp/bin:/usr/local/opt/graphicsmagick/bin:/usr/local/opt/gcc/bin:/usr/local/opt/hdf5/bin:/usr/local/opt/netcdf/bin:/usr/local/opt/udunits/bin:/usr/local/opt/openssl/bin:/usr/local/opt/libevent/bin:/usr/local/opt/open-mpi/bin:/usr/local/opt/fftw/bin:/usr/local/opt/fontconfig/bin:/usr/local/opt/gettext/bin:/usr/local/opt/pcre/bin:/usr/local/opt/glib/bin:/usr/local/opt/cairo/bin:/usr/local/opt/fribidi/bin:/usr/local/opt/graphite2/bin:/usr/local/opt/icu4c/bin:/usr/local/opt/harfbuzz/bin:/usr/local/opt/pango/bin:/opt/X11/bin:/usr/bin:/bin:/usr/sbin:/sbin

Error: brewsci/science/gnudatalanguage 0.9.7 did not build
Logs:
/Users/jtorresh/Library/Logs/Homebrew/gnudatalanguage/00.options.out
/Users/jtorresh/Library/Logs/Homebrew/gnudatalanguage/01.cmake.cc
/Users/jtorresh/Library/Logs/Homebrew/gnudatalanguage/01.cmake
/Users/jtorresh/Library/Logs/Homebrew/gnudatalanguage/02.make.cc
/Users/jtorresh/Library/Logs/Homebrew/gnudatalanguage/02.make
If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/brewsci/homebrew-science/issues

00.options.out.zip
01.cmake.zip
01.cmake.cc.zip
02.make.zip
02.make.cc.zip

==> cmake .. -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/superlu_dist/5.1.0
==> make
==> make install
==> make test
Last 15 lines from /Users/ning/Library/Logs/Homebrew/superlu_dist/04.make:
Test project /tmp/superlu_dist-20180116-66311-3vvpm4/SuperLU_DIST_5.1.0/build
    Start 1: pddrive
1/2 Test #1: pddrive ..........................***Failed    0.13 sec
    Start 2: pddrive1
2/2 Test #2: pddrive1 .........................***Failed    0.05 sec

0% tests passed, 2 tests failed out of 2

Total Test time (real) =   0.19 sec

The following tests FAILED:
	  1 - pddrive (Failed)
	  2 - pddrive1 (Failed)
Errors while running CTest
make: *** [test] Error 8

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/brewsci/homebrew-science/issues

This tap is not maintained. Please consider opening a pull request to migrate this formula to Homebrew/core or a different tap within the Brewsci organization. Please open an issue if you are interested in creating and maintaining a new tap within the Brewsci organization.

Hosting Your Own Tap

Anyone can host their own tap. See Interesting Taps & Forks and How to Create and Maintain a Tap

I got an error in installing arb on Mojave 10.14.4.
I wrote
brew install brewsci/science/arb
and got the following

Updating Homebrew...
==> Auto-updated Homebrew!
Updated 1 tap (homebrew/cask).
No changes to formulae.

==> Installing arb from brewsci/science
==> Downloading https://homebrew.bintray.com/bottles-science/arb-2.11.1.sierra.bottle.tar.gz

curl: (22) The requested URL returned error: 404 Not Found
Error: Failed to download resource "arb"
Download failed: https://homebrew.bintray.com/bottles-science/arb-2.11.1.sierra.bottle.tar.gz
Warning: Bottle installation failed: building from source.
==> Downloading https://github.com/fredrik-johansson/arb/archive/2.11.1.tar.gz
Already downloaded: /Users/languasc/Library/Caches/Homebrew/downloads/7920f35fc5adfab9fd30d73f833965568100175a5e801547ad3948a692ef0c02--2.11.1.tar.gz
==> ./configure --prefix=/usr/local/Cellar/arb/2.11.1 --with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr --with-flint=/usr/local/opt/flint
==> make
==> make install
==> make check
Last 15 lines from /Users/languasc/Library/Logs/Homebrew/arb/04.make:
det....exp....exp_sum_taylor....PASS
frobenius_norm....PASS
inv....PASS
inv_cho_precomp....PASS
inv_ldl_precomp....PASS
ldl....PASS
lu....PASS
mul....PASS
mul_entrywise....PASS
mul_threaded....make[1]: *** [../build/arb_mat/test/t-mul_threaded_RUN] Abort trap: 6
make[1]: *** Waiting for unfinished jobs....
PASS
PASS
PASS
make: *** [check] Error 2

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/brewsci/homebrew-science/issues

Do you have any suggestion? Thanks a lot !

I'll post news about significant developments in Brewsci/science to this issue. Subscribe to this issue to receive notifications of these updates.

Logs:

https://gist.github.com/d2405ddb9b1928937f4769b6dfa081d2

Error:

Last 15 lines from /home/linuxbrew/.cache/Homebrew/Logs/rapsearch2/01.make:
                 from HashSearch.cpp:16:
/home/linuxbrew/.linuxbrew/opt/boost/include/boost/iterator/advance.hpp:68:9: note: candidate: void boost::iterators::advance_adl_barrier::advance(InputIterator&, Distance) [with InputIterator = __gnu_cxx::__normal_iterator<char*, std::vector<char> >; Distance = long unsigned int]
         advance(InputIterator& it, Distance n)
         ^
In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.5.0/include/c++/5.5.0/bits/stl_algobase.h:66:0,
                 from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.5.0/include/c++/5.5.0/bits/char_traits.h:39,
                 from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.5.0/include/c++/5.5.0/ios:40,
                 from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.5.0/include/c++/5.5.0/ostream:38,
                 from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.5.0/include/c++/5.5.0/iostream:39,
                 from HashSearch.h:5,
                 from HashSearch.cpp:2:
/home/linuxbrew/.linuxbrew/Cellar/gcc/5.5.0/include/c++/5.5.0/bits/stl_iterator_base_funcs.h:173:5: note: candidate: void std::advance(_InputIterator&, _Distance) [with _InputIterator = __gnu_cxx::__normal_iterator<char*, std::vector<char> >; _Distance = long unsigned int]
     advance(_InputIterator& __i, _Distance __n)
     ^
make: *** [HashSearch.o] Error 1

make -C ccx_2.13/src ccx_2.13 CC=clang FC= CFLAGS=-O2 -I../../spooles -DARCH
Last 15 lines from /Users/elsasilva/Library/Logs/Homebrew/calculix-ccx/03.make:
a - strcpy1.o
a - stress_sen.o
a - strsplt.o
a - tau.o
a - thicknessmain.o
a - tiedcontact.o
a - transitionmain.o
a - u_calloc.o
a - u_free.o
a - u_realloc.o
a - v_betrag.o
a - v_prod.o
a - v_result.o
a - writeheading.o
make: *** [ccx_2.13.a] Error 1

Hello,
I try to install openni2, so I launched the following commands:
$brew tap brewsci/science
$brew install openni2

The terminal returns the following message:

Broken pipe EPIPE

Can you help me?

Bye, Sébastien

PS. Please find attached the logs.
openni2.txt

This tap is not maintained. Please consider opening a pull request to migrate this formula to Homebrew/core or a different tap within the Brewsci organization. Please open an issue if you are interested in creating and maintaining a new tap within the Brewsci organization.

Hosting Your Own Tap

Anyone can host their own tap. See Interesting Taps & Forks and How to Create and Maintain a Tap

This tap is not maintained. Please consider opening a pull request to migrate this formula to Homebrew/core or a different tap within the Brewsci organization. Please open an issue if you are interested in creating and maintaining a new tap within the Brewsci organization.

Hosting Your Own Tap

Anyone can host their own tap. See Interesting Taps & Forks and How to Create and Maintain a Tap

Hi @sjackman,

I am interested in migrating https://github.com/randy3k/homebrew-r to brewsci. I have been trying a model of bottling based on github releases. The procedure is as follows: say if one wants to bottle rstudio-server-1.1.419, one will need to create a branch rstudio-server-1.1.419#bottle (with #bottle suffix) and push it to github. The circle ci service will then be triggered: the bottles will be created and uploaded to github releases. At last, a pull request about the bottling information will be made (see this PR for an example).

One major issue of my approach is that it doesn't build bottles directly from PR. I would need to create a branch in order to bottle each formula. However, I think it is not a big issue for a small tap. Especially, I don't have to deal with the potential hassles of bintray and amazon lambda services.

Nevertheless, I am open to switching to the model of using bintray once homebrew-r is migrated.

Hi,

I tried to install blasr on Mac OSX using homebrew but I got this error:

brew tap brewsci/science     
brew install blasr
Updating Homebrew...
==> Auto-updated Homebrew!
Updated 2 taps (caskroom/cask, caskroom/versions).
Warning: Calling 'depends_on :mysql' is deprecated!
Use 'depends_on "mysql"' instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blat.rb:19:in `<class:Blat>'
Please report this to the brewsci/science tap!

Warning: Calling 'depends_on :python3' is deprecated!
Use 'depends_on "python3"' instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/matplotlib.rb:56:in `<class:Matplotlib>'
Please report this to the brewsci/science tap!

Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/plink.rb:23:in `block in <class:Plink>'
Please report this to the brewsci/science tap!

Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/plink.rb:23:in `block in <class:Plink>'
Please report this to the brewsci/science tap!

Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/plink.rb:23:in `block in <class:Plink>'
Please report this to the brewsci/science tap!


Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!

Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!

Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!

Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!

Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!

Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!

==> Installing blasr from brewsci/science
Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!

Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!

Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!

Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!

Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!

Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!

==> Downloading https://github.com/PacificBiosciences/blasr/archive/smrtanalysis
Already downloaded: /Users/cr517/Library/Caches/Homebrew/blasr-2.2.tar.gz
==> make STATIC= HDF5INCLUDEDIR=/usr/local/opt/hdf5/include HDF5LIBDIR=/usr/loca
Last 15 lines from /Users/cr517/Library/Logs/Homebrew/blasr/01.make:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/memory:4912:1: note: candidate template ignored: could not match 'shared_ptr<type-parameter-0-0>' against 'const RegionAnnotation'
operator<(const shared_ptr<_Tp>& __x, const shared_ptr<_Up>& __y) _NOEXCEPT
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/memory:4977:1: note: candidate template ignored: could not match 'shared_ptr<type-parameter-0-0>' against 'const RegionAnnotation'
operator<(const shared_ptr<_Tp>& __x, nullptr_t) _NOEXCEPT
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/memory:4985:1: note: candidate template ignored: could not match 'shared_ptr<type-parameter-0-0>' against 'const int'
operator<(nullptr_t, const shared_ptr<_Tp>& __x) _NOEXCEPT
^
1 error generated.
make[1]: *** [bin/KBandMatcher.o] Error 1
make: *** [alignment-build] Error 2
make: *** [sequtils-build] Error 2
clang++  -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include bin/PrintPBBWT.o -o bin/bwtpbPrint -L/usr/local/opt/hdf5/lib -lz -lpthread
clang++  -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include bin/BWTQuery.o -o bin/bwtquery -L/usr/local/opt/hdf5/lib -lz -lpthread

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/brewsci/homebrew-science/issues

Hello, I am attempting to install an annotation package via brew install on my RHEL-7 workstation. When I do, I run into a make error with eXpress.

When attempting to install eXpress, I receive this error:

==> Installing express from brewsci/science
==> Downloading https://pachterlab.github.io/eXpress/downloads/express-1.5.1/express-1.5.1-src.tgz
Already downloaded: /home/cwu/.cache/Homebrew/express-1.5.1.tgz
==> cmake . -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -DCMAKE_INSTALL_PREFIX=/home/linuxbrew/.linuxbrew/Cellar
==> make install
Last 15 lines from /home/cwu/.cache/Homebrew/Logs/express/02.make:
/tmp/express-20180627-38645-i64hxv/express-1.5.1-src/src/alignments.pb.h:543:30: error: expected '}' before end of line
/tmp/express-20180627-38645-i64hxv/express-1.5.1-src/src/alignments.pb.h:543:30: error: expected unqualified-id before end of line
/tmp/express-20180627-38645-i64hxv/express-1.5.1-src/src/alignments.pb.h:543:30: error: expected '}' before end of line
/tmp/express-20180627-38645-i64hxv/express-1.5.1-src/src/alignments.pb.h:543:30: error: expected '}' before end of line
/tmp/express-20180627-38645-i64hxv/express-1.5.1-src/src/alignments.pb.h:543:30: error: expected '}' before end of line
/tmp/express-20180627-38645-i64hxv/express-1.5.1-src/src/alignments.pb.h:543:30: error: expected declaration before end of line
In file included from /tmp/express-20180627-38645-i64hxv/express-1.5.1-src/src/main.cpp:20:0:
/tmp/express-20180627-38645-i64hxv/express-1.5.1-src/src/main.h:94:14: warning: 'LOG_MAX' defined but not used [-Wunused-variable]
const double LOG_MAX = log(std::numeric_limits::max());
^
make[2]: *** [src/CMakeFiles/express.dir/main.cpp.o] Error 1
make[2]: Leaving directory /tmp/express-20180627-38645-i64hxv/express-1.5.1-src' make[1]: *** [src/CMakeFiles/express.dir/all] Error 2 make[1]: Leaving directory /tmp/express-20180627-38645-i64hxv/express-1.5.1-src'
make: *** [all] Error 2

From there the install fails. Any help resolving this issue would be greatly appreciated.

Best,

Michael

==> cmake .. -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/superlu_dist/5.1.0_3 -DCMAKE_BUILD
Last 15 lines from /Users/konstantin/Library/Logs/Homebrew/superlu_dist/01.cmake:
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- The Fortran compiler identification is unknown
CMake Error at CMakeLists.txt:71 (enable_language):
No CMAKE_Fortran_COMPILER could be found.

Tell CMake where to find the compiler by setting either the environment
variable "FC" or the CMake cache entry CMAKE_Fortran_COMPILER to the full
path to the compiler, or to the compiler name if it is in the PATH.

-- Configuring incomplete, errors occurred!
See also "/tmp/superlu_dist-20190113-2626-1ph20pj/SuperLU_DIST_5.1.0/build/CMakeFiles/CMakeOutput.log".
See also "/tmp/superlu_dist-20190113-2626-1ph20pj/SuperLU_DIST_5.1.0/build/CMakeFiles/CMakeError.log".

https://github.com/Homebrew/homebrew-core/blob/master/Formula/orocos-kdl.rb

Therefore the orocos-kdl formula should be removed from this tap to avoid conflicts.

Popular or notable formulae can be migrated to Homebrew/core.
Bioinformatics formulae can be migrated to Brewsci/bio.

Metrics of popularity (number of installations) and notariety (GitHub watchers, stars, forks)

• Bioinformatics formulae
• All formulae

• a5
• abacas
• abyss-explorer
• ace-corrector
• adam
• adapterremoval
• afra
• alien-hunter
• allpaths-lg
• amos
• analysis
• andi
• anvio
• aragorn
• arcs
• art
• artemis
• astral
• atram
• augustus
• bam-readcount
• bam2wig
• bamhash
• bamm
• bamutil
• barrnap
• bbtools
• bcalm
• beagle
• beast2
• beetl
• bfc
• bioawk
• biobloomtools
• biointerchange
• biomake
• biopieces
• blasr
• blast
• blat
• bless
• bowtie
• bpipe
• breseq
• busco
• canu
• cap3
• cd-hit
• cegma
• celera-assembler
• centrifuge
• cerulean
• circlator
• clark
• clonalframeml
• clonehd
• clustal-omega
• clustal-w
• corset
• cutadapt
• cytoscape
• daligner
• dazz_db
• delly
• dextractor
• dida
• discovar
• discovardenovo
• dsk
• dwgsim
• e-mem
• edirect
• ensembl-tools
• exonerate
• express
• fasta
• fastml
• fastq-tools
• fasttree
• fastuniq
• fastx_toolkit
• fermi
• fermi-lite
• fermi2
• fermikit
• flash
• flexbar
• fqzcomp
• freebayes
• freec
• fsa
• fwdpp
• gaemr
• garli
• gatb
• gatk
• geneid
• genewise
• gingr
• glimmerhmm
• gmap-gsnap
• grabix
• graphlan
• gubbins
• harvest-tools
• hisat
• hisat2
• hlaminer
• hmmer
• hmmer2
• htsbox
• humann2
• idba
• igvtools
• impute2
• infernal
• iqtree
• iva
• jellyfish
• jellyfish-1.1
• kaiju
• kat
• kent-tools
• kmacs
• kmc
• kmergenie
• kmerstream
• kollector
• kraken
• last
• lastz
• libbigwig
• libpll
• libsequence
• lighter
• links-scaffolder
• lobstr
• lrsim
• lsd
• lumpy-sv
• macse
• mafft
• maker
• mapsembler2
• maq
• mash
• masurca
• mcl
• megahit
• meme
• meraculous
• metaphlan
• methpipe
• mhap
• minced
• minia
• miniasm
• minimap
• mir-prefer
• mira
• mitofy
• mlst
• mothur
• mrbayes
• multi-worm-tracker
• mummer
• muscle
• nanopolish
• ncbi-c++-toolkit
• ncl
• newick-utils
• newicktools
• nextflow
• nonpareil
• novoalign
• ntcard
• nxtrim
• oases
• ogdraw
• oma
• orthofinder
• paml
• pandaseq
• parsnp
• pathd8
• pathvisio
• pbsuite
• pear
• phipack
• phlawd
• phylip
• phyml
• phyutility
• phyx
• piler
• pilercr
• pilon
• platypusvar
• plink
• plink2
• poa
• populations
• poretools
• prokka
• proteinortho
• psmc
• quaff
• quake
• quast
• quest
• quicktree
• quorum
• r8s
• racon
• rampart
• rapsearch2
• raxml
• ray
• rcorrector
• readseq
• readsim
• reapr
• recon
• repeatmasker
• repeatmodeler
• repeatscout
• rmblast
• rna-star
• rnammer
• ropebwt2
• sailfish
• salmon
• sambamba
• samblaster
• [email protected]
• scarpa
• sdsl-lite
• seq-gen
• seqan
• seqdb
• sequel
• sga
• shrimp
• sickle
• simulate-pcr
• skewer
• smalt
• smrtanalysis
• snap
• snap-aligner
• snoscan
• snp-sites
• snpeff
• soapdenovo
• sortmerna
• spaced
• spici
• squeezambler
• ssake
• stacks
• stringtie
• swarm
• tabtk
• tagdust
• tasr
• tbl2asn
• tophat
• trans-abyss
• trans_proteomic_pipeline
• transdecoder
• transrate-tools
• trf
• trimadap
• trimal
• trimmomatic
• trinity
• trnascan
• ucsc-genome-browser
• unicycler
• uproc
• vague
• varscan
• vcake
• vcflib
• velvet
• velvetoptimiser
• viennarna
• vsearch
• vt
• weblogo
• wiggletools
• yaha

Logs:

https://gist.github.com/70e584af599d7611270cdaa568bc141e

Error:

cd /tmp/sailfish-20180111-151804-1wkjpkf/sailfish-0.10.1/build/src && /home/linuxbrew/.linuxbrew/Cellar/cmake/3.10.1/bin/cmake -E cmake_link_script CMakeFiles/sailfish.dir/link.txt --verbose=1
/home/linuxbrew/.linuxbrew/Library/Homebrew/shims/linux/super/g++-5  -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -DRAPMAP_SALMON_SUPPORT -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -DRAPMAP_SALMON_SUPPORT -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs  -rdynamic CMakeFiles/sailfish.dir/Sailfish.cpp.o  -o sailfish  -L/tmp/sailfish-20180111-151804-1wkjpkf/sailfish-0.10.1/lib  -L/tmp/sailfish-20180111-151804-1wkjpkf/sailfish-0.10.1/external/install/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib" libsailfish_core.a -lpthread -Wl,-Bstatic -lboost_iostreams-mt -lboost_filesystem-mt -lboost_system-mt -lboost_thread-mt -lboost_timer-mt -lboost_chrono-mt -lboost_program_options-mt -lboost_serialization-mt -lboost_regex-mt -lboost_date_time-mt -lboost_atomic-mt -Wl,-Bdynamic -lgff -Wl,-Bstatic -lz -Wl,-Bdynamic ../../external/install/lib/libdivsufsort.a ../../external/install/lib/libdivsufsort64.a ../../external/install/lib/libjellyfish-2.0.a -lm -ltbb -ltbbmalloc -lgomp -lrt -Wl,-Bstatic -ljemalloc -Wl,-Bdynamic
/home/linuxbrew/.linuxbrew/bin/ld: /home/linuxbrew/.linuxbrew/lib/libjemalloc.a(background_thread.o): undefined reference to symbol 'dlsym@@GLIBC_2.2.5'
//home/linuxbrew/.linuxbrew/lib/libdl.so.2: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make[2]: *** [src/sailfish] Error 1
make[2]: Leaving directory `/tmp/sailfish-20180111-151804-1wkjpkf/sailfish-0.10.1/build'
make[1]: *** [src/CMakeFiles/sailfish.dir/all] Error 2
make[1]: Leaving directory `/tmp/sailfish-20180111-151804-1wkjpkf/sailfish-0.10.1/build'
make: *** [all] Error 2

hi there,
i've seen the message about this not being maintained. i can't find this formula anywhere else though, where should I post this issue? thanks

➜  Students git:(master) brew install ipopt
Warning: Calling 'depends_on :fortran' is deprecated!
Use 'depends_on "gcc"' instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/ipopt.rb:21:in `<class:Ipopt>'
Please report this to the brewsci/science tap!

==> Installing ipopt from brewsci/science
Warning: Calling 'depends_on :mpi' is deprecated!
Use 'depends_on "open-mpi"' instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/mumps.rb:11:in `<class:Mumps>'
Please report this to the brewsci/science tap!

==> Installing dependencies for brewsci/science/ipopt: mumps
==> Installing brewsci/science/ipopt dependency: mumps
Warning: Calling 'depends_on :mpi' is deprecated!
Use 'depends_on "open-mpi"' instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/mumps.rb:11:in `<class:Mumps>'
Please report this to the brewsci/science tap!

Warning: Calling 'depends_on :fortran' is deprecated!
Use 'depends_on "gcc"' instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/mumps.rb:14:in `<class:Mumps>'
Please report this to the brewsci/science tap!

==> Downloading http://mumps.enseeiht.fr/MUMPS_5.1.1.tar.gz
######################################################################## 100.0%
==> make alllib LIBEXT=.dylib AR= -dynamiclib -Wl,-install_name -Wl,/usr/local/Cellar/mumps/5.1.1_1/lib/$(notdir $@) -undefined dynamic_lookup -o  RANLIB=echo 
Last 15 lines from /Users/florian.oswald/Library/Logs/Homebrew/mumps/01.make:
clang -fPIC -I../include -O  -c symbfac.c -o symbfac.o
clang -fPIC -I../include -O  -c interface.c -o interface.o
clang -fPIC -I../include -O  -c sort.c -o sort.o
clang -fPIC -I../include -O  -c minpriority.c -o minpriority.o
dynamiclib -Wl,-install_name -Wl,/usr/local/Cellar/mumps/5.1.1_1/lib/libpord.dylib -undefined dynamic_lookup -o libpord.dylib graph.o gbipart.o gbisect.o ddcreate.o ddbisect.o nestdiss.o multisector.o gelim.o bucket.o tree.o symbfac.o interface.o sort.o minpriority.o 
make[2]: dynamiclib: No such file or directory
make[2]: [libpord.dylib] Error 1 (ignored)
echo libpord.dylib
libpord.dylib
if [ "./PORD/lib/" != "" ] ; then \
	  cp ./PORD/lib//libpord.dylib lib/libpord.dylib; \
	fi;
cp: ./PORD/lib//libpord.dylib: No such file or directory
make[1]: *** [lib/libpord.dylib] Error 1
make: *** [c] Error 2

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/brewsci/homebrew-science/issues

Should the following text be removed from the pull request template?

New formula:

We will no longer accept new formula in homebrew-science, as this tap is being phased out.
Please consider submitting your formulae to https://github.com/Homebrew/homebrew-core or host it in your own tap (https://docs.brew.sh/How-to-Create-and-Maintain-a-Tap.html).

Hello,

I encounter this build issue (Mojave):

[–]$ brew install ome-files
==> Installing ome-files from brewsci/science
==> Installing dependencies for brewsci/science/ome-files: ome-common and ome-xml
==> Installing brewsci/science/ome-files dependency: ome-common
==> Downloading https://downloads.openmicroscopy.org/ome-common-cpp/5.5.0/source/ome-common-cpp-5.5.0.tar.xz
######################################################################## 100.0%
==> Downloading https://github.com/google/googletest/archive/release-1.8.0.tar.gz
==> Downloading from https://codeload.github.com/google/googletest/tar.gz/release-1.8.0
######################################################################## 100.0%
==> cmake . -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/ome-common/5.5.0_1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_VERBOSE_MAKEFI
==> make install
==> cmake .. -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/ome-common/5.5.0_1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_VERBOSE_MAKEF
==> make
Last 15 lines from /Users/Turlier/Library/Logs/Homebrew/ome-common/04.make:
make[1]: *** [test/ome-common/CMakeFiles/xalan.dir/all] Error 2
[ 59%] Linking CXX executable xerces
cd /tmp/ome-common-20190502-89835-hk2g6e/ome-common-cpp-5.5.0/build/test/ome-common && /usr/local/Cellar/cmake/3.14.3/bin/cmake -E cmake_link_script CMakeFiles/xerces.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++ -pedantic -Wall -Wcast-align -Wcast-qual -Wctor-dtor-privacy -Wextra -Wformat=2 -Wimplicit-atomic-properties -Wmissing-declarations -Wno-long-long -Wnon-virtual-dtor -Woverlength-strings -Woverloaded-virtual -Wredundant-decls -Wreorder -Wswitch-default -Wunused-variable -Wwrite-strings -Wno-variadic-macros -fstrict-aliasing -Wno-unused-local-typedef -Wno-language-extension-token -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/xerces.dir/xerces.cpp.o -o xerces -Wl,-rpath,/tmp/ome-common-20190502-89835-hk2g6e/ome-common-cpp-5.5.0/build/lib/ome/common ../../lib/ome/test/libome-test.a ../../lib/ome/common/libome-common.5.5.0.dylib /usr/local/lib/libboost_log-mt.dylib /usr/local/lib/libboost_log_setup-mt.dylib /usr/local/lib/libboost_thread-mt.dylib /usr/local/lib/libboost_date_time-mt.dylib /usr/local/lib/libboost_chrono-mt.dylib /usr/local/lib/libboost_atomic-mt.dylib /usr/local/lib/libboost_iostreams-mt.dylib /usr/local/lib/libboost_regex-mt.dylib /usr/local/lib/libboost_filesystem-mt.dylib /usr/local/lib/libboost_system-mt.dylib /usr/local/lib/libxalan-c.dylib /usr/local/lib/libxerces-c.so /usr/local/lib/libgtest.dylib
Undefined symbols for architecture x86_64:
"testing::internal::MakeAndRegisterTestInfo(char const*, char const*, char const*, char const*, testing::internal::CodeLocation, void const*, void ()(), void ()(), testing::internal::TestFactoryBase*)", referenced from:
testing::internal::ParameterizedTestCaseInfo::RegisterTests() in xerces.cpp.o
__GLOBAL__sub_I_xerces.cpp in xerces.cpp.o
"testing::internal::ReportInvalidTestCaseType(char const*, testing::internal::CodeLocation)", referenced from:
testing::internal::ParameterizedTestCaseInfo* testing::internal::ParameterizedTestCaseRegistry::GetTestCasePatternHolder(char const*, testing::internal::CodeLocation) in xerces.cpp.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [test/ome-common/xerces] Error 1
make[1]: *** [test/ome-common/CMakeFiles/xerces.dir/all] Error 2
make: *** [all] Error 2

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/brewsci/homebrew-science/issues

I am trying to install ipopt by running: brew install ipopt.rb --with-openblas and got this error:

==> Installing dependencies for ipopt: mumps
==> Installing ipopt dependency: mumps
==> Downloading http://mumps.enseeiht.fr/MUMPS_5.1.1.tar.gz
Already downloaded: /Users/yufeiliu/Library/Caches/Homebrew/mumps-5.1.1.tar.gz
==> make alllib LIBEXT=.dylib AR= -dynamiclib -Wl,-install_name -Wl,/usr/local/Cellar/mumps/5.1.
Last 15 lines from /Users/yufeiliu/Library/Logs/Homebrew/mumps/01.make:
clang -fPIC -I../include -O -c symbfac.c -o symbfac.o
clang -fPIC -I../include -O -c interface.c -o interface.o
clang -fPIC -I../include -O -c sort.c -o sort.o
clang -fPIC -I../include -O -c minpriority.c -o minpriority.o
dynamiclib -Wl,-install_name -Wl,/usr/local/Cellar/mumps/5.1.1_1/lib/libpord.dylib -undefined dynamic_lookup -o libpord.dylib graph.o gbipart.o gbisect.o ddcreate.o ddbisect.o nestdiss.o multisector.o gelim.o bucket.o tree.o symbfac.o interface.o sort.o minpriority.o
make[2]: dynamiclib: No such file or directory
make[2]: [libpord.dylib] Error 1 (ignored)
echo libpord.dylib
libpord.dylib
if [ "./PORD/lib/" != "" ] ; then
cp ./PORD/lib//libpord.dylib lib/libpord.dylib;
fi;
cp: ./PORD/lib//libpord.dylib: No such file or directory
make[1]: *** [lib/libpord.dylib] Error 1
make: *** [c] Error 2

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/brewsci/homebrew-science/issues

Does anyone know how to resolve this?

When I attempt to build calculix-ccx from source (ie brew install --build-from-source calculix-ccx) I get an error. Further more the standard install method works but the installed file doesn't seem to work. I'm using macOS High Sierra 10.13.4. Error codes below.

brew install --build-from-source calculix-ccx
==> make -C ccx_2.13/src ccx_2.13 CC=clang FC= CFLAGS=-O2 -I../../spooles -DARCH
Last 15 lines from /Users/tom/Library/Logs/Homebrew/calculix-ccx/03.make:
a - strcpy1.o
a - stress_sen.o
a - strsplt.o
a - tau.o
a - thicknessmain.o
a - tiedcontact.o
a - transitionmain.o
a - u_calloc.o
a - u_free.o
a - u_realloc.o
a - v_betrag.o
a - v_prod.o
a - v_result.o
a - writeheading.o
make: *** [ccx_2.13.a] Error 1

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/brewsci/homebrew-science/issues

==> Installing scotch from brewsci/science
==> Downloading https://gforge.inria.fr/frs/download.php/file/34618/scotch_6.0.4.tar.gz
Already downloaded: /Users/walham/Library/Caches/Homebrew/downloads/2bd1ac66828c15a1bdf933512b701013a9c8caf78030a82d03da9be8228063a5--scotch_6.0.4.tar.gz
==> make scotch VERBOSE=ON CCS=clang CCP= CCD= RANLIB=echo CFLAGS=-O3 -fPIC -Drestrict=__restrict -DCOMMON_PTHREAD_B
==> make ptscotch VERBOSE=ON CCS=clang CCP= CCD= RANLIB=echo CFLAGS=-O3 -fPIC -Drestrict=__restrict -DCOMMON_PTHREAD
Last 15 lines from /Users/walham/Library/Logs/Homebrew/scotch/02.make:
make[2]: `libscotcherrexit.dylib' is up to date.
make CFLAGS="-O3 -fPIC -Drestrict=__restrict -DCOMMON_PTHREAD_BARRIER -DCOMMON_PTHREAD -DSCOTCH_CHECK_AUTO -DCOMMON_RANDOM_FIXED_SEED -DCOMMON_TIMING_OLD -DSCOTCH_RENAME -DCOMMON_FILE_COMPRESS_BZ2 -DCOMMON_FILE_COMPRESS_GZ -DSCOTCH_PTSCOTCH" CC=""
ptscotch.h
ptscotchf.h
libptscotch.dylib
libptscotcherr.dylib
libptscotcherrexit.dylib
O3 -fPIC -Drestrict=__restrict -DCOMMON_PTHREAD_BARRIER -DCOMMON_PTHREAD -DSCOTCH_CHECK_AUTO -DCOMMON_RANDOM_FIXED_SEED -DCOMMON_TIMING_OLD -DSCOTCH_RENAME -DCOMMON_FILE_COMPRESS_BZ2 -DCOMMON_FILE_COMPRESS_GZ -DSCOTCH_PTSCOTCH -DSCOTCH_VERSION=6 -DSCOTCH_RELEASE=0 -DSCOTCH_PATCHLEVEL=4 dummysizes.c -o ptdummysizes -lm -lz -lpthread -lbz2
make[2]: O3: No such file or directory
make[2]: [ptdummysizes] Error 1 (ignored)
./ptdummysizes library_pt.h ptscotch.h
make[2]: ./ptdummysizes: No such file or directory
make[2]: *** [ptscotch.h] Error 1
make[1]: *** [ptscotch] Error 2
make: *** [ptscotch] Error 2

I have many questions on how this repository will evolve...
-is brewsci/homebrew-science an archive or supposed to be a new maintained home for scientific software?
-do you aim at splitting brewsci/homebrew-science into smaller repositories according to discipline as you have done with homebrew-bio? if yes, I could help setting up homebrew-numerics.
-some formula have been previously moved from homebrew-science to core but have been crippled down in features during the process, i.e. from my point of view as a computational scientist important options were removed. Are these formulas now welcome to be reimported? (e.g. Octave, SuiteSparse etc.)
-I suggested during previous discussions to define a maintainer for each formula to (hopefully) improve code quality. Is that option still considered?

Thanks for your initiative @sjackman!

When I want to install mumps, I have the following issue:

Warning: Calling 'depends_on :mpi' is deprecated!
Use 'depends_on "open-mpi"' instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/mumps.rb:11:in `class:Mumps'
Please report this to the brewsci/science tap!

Warning: Calling 'depends_on :fortran' is deprecated!
Use 'depends_on "gcc"' instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/mumps.rb:14:in `class:Mumps'
Please report this to the brewsci/science tap!

==> Installing mumps from brewsci/science
Warning: Calling 'depends_on :mpi' is deprecated!
Use 'depends_on "open-mpi"' instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/mumps.rb:11:in `class:Mumps'
Please report this to the brewsci/science tap!

Warning: Calling 'depends_on :fortran' is deprecated!
Use 'depends_on "gcc"' instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/mumps.rb:14:in `class:Mumps'
Please report this to the brewsci/science tap!

==> Downloading http://mumps.enseeiht.fr/MUMPS_5.1.1.tar.gz
Already downloaded: /Users/serge/Library/Caches/Homebrew/mumps-5.1.1.tar.gz
==> make alllib LIBEXT=.dylib AR= -dynamiclib -Wl,-install_name -Wl,/usr/local/C
Last 15 lines from /Users/serge/Library/Logs/Homebrew/mumps/01.make:
clang -fPIC -I../include -O -c symbfac.c -o symbfac.o
clang -fPIC -I../include -O -c interface.c -o interface.o
clang -fPIC -I../include -O -c sort.c -o sort.o
clang -fPIC -I../include -O -c minpriority.c -o minpriority.o
dynamiclib -Wl,-install_name -Wl,/usr/local/Cellar/mumps/5.1.1_1/lib/libpord.dylib -undefined dynamic_lookup -o libpord.dylib graph.o gbipart.o gbisect.o ddcreate.o ddbisect.o nestdiss.o multisector.o gelim.o bucket.o tree.o symbfac.o interface.o sort.o minpriority.o
make[2]: dynamiclib: No such file or directory
make[2]: [libpord.dylib] Error 1 (ignored)
echo libpord.dylib
libpord.dylib
if [ "./PORD/lib/" != "" ] ; then
cp ./PORD/lib//libpord.dylib lib/libpord.dylib;
fi;
cp: ./PORD/lib//libpord.dylib: No such file or directory
make[1]: *** [lib/libpord.dylib] Error 1
make: *** [c] Error 2

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/brewsci/homebrew-science/issues

How can I fix it ?

Yours

This tap is not maintained. Please consider opening a pull request to migrate this formula to Homebrew/core or a different tap within the Brewsci organization. Please open an issue if you are interested in creating and maintaining a new tap within the Brewsci organization.

Hosting Your Own Tap

Anyone can host their own tap. See Interesting Taps & Forks and How to Create and Maintain a Tap

My os is Mac OS High Sierra 10.13.6 (17G4015)
When attempting to install calculix-ccx I got the error:

~/programming/pycalculix (v1.1.3_development)$ brew install brewsci/science/calculix-ccx
Updating Homebrew...
==> Installing calculix-ccx from brewsci/science
==> Downloading https://homebrew.bintray.com/bottles-science/calculix-ccx-2.13.high_sierra.bottle.tar.gz

curl: (22) The requested URL returned error: 404 Not Found
Error: Failed to download resource "calculix-ccx"
Download failed: https://homebrew.bintray.com/bottles-science/calculix-ccx-2.13.high_sierra.bottle.tar.gz
Warning: Bottle installation failed: building from source.
==> Downloading http://www.dhondt.de/ccx_2.13.src.tar.bz2
######################################################################## 100.0%
==> Patching
patching file ccx_2.13/src/CalculiX.h
patching file ccx_2.13/src/Makefile
patching file ccx_2.13/src/u_free.c
==> Downloading http://www.netlib.org/linalg/spooles/spooles.2.2.tgz
######################################################################## 100.0%
==> make -C spooles lib
==> make -C spooles/MT/src makeLib
==> make -C ccx_2.13/src ccx_2.13 CC=clang FC= CFLAGS=-O2 -I../../spooles -DARCH=Linux -DSPOOLES -DARPACK -DMATRIXSTORAGE FFLAGS=-O2 D
Last 15 lines from /Users/justin/Library/Logs/Homebrew/calculix-ccx/03.make:
a - strcpy1.o
a - stress_sen.o
a - strsplt.o
a - tau.o
a - thicknessmain.o
a - tiedcontact.o
a - transitionmain.o
a - u_calloc.o
a - u_free.o
a - u_realloc.o
a - v_betrag.o
a - v_prod.o
a - v_result.o
a - writeheading.o
make: *** [ccx_2.13.a] Error 1

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
  https://github.com/brewsci/homebrew-science/issues

I have this err. could you help me?

brew install tamarin-prover
Updating Homebrew...
==> Auto-updated Homebrew!
Updated 1 tap (homebrew/core).
==> Updated Formulae
cloog                                                                                              [email protected]
==> Deleted Formulae
gmp@4                                            [email protected]                                         [email protected]                                       mpfr@2

==> Installing tamarin-prover from brewsci/science
==> Downloading https://github.com/tamarin-prover/tamarin-prover/archive/1.2.2.tar.gz
Already downloaded: /Users/foiman/Library/Caches/Homebrew/tamarin-prover-1.2.2.tar.gz
==> stack -j1 setup
Last 15 lines from /Users/foiman/Library/Logs/Homebrew/tamarin-prover/01.stack:
Installing GHC ...
Running /usr/local/Homebrew/Library/Homebrew/shims/super/gmake install in directory /private/tmp/tamarin-prover-20180124-66778-1r233dc/tamarin-prover-1.2.2/.brew_home/.stack/programs/x86_64-osx/ghc-8.0.2.temp/ghc-8.0.2/ exited with ExitFailure 2


mk/config.mk:521: *** missing separator.  Stop.


Error: Error encountered while installing GHC with
         gmake install
         run in /private/tmp/tamarin-prover-20180124-66778-1r233dc/tamarin-prover-1.2.2/.brew_home/.stack/programs/x86_64-osx/ghc-8.0.2.temp/ghc-8.0.2/
       
       The following directories may now contain files, but won't be used by stack:
         - /private/tmp/tamarin-prover-20180124-66778-1r233dc/tamarin-prover-1.2.2/.brew_home/.stack/programs/x86_64-osx/ghc-8.0.2.temp/
         - /private/tmp/tamarin-prover-20180124-66778-1r233dc/tamarin-prover-1.2.2/.brew_home/.stack/programs/x86_64-osx/ghc-8.0.2/
       

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/brewsci/homebrew-science/issues

I got this!

==> Installing molden from brewsci/science
Warning: Calling 'depends_on :fortran' is deprecated!
Use 'depends_on "gcc"' instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/molden.rb:18:in `class:Molden'
Please report this to the brewsci/science tap!

Last 15 lines from /Users/agaspar/Library/Logs/Homebrew/ds9/01.make:
inline _LIBCPP_INLINE_VISIBILITY long double tanh(long double __lcpp_x) _NOEXCEPT {return ::tanhl(__lcpp_x);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/math.h:1055:46: note: candidate function
inline _LIBCPP_INLINE_VISIBILITY float tanh(float __lcpp_x) _NOEXCEPT {return ::tanhf(__lcpp_x);}
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/math.h:357:15: note: candidate function
extern double tanh(double);
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/math.h:1062:1: note: candidate template ignored: could not match 'typename std::enable_if<std::is_integral<_A1>::value, double>::type (_A1) throw()' against 'void'
tanh(_A1 __lcpp_x) _NOEXCEPT {return ::tanh((double)__lcpp_x);}
^
15 errors generated.

I'm using brew bundle on travis ci and tapping into the brewsci/science tap results in following issue:

Cloning into '/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science'...
Error: Invalid formula: /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/ome-common.rb
Error: Invalid formula: /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/ome-files.rb
Error: Invalid formula: /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/ome-xml.rb
Error: Invalid formula: /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/osgearth.rb
Error: Cannot tap brewsci/science: invalid syntax in tap!
uninitialized constant #<Class:0x0000000101e9c9b8>::MinimumMacOSRequirement
Did you mean?  MaximumMacOSRequirement
uninitialized constant #<Class:0x0000000101e0c020>::MinimumMacOSRequirement
Did you mean?  MaximumMacOSRequirement
uninitialized constant #<Class:0x000000010148fda8>::MinimumMacOSRequirement
Did you mean?  MaximumMacOSRequirement
uninitialized constant #<Class:0x0000000101b46cc8>::MinimumMacOSRequirement
Did you mean?  MaximumMacOSRequirement
Tapping brewsci/science has failed!```

Best, 
Joschka

Good afternoon,

The command brew install brewsci/science/qcl is not working anymore. Anyone can help me?

Thanks

Hello,

Show error when try to make DSSP on macOS High Sierra 10.13.4.

==> make install DEST_DIR=/Users//Programs/brew-1.6.3/Cellar/dssp/3.0.0 M
Last 15 lines from /Users//Library/Logs/Homebrew/dssp/01.make:
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/memory:2037:8: note: candidate constructor (the implicit move constructor) not viable: no known conversion from 'long' to 'std::__1::__compressed_pair_elem<const char **, 0, false>' for 1st argument
struct __compressed_pair_elem {
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/memory:2050:3: note: candidate template ignored: substitution failure [with _Up = long, $1 = void]
__compressed_pair_elem(_Up&& __u)
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/memory:2055:3: note: candidate constructor template not viable: requires 3 arguments, but 1 was provided
__compressed_pair_elem(piecewise_construct_t, tuple<_Args...> __args,
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/memory:2043:39: note: candidate constructor not viable: requires 0 arguments, but 1 was provided
_LIBCPP_INLINE_VISIBILITY constexpr __compressed_pair_elem() : _value() {}
^
13 errors generated.
make: *** [obj/utils.o] Error 1

Could anyone please help me with this issue?

Thanks

Just tried to install ds9 and got this error.
"""
brian:~$ brew install brewsci/science/ds9
==> Installing ds9 from brewsci/science
==> Downloading http://ds9.si.edu/archive/source/ds9.7.3.2.tar.gz
Already downloaded: /Users/brian/Library/Caches/Homebrew/ds9-7.3.2.tar.gz
==> make
Last 15 lines from /Users/brian/Library/Logs/Homebrew/ds9/01.make:
inline _LIBCPP_INLINE_VISIBILITY long double tanh(long double __lcpp_x) _NOEXCEPT {return ::tanhl(__lcpp_x);}
^
/Library/Developer/CommandLineTools/usr/include/c++/v1/math.h:1027:46: note: candidate function
inline _LIBCPP_INLINE_VISIBILITY float tanh(float __lcpp_x) _NOEXCEPT {return ::tanhf(__lcpp_x);}
^
/usr/include/math.h:371:15: note: candidate function
extern double tanh(double);
^
/Library/Developer/CommandLineTools/usr/include/c++/v1/math.h:1034:1: note: candidate template ignored: could not match 'typename std::enable_if<std::is_integral<_A1>::value, double>::type (_A1) throw()' against 'void'
tanh(_A1 __lcpp_x) _NOEXCEPT {return ::tanh((double)__lcpp_x);}
^
15 errors generated.
make[1]: *** [bltVecMath.o] Error 1
make[1]: *** Waiting for unfinished jobs....
make: *** [tkblt] Error 2

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/brewsci/homebrew-science/issues
"""

Sorry if that's not the right place to file this issue.
When installing petsc from homebrew, the symlink that is generated seems wrong :

>> ls /usr/local/lib/petsc 
lrwxr-xr-x  1 viquerat  admin    34B May 13 09:01 /usr/local/lib/petsc -> usr/local/Cellar/petsc/3.10.3_2/lib/petsc

I would expect it to link to /usr/local/Cellar/petsc/3.10.3_2. The current linking pattern generates conflict when building projects relying on petsc with cmake.

I am using Osx Mojave, 10.14.4.

This tap is not maintained. Please consider opening a pull request to migrate this formula to Homebrew/core or a different tap within the Brewsci organization. Please open an issue if you are interested in creating and maintaining a new tap within the Brewsci organization.

Hosting Your Own Tap

Anyone can host their own tap. See Interesting Taps & Forks and How to Create and Maintain a Tap

Brew Log
https://gist.github.com/1d6e6a7c8e7b7138f04dcfe60ada92bc

-- I ran brew upgrade numpy

-- got this error:
File "/usr/local/Cellar/python@2/2.7.15_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/command/build_ext.py", line 159, in finalize_options
self.include_dirs.append(py_include)
AttributeError: 'unicode' object has no attribute 'append'

-- Thanks!

This tap is not maintained. Please consider opening a pull request to migrate this formula to Homebrew/core or a different tap within the Brewsci organization. Please open an issue if you are interested in creating and maintaining a new tap within the Brewsci organization.

Hosting Your Own Tap

Anyone can host their own tap. See Interesting Taps & Forks and How to Create and Maintain a Tap

I now get the following runtime error:

$ gdl
Assertion failed: (semaphore_info != (SemaphoreInfo *) NULL), function LockSemaphoreInfo, file magick/semaphore.c, line 601.
Abort trap: 6

Here is the reinstallation/compile step:

==> Reinstalling 1 broken dependent from source:
brewsci/science/gnudatalanguage
==> Reinstalling brewsci/science/gnudatalanguage 
==> Downloading https://downloads.sourceforge.net/project/gnudatalanguage/gdl/0.9.7/gdl-0.9.7.tgz
==> Downloading from https://netcologne.dl.sourceforge.net/project/gnudatalanguage/gdl/0.9.7/gdl-0.9.7.tgz
######################################################################## 100.0%
==> Downloading https://gist.githubusercontent.com/sjackman/00fb95e10b7775d16924efb6faf462f6/raw/71ed3e05138a20b824c9e68707e403afc0f92c98/gnudatalanguage-hdf5-1.10.patch
######################################################################## 100.0%
==> Patching
==> Applying gnudatalanguage-hdf5-1.10.patch
patching file src/hdf5_fun.cpp
==> Downloading https://downloads.sourceforge.net/project/plplot/plplot/5.12.0%20Source/plplot-5.12.0.tar.gz
==> Downloading from https://netix.dl.sourceforge.net/project/plplot/plplot/5.12.0%20Source/plplot-5.12.0.tar.gz
######################################################################## 100.0%
==> cmake .. -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/gnudatalanguage/0.9.7_4 -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_VERB
==> make
==> make install
==> cmake .. -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/gnudatalanguage/0.9.7_4 -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_VERB
==> make
==> make install
Warning: brewsci/science/gnudatalanguage dependency gcc was built with a different C++ standard
library (libstdc++ from clang). This may cause problems at runtime.
🍺  /usr/local/Cellar/gnudatalanguage/0.9.7_4: 332 files, 11MB, built in 3 minutes 14 seconds

It is possibly related to this known gdl issue?

Good morning,

I have the following error when trying to install SLEPc via Homebrew

==> ./configure --prefix=/usr/local/Cellar/slepc/3.7.4_1/real --with-clean=true --with-arpack-dir=/usr/local/opt/arpack/lib --with-arpack-flags=-lparpack,-larpack


./configure
--prefix=/usr/local/Cellar/slepc/3.7.4_1/real
--with-clean=true
--with-arpack-dir=/usr/local/opt/arpack/lib
--with-arpack-flags=-lparpack,-larpack

Checking environment...
ERROR: PETSC_DIR environment variable is not valid

Moreover, the SLEPc version that is brewed is 3.7 and it should not be compatible with the current PETSc version.

Produced in the linuxbrew docker container.

brew install emboss

Warning: Calling 'depends_on :postgresql' is deprecated!
Use 'depends_on "postgresql"' instead.
/home/linuxbrew/.linuxbrew/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/emboss.rb:22:in `<class:Emboss>'
Please report this to the brewsci/science tap!

Warning: Calling 'depends_on :mysql' is deprecated!
Use 'depends_on "mysql"' instead.

/home/linuxbrew/.linuxbrew/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/emboss.rb:23:in `<class:Emboss>'
Please report this to the brewsci/science tap!
==> Installing emboss from brewsci/science
Error: no implicit conversion of Symbol into String
Please report this bug:
  https://github.com/Linuxbrew/brew/blob/master/docs/Troubleshooting.md#troubleshooting
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/formulary.rb:363:in `extname'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/formulary.rb:363:in `loader_for'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/formulary.rb:280:in `factory'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/dependency.rb:33:in `to_formula'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/formula_installer.rb:498:in `block in expand_dependencies'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/dependency.rb:109:in `block in action'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/dependency.rb:107:in `catch'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/dependency.rb:107:in `action'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/dependency.rb:86:in `block in expand'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/dependency.rb:83:in `each'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/dependency.rb:83:in `expand'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/formula_installer.rb:492:in `expand_dependencies'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/formula_installer.rb:379:in `compute_dependencies'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/formula_installer.rb:134:in `verify_deps_exist'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/formula_installer.rb:127:in `prelude'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/cmd/install.rb:371:in `install_formula'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/cmd/install.rb:227:in `block in install'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/cmd/install.rb:225:in `each'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/cmd/install.rb:225:in `install'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/brew.rb:100:in `<main>'

Hello. Is this tap maintained?

I met an error message when paraview installing although python@2 is installed.

No libpythonX.Y.{dylib|so|a} file found!

How about changing paraview.rb

58         python_executable = `which python`.strip

to

python_executable = Utils.popen_read("which python").strip

?
Thank you.