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Does not install with homebrew
See original GitHub issuebrew install homebrew/science/butterflow
==> Tapping homebrew/science
Cloning into '/usr/local/Library/Taps/homebrew/homebrew-science'...
remote: Counting objects: 694, done.
remote: Compressing objects: 100% (687/687), done.
remote: Total 694 (delta 0), reused 52 (delta 0), pack-reused 0
Receiving objects: 100% (694/694), 635.30 KiB | 0 bytes/s, done.
Checking connectivity... done.
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/ann.rb
undefined method `rebuild' for #<BottleSpecification:0x10492d858>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/aragorn.rb
undefined method `rebuild' for #<BottleSpecification:0x10490e070>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/bayestraits.rb
compile error
/usr/local/Library/Taps/homebrew/homebrew-science/bayestraits.rb:35: syntax error, unexpected tSTRING_BEG, expecting tAMPER
system ENV.cc, *args, "-o", "bayestraits"
^
/usr/local/Library/Taps/homebrew/homebrew-science/bayestraits.rb:35: syntax error, unexpected ',', expecting kEND
system ENV.cc, *args, "-o", "bayestraits"
^
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/beagle.rb
undefined method `rebuild' for #<BottleSpecification:0x1047ca6c8>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/biopp.rb
undefined method `rebuild' for #<BottleSpecification:0x1045854d0>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/clustal-w.rb
undefined method `rebuild' for #<BottleSpecification:0x1049c4aa0>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/colpack.rb
undefined method `rebuild' for #<BottleSpecification:0x1049961f0>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/cufflinks.rb
undefined method `rebuild' for #<BottleSpecification:0x1049195d8>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/einspline.rb
undefined method `rebuild' for #<BottleSpecification:0x1053c60d0>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/exonerate.rb
undefined method `rebuild' for #<BottleSpecification:0x10537f6a8>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/fasttree.rb
undefined method `rebuild' for #<BottleSpecification:0x10535aba0>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/flint.rb
undefined method `rebuild' for #<BottleSpecification:0x105314f60>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/geneid.rb
undefined method `rebuild' for #<BottleSpecification:0x10527dae8>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/grabix.rb
undefined method `rebuild' for #<BottleSpecification:0x1051e0860>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/harry.rb
undefined method `rebuild' for #<BottleSpecification:0x105195018>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/hdf5@1.8.rb
No available formula with the name "hdf5@1.8"
In formula file: /usr/local/Library/Taps/homebrew/homebrew-science/hdf5@1.8.rb
Expected to find class Hdf5@18, but only found: Hdf5AT18.
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/hlaminer.rb
undefined method `rebuild' for #<BottleSpecification:0x1051550a8>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/hmmer2.rb
undefined method `rebuild' for #<BottleSpecification:0x10514ad88>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/hyphy.rb
compile error
/usr/local/Library/Taps/homebrew/homebrew-science/hyphy.rb:20: syntax error, unexpected ':', expecting kEND
depends_on mpi: :optional
^
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/iva.rb
undefined method `rebuild' for #<BottleSpecification:0x10509b590>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/jellyfish-1.1.rb
undefined method `rebuild' for #<BottleSpecification:0x1050942e0>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/kmc.rb
"cxx14" is not a recognized standard
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/links-scaffolder.rb
compile error
/usr/local/Library/Taps/homebrew/homebrew-science/links-scaffolder.rb:34: syntax error, unexpected tSTRING_BEG, expecting tAMPER
... system ENV.cxx, *cxxflags, "-c", "-fPIC", "-I#{perl}", "Bl...
^
/usr/local/Library/Taps/homebrew/homebrew-science/links-scaffolder.rb:34: syntax error, unexpected ',', expecting kEND
...stem ENV.cxx, *cxxflags, "-c", "-fPIC", "-I#{perl}", "BloomF...
^
/usr/local/Library/Taps/homebrew/homebrew-science/links-scaffolder.rb:34: syntax error, unexpected ',', expecting kEND
...cxx, *cxxflags, "-c", "-fPIC", "-I#{perl}", "BloomFilter_wra...
^
/usr/local/Library/Taps/homebrew/homebrew-science/links-scaffolder.rb:34: syntax error, unexpected ',', expecting kEND
...s, "-c", "-fPIC", "-I#{perl}", "BloomFilter_wrap.cxx"
^
/usr/local/Library/Taps/homebrew/homebrew-science/links-scaffolder.rb:35: syntax error, unexpected tSTRING_BEG, expecting tAMPER
... system ENV.cxx, *cxxflags, "-shared", "-o", "BloomFilter.#...
^
/usr/local/Library/Taps/homebrew/homebrew-science/links-scaffolder.rb:35: syntax error, unexpected ',', expecting kEND
...ENV.cxx, *cxxflags, "-shared", "-o", "BloomFilter.#{so}", "B...
^
/usr/local/Library/Taps/homebrew/homebrew-science/links-scaffolder.rb:35: syntax error, unexpected ',', expecting kEND
...x, *cxxflags, "-shared", "-o", "BloomFilter.#{so}", "BloomFi...
^
/usr/local/Library/Taps/homebrew/homebrew-science/links-scaffolder.rb:35: syntax error, unexpected ',', expecting kEND
...d", "-o", "BloomFilter.#{so}", "BloomFilter_wrap.o", "-L#{pe...
^
/usr/local/Library/Taps/homebrew/homebrew-science/links-scaffolder.rb:35: syntax error, unexpected ',', expecting kEND
....#{so}", "BloomFilter_wrap.o", "-L#{perl}", "-lperl"
^
/usr/local/Library/Taps/homebrew/homebrew-science/links-scaffolder.rb:35: syntax error, unexpected ',', expecting kEND
...omFilter_wrap.o", "-L#{perl}", "-lperl"
^
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/mcl.rb
undefined method `rebuild' for #<BottleSpecification:0x1051a1340>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/metaphlan.rb
undefined method `rebuild' for #<BottleSpecification:0x105167e38>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/metis.rb
undefined method `rebuild' for #<BottleSpecification:0x105156f48>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/multi-worm-tracker.rb
undefined method `rebuild' for #<BottleSpecification:0x10505d0d8>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/ncl.rb
undefined method `rebuild' for #<BottleSpecification:0x104fe6fa0>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/neuron.rb
undefined method `rebuild' for #<BottleSpecification:0x104fa8db8>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/nfft.rb
undefined method `rebuild' for #<BottleSpecification:0x104f8a890>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/oases.rb
undefined method `rebuild' for #<BottleSpecification:0x104f393a0>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/opencv.rb
undefined method `rebuild' for #<BottleSpecification:0x104e5a650>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/openni2.rb
undefined method `version_scheme' for #<Class:0x105318598>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/pcb.rb
undefined method `version_scheme' for Formulary::FormulaNamespacec5091eb1842699f6ce3d04293a715f7d::Pcb:Class
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/phlawd.rb
undefined method `rebuild' for #<BottleSpecification:0x1050c6da8>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/plink.rb
undefined method `rebuild' for #<BottleSpecification:0x104fe89b8>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/populations.rb
compile error
/usr/local/Library/Taps/homebrew/homebrew-science/populations.rb:30: syntax error, unexpected tSTRING_BEG, expecting tAMPER
...make", ".", *std_cmake_args, "-DCMAKE_PREFIX_PATH=#{Formula[...
^
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/r-gui.rb
compile error
/usr/local/Library/Taps/homebrew/homebrew-science/r-gui.rb:3: syntax error, unexpected ':', expecting ')'
satisfy(build_env: false) { OS.mac? }
^
/usr/local/Library/Taps/homebrew/homebrew-science/r-gui.rb:3: syntax error, unexpected '}', expecting kEND
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/repeatscout.rb
undefined method `rebuild' for #<BottleSpecification:0x104ddd1f0>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/rnammer.rb
undefined method `rebuild' for #<BottleSpecification:0x104dc95d8>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/rstudio-server.rb
compile error
/usr/local/Library/Taps/homebrew/homebrew-science/rstudio-server.rb:216: syntax error, unexpected ')'
/usr/local/Library/Taps/homebrew/homebrew-science/rstudio-server.rb:265: syntax error, unexpected $end, expecting kEND
__END__
^
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/samtools@0.1.rb
No available formula with the name "samtools@0.1"
In formula file: /usr/local/Library/Taps/homebrew/homebrew-science/samtools@0.1.rb
Expected to find class Samtools@01, but only found: SamtoolsAT01.
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/scram.rb
"cxx14" is not a recognized standard
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/sdsl-lite.rb
compile error
/usr/local/Library/Taps/homebrew/homebrew-science/sdsl-lite.rb:40: syntax error, unexpected tSTRING_BEG, expecting tAMPER
system *ENV.cxx.split, "-o", exe,
^
/usr/local/Library/Taps/homebrew/homebrew-science/sdsl-lite.rb:40: syntax error, unexpected ',', expecting kEND
system *ENV.cxx.split, "-o", exe,
^
/usr/local/Library/Taps/homebrew/homebrew-science/sdsl-lite.rb:41: syntax error, unexpected ',', expecting tCOLON2 or '[' or '.'
"-I#{opt_include}", pkgshare/"examples/fm-index.cpp",
^
/usr/local/Library/Taps/homebrew/homebrew-science/sdsl-lite.rb:41: syntax error, unexpected ',', expecting kEND
/usr/local/Library/Taps/homebrew/homebrew-science/sdsl-lite.rb:42: syntax error, unexpected ',', expecting kEND
"-L#{opt_lib}", "-lsdsl", "-ldivsufsort", "-ldivsufsort64"
^
/usr/local/Library/Taps/homebrew/homebrew-science/sdsl-lite.rb:42: syntax error, unexpected ',', expecting kEND
"-L#{opt_lib}", "-lsdsl", "-ldivsufsort", "-ldivsufsort64"
^
/usr/local/Library/Taps/homebrew/homebrew-science/sdsl-lite.rb:42: syntax error, unexpected ',', expecting kEND
"-L#{opt_lib}", "-lsdsl", "-ldivsufsort", "-ldivsufsort64"
^
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/sfscode.rb
undefined method `rebuild' for #<BottleSpecification:0x104cf6d18>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/simpleitk.rb
undefined method `version_scheme' for #<Class:0x1053d0210>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/siril.rb
undefined method `rebuild' for #<BottleSpecification:0x1053aaad8>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/snap.rb
undefined method `rebuild' for #<BottleSpecification:0x1052cae10>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/tamarin-prover.rb
compile error
/usr/local/Library/Taps/homebrew/homebrew-science/tamarin-prover.rb:34: syntax error, unexpected tSTRING_BEG, expecting tAMPER
..."stack", "-j#{jobs}", *args, "install", "--flag", "tamarin-p...
^
/usr/local/Library/Taps/homebrew/homebrew-science/tamarin-prover.rb:34: syntax error, unexpected ',', expecting kEND
..."-j#{jobs}", *args, "install", "--flag", "tamarin-prover:thr...
^
/usr/local/Library/Taps/homebrew/homebrew-science/tamarin-prover.rb:34: syntax error, unexpected ',', expecting kEND
...", *args, "install", "--flag", "tamarin-prover:threaded"
^
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/trimal.rb
undefined method `rebuild' for #<BottleSpecification:0x104d49590>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/veclibfort.rb
compile error
/usr/local/Library/Taps/homebrew/homebrew-science/veclibfort.rb:3: syntax error, unexpected ':', expecting ')'
satisfy(build_env: false) { OS.mac? }
^
/usr/local/Library/Taps/homebrew/homebrew-science/veclibfort.rb:3: syntax error, unexpected '}', expecting kEND
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/velvet.rb
undefined method `rebuild' for #<BottleSpecification:0x104ca85f0>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/weblogo.rb
undefined method `rebuild' for #<BottleSpecification:0x104a59790>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/wfdb.rb
undefined method `rebuild' for #<BottleSpecification:0x104a49930>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/wiggletools.rb
undefined method `rebuild' for #<BottleSpecification:0x104a408f8>
Error: Invalid formula: /usr/local/Library/Taps/homebrew/homebrew-science/xraylib.rb
undefined method `rebuild' for #<BottleSpecification:0x1049cc020>
Error: Cannot tap homebrew/science: invalid syntax in tap!
Issue Analytics
- State:
- Created 6 years ago
- Comments:5
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python setuptools is not using clang++ for c++ files. Brew installation is broken as well
`building ‘butterflow.ocl’ extension
/usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c butterflow/ocl.cpp -o build/temp.macosx-10.6-intel-2.7/butterflow/ocl.o -I/usr/local/opt/opencv@2/include -Wno-unused-variable -Wno-unused-function -Wno-shorten-64-to-32 -Wno-overloaded-virtual -Wno-#warnings
warning: include path for stdlibc++ headers not found; pass ‘-stdlib=libc++’ on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
butterflow/ocl.cpp:2:10: fatal error: ‘iostream’ file not found `
try this - twice
brew update