Formulae fail after updating boost, linuxbrew

[tmozgach]

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 gcc@4.9 solves
• [x] express => RUN brew install gcc@4.9 solves
• [x] kat RUN brew install gcc@4.9 solves
• [x] mapsembler2 RUN brew install gcc@4.9 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

[tmozgach]

matplotlib is probably responsible for errors (poretools).

[tmozgach]

• [ ] 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

[sjackman]

sga works in empty image =>something influences on it

What's the error message? Please report brew gist-logs sga

[sjackman]

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.

[sjackman]

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

[tmozgach]

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?

[sjackman]

discovar shouldn't need a fix. Is brew test discovar failing? What's the error message?

[sjackman]

Oh, you mean brew install discovar is failing. In that case, add

depends_on "gcc@4.9" => :build

[sjackman]

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?

[tmozgach]

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.

[sjackman]

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?

[tmozgach]

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>'

[tmozgach]

linuxbrew@13b6730f2934:~$ which gcc
/home/linuxbrew/.linuxbrew/bin/gcc

linuxbrew@13b6730f2934:~$ gcc --version
gcc (Homebrew gcc 5.4.0) 5.4.0

[sjackman]

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 gcc@4.9 to the ORCA image it should work.

[tmozgach]

Just instaliing gcc@4.9 works!

[tmozgach]

2017.10.12 Install:

• [ ] kent-tools

[sjackman]

What's the error message?

[tmozgach]

@sjackman It is an automated build, I haven't checked that using a terminal yet.

[91mcurl: (23) Failed writing body (9776 != 16160)

Error: Failed to download resource "kent-tools"
Download failed: https://linuxbrew.bintray.com/bottles-science/kent-tools-353.x86_64_linux.bottle.tar.gz

Warning: Bottle installation failed: building from source.


Error: No space left on device @ dir_s_mkdir - /tmp/homebrew20171013-5-19ydkj3

Removing intermediate container 011074aec7b9

[sjackman]

No space left on device

The disk is full.