Error - installation latest biobloom

[KristinaGagalova]

Hi Justin I am having the following error

Making install in Common
make[1]: Entering directory '/home/kgagalova/src/biobloom/Common'
make[2]: Entering directory '/home/kgagalova/src/biobloom/Common'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/kgagalova/src/biobloom/Common'
make[1]: Leaving directory '/home/kgagalova/src/biobloom/Common'
Making install in BioBloomMaker
make[1]: Entering directory '/home/kgagalova/src/biobloom/BioBloomMaker'
/home/kgagalova/miniconda3/envs/py3.6/bin/x86_64-conda_cos6-linux-gnu-c++ -DHAVE_CONFIG_H -I. -I..  -I/home/kgagalova/src/biobloom/BioBloomMaker -I/home/kgagalova/src/biobloom/Common -I/home/kgagalova/src/biobloom -I/home/kgagalova/src/biobloom -isystem/home/kgagalova/bin/boost/include   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/kgagalova/miniconda3/envs/py3.6/include -Wall -Wextra -Werror  -fopenmp -std=c++11 -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/kgagalova/miniconda3/envs/py3.6/include -MT biobloommimaker-BioBloomMIMaker.o -MD -MP -MF .deps/biobloommimaker-BioBloomMIMaker.Tpo -c -o biobloommimaker-BioBloomMIMaker.o `test -f 'BioBloomMIMaker.cpp' || echo '/home/kgagalova/src/biobloom/BioBloomMaker/'`BioBloomMIMaker.cpp
In file included from MIBFGen.hpp:20:0,
                 from BioBloomMIMaker.cpp:18:
../Common/sntHashIterator.hpp: In constructor 'sntHashIterator::sntHashIterator(const string&, const std::vector<std::vector<unsigned int> >&, unsigned int, unsigned int, unsigned int, size_t)':
../Common/sntHashIterator.hpp:30:47: error: unused parameter 'seed' [-Werror=unused-parameter]
    const std::vector<std::vector<unsigned> > &seed, unsigned h,
                                               ^~~~
../Common/sntHashIterator.hpp:31:13: error: unused parameter 'h2' [-Werror=unused-parameter]
    unsigned h2, unsigned k, size_t pos = 0) :
             ^~
cc1plus: all warnings being treated as errors
make[1]: *** [Makefile:452: biobloommimaker-BioBloomMIMaker.o] Error 1
make[1]: Leaving directory '/home/kgagalova/src/biobloom/BioBloomMaker'
make: *** [Makefile:429: install-recursive] Error 1

boost library is 1.55. Any suggestions on that? Thank you iin advance

[JustinChu]

What version of GCC are you using?

[KristinaGagalova]

gcc --version
gcc (Ubuntu 9.3.0-10ubuntu2) 9.3.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE

[KristinaGagalova]

Also: I am trying to install with linuxbrew but gives me

brew install biobloomtools
Error: No available formula with the name "biobloomtools" 
==> Searching for a previously deleted formula (in the last month)...
Error: No previously deleted formula found.
==> Searching for similarly named formulae...
Error: No similarly named formulae found.
==> Searching taps...
==> Searching taps on GitHub...
Error: No formulae found in taps.

Never, mind - this is the correct formula name

brew install brewsci/bio/biobloomtools

[lcoombe]

@KristinaGagalova - Looks like there might be an issue with using gcc 9.3.0? In the meantime, try using the linuxbrew gcc:

[lcoombe@hpce705 biobloom]$ g++ --version
g++ (Homebrew GCC 5.5.0_7) 5.5.0

I was able to successfully compile biobloomtools on my end using that version. We are also seeing some installation issues with clang which is currently holding back biobloomtools from being merged into bioconda.

Also, for linuxbrew installations, if you do this, you won't have to worry about remembering which packages are in brewsci/bio and which are in core:

brew tap brewsci/bio

[KristinaGagalova]

Sounds good, I successfully installed it with linuxbrew

[JustinChu]

Determined to be an issue with BBT and conda the gcc flags it adds. Since I want to make BBT work with conda hopefully this issue will be resolved when I get around to fixing the code for conda.