bcgsc
Formulae fail after updating boost, linuxbrew
Install:
- [x] sga works in empty image =>something influences on it
Test:
- [ ] circlator https://github.com/Homebrew/homebrew-science/pull/6216
- [x] discovar https://github.com/Homebrew/homebrew-science/pull/6275 => RUN brew install [email protected] solves
- [x] express => RUN brew install [email protected] solves
- [x] kat RUN brew install [email protected] solves
- [x] mapsembler2 RUN brew install [email protected] solves
- [ ] mummer works in empty image =>something influences on it
/home/linuxbrew/.linuxbrew/Cellar/mummer/3.23_2/mummerplot -h 2>&1
Error: homebrew/science/mummer: failed
</U(sage|SAGE)/> expected to be =~
<"Can't use 'defined(%hash)' (Maybe you should just omit the defined()?) at /home/linuxbrew/.linuxbrew/Cellar/mummer/3.23_2/mummerplot line 884.\n">.
- [ ] poretools works in empty image =>something influences on it
==> /home/linuxbrew/.linuxbrew/Cellar/poretools/0.6.0_6/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /tmp/poretools--h5py-20170901-18
Last 15 lines from /home/linuxbrew/.cache/Homebrew/Logs/poretools/06.pip:
Removing source in /tmp/pip-C409WA-build
Command "/home/linuxbrew/.linuxbrew/Cellar/poretools/0.6.0_6/libexec/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-C409WA-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-hdaw0X-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/linuxbrew/.linuxbrew/Cellar/poretools/0.6.0_6/libexec/include/site/python2.7/h5py" failed with error code 1 in /tmp/pip-C409WA-build/
Exception information:
Traceback (most recent call last):
File "/home/linuxbrew/.linuxbrew/lib/python2.7/site-packages/pip/basecommand.py", line 215, in main
status = self.run(options, args)
File "/home/linuxbrew/.linuxbrew/lib/python2.7/site-packages/pip/commands/install.py", line 342, in run
prefix=options.prefix_path,
File "/home/linuxbrew/.linuxbrew/lib/python2.7/site-packages/pip/req/req_set.py", line 784, in install
**kwargs
File "/home/linuxbrew/.linuxbrew/lib/python2.7/site-packages/pip/req/req_install.py", line 878, in install
spinner=spinner,
File "/home/linuxbrew/.linuxbrew/lib/python2.7/site-packages/pip/utils/__init__.py", line 707, in call_subprocess
% (command_desc, proc.returncode, cwd))
InstallationError: Command "/home/linuxbrew/.linuxbrew/Cellar/poretools/0.6.0_6/libexec/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-C409WA-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-hdaw0X-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/linuxbrew/.linuxbrew/Cellar/poretools/0.6.0_6/libexec/include/site/python2.7/h5py" failed with error code 1 in /tmp/pip-C409WA-build/
- [ ] repeatmasker
- [x] sdsl-lite brew test sdsl-lite --cc=gcc-4.9
- [ ] discovar 4.9
- [ ] kat 4.9
- [x] lrsim - perl, solved
- [ ] mapsembler2 4.9
- [ ] mummer not perl.
- [ ] poretools not perl
- [ ] repeatmasker not perl
- [ ] sdsl-lite 4.9
sga works in empty image =>something influences on it
What's the error message? Please report brew gist-logs sga
mummer works in empty image =>something influences on it
That's the version of perl I believe. It doesn't like newer versions of Perl.
poretools works in empty image =>something influences on it
The error message is from h5py. See if you can get a more helpful and verbose error message from brew gist-logs poretools
in the formulae discovar there is
fails_with :gcc => "5" do
cause "error: reference to 'align' is ambiguous. See https://groups.google.com/a/broadinstitute.org/forum/?hl=en&fromgroups=#!topic/discovar-user-forum/zuqNcaRUetA"
end
So, fixing will be tricky?
discovar shouldn't need a fix. Is brew test discovar failing? What's the error message?
Oh, you mean brew install discovar is failing. In that case, add
depends_on "[email protected]" => :build
No need to bump the revision for discovar. brew install discovar should use the bottle and should succeed. What command is failing, and what is the error message?
discovar fails a test. If I compile that with 4.9, it works, but in my image there is no 4.9 and you said that it should work with 5 otherwise it is a bug.
brew install discovar should use the precompiled bottle and succeed. brew test discovar should succeed with gcc-5 (I think). Which command is failing, and what is the error message?
Testing homebrew/science/discovar
Error: homebrew/science/discovar: failed
homebrew/science/discovar cannot be built with any available compilers.
Install Clang or brew install gcc
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/compilers.rb:127:in `compiler'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/compilers.rb:109:in `select_for'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/extend/ENV/shared.rb:176:in `compiler'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/extend/ENV/std.rb:78:in `setup_build_environment'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/test.rb:22:in `<main>'
linuxbrew@13b6730f2934:~$ which gcc
/home/linuxbrew/.linuxbrew/bin/gcc
linuxbrew@13b6730f2934:~$ gcc --version
gcc (Homebrew gcc 5.4.0) 5.4.0
Okay. Good to know. That's kind of a bug in brew test, sort of. It'd be tricky to fix though. If you add [email protected] to the ORCA image it should work.
@sjackman It is an automated build, I haven't checked that using a terminal yet.
[91mcurl: (23) Failed writing body (9776 != 16160)
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[91mError: Failed to download resource "kent-tools"
Download failed: https://linuxbrew.bintray.com/bottles-science/kent-tools-353.x86_64_linux.bottle.tar.gz
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[91mWarning: Bottle installation failed: building from source.[0m
[91m
[0m
[91mError: No space left on device @ dir_s_mkdir - /tmp/homebrew20171013-5-19ydkj3
[0m
Removing intermediate container 011074aec7b9