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New g++5, boost. Lobsrt fails. #88

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tmozgach opened this issue Sep 1, 2017 · 1 comment
Open

New g++5, boost. Lobsrt fails. #88

tmozgach opened this issue Sep 1, 2017 · 1 comment

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@tmozgach
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tmozgach commented Sep 1, 2017

Hello, I am on of the contributor for homebrew and recently new version of g++5 and boost have been updated and there is error:


==> brew install --build-bottle --verbose homebrew/science/lobstr
==> Installing lobstr from homebrew/science
git config --replace-all homebrew.private false
==> Downloading https://github.com/mgymrek/lobstr-code/releases/download/v4.0.6/lobSTR-4.0.6.tar.gz
Already downloaded: /home/linuxbrew/.cache/Homebrew/lobstr-4.0.6.tar.gz
==> Verifying lobstr-4.0.6.tar.gz checksum
tar xzf /home/linuxbrew/.cache/Homebrew/lobstr-4.0.6.tar.gz
==> ./configure --prefix=/home/linuxbrew/.linuxbrew/Cellar/lobstr/4.0.6_3 --disable-dependency-tracking
.
==> make
.
Last 150 lines from /home/linuxbrew/.cache/Homebrew/Logs/lobstr/02.make:
2017-08-31 19:09:28 +0000

make

make  all-recursive
make[1]: Entering directory '/tmp/lobstr-20170831-4088-1ol7xyc/lobSTR-4.0.6'
Making all in m4
make[2]: Entering directory '/tmp/lobstr-20170831-4088-1ol7xyc/lobSTR-4.0.6/m4'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/tmp/lobstr-20170831-4088-1ol7xyc/lobSTR-4.0.6/m4'
Making all in src
make[2]: Entering directory '/tmp/lobstr-20170831-4088-1ol7xyc/lobSTR-4.0.6/src'
g++-5 -DHAVE_CONFIG_H -I. -I..   -I../src/ -I../ -I/home/linuxbrew/.linuxbrew/Cellar/gsl/2.4/include -I/usr/include   -g -O2 -Wall -Wextra -Wswitch-default -Wno-strict-aliasing -pthread -D_GIT_VERSION="\"4.0.6\"" -D_MACHTYPE="\"x86_64\""  -c -o liblobstr_a-AlignmentUtils.o `test -f 'AlignmentUtils.cpp' || echo './'`AlignmentUtils.cpp
g++-5 -DHAVE_CONFIG_H -I. -I..   -I../src/ -I../ -I/home/linuxbrew/.linuxbrew/Cellar/gsl/2.4/include -I/usr/include   -g -O2 -Wall -Wextra -Wswitch-default -Wno-strict-aliasing -pthread -D_GIT_VERSION="\"4.0.6\"" -D_MACHTYPE="\"x86_64\""  -c -o liblobstr_a-BamFileReader.o `test -f 'BamFileReader.cpp' || echo './'`BamFileReader.cpp
g++-5 -DHAVE_CONFIG_H -I. -I..   -I../src/ -I../ -I/home/linuxbrew/.linuxbrew/Cellar/gsl/2.4/include -I/usr/include   -g -O2 -Wall -Wextra -Wswitch-default -Wno-strict-aliasing -pthread -D_GIT_VERSION="\"4.0.6\"" -D_MACHTYPE="\"x86_64\""  -c -o liblobstr_a-BamPairedFileReader.o `test -f 'BamPairedFileReader.cpp' || echo './'`BamPairedFileReader.cpp
g++-5 -DHAVE_CONFIG_H -I. -I..   -I../src/ -I../ -I/home/linuxbrew/.linuxbrew/Cellar/gsl/2.4/include -I/usr/include   -g -O2 -Wall -Wextra -Wswitch-default -Wno-strict-aliasing -pthread -D_GIT_VERSION="\"4.0.6\"" -D_MACHTYPE="\"x86_64\""  -c -o liblobstr_a-BWAReadAligner.o `test -f 'BWAReadAligner.cpp' || echo './'`BWAReadAligner.cpp
g++-5 -DHAVE_CONFIG_H -I. -I..   -I../src/ -I../ -I/home/linuxbrew/.linuxbrew/Cellar/gsl/2.4/include -I/usr/include   -g -O2 -Wall -Wextra -Wswitch-default -Wno-strict-aliasing -pthread -D_GIT_VERSION="\"4.0.6\"" -D_MACHTYPE="\"x86_64\""  -c -o liblobstr_a-common.o `test -f 'common.cpp' || echo './'`common.cpp
g++-5 -DHAVE_CONFIG_H -I. -I..   -I../src/ -I../ -I/home/linuxbrew/.linuxbrew/Cellar/gsl/2.4/include -I/usr/include   -g -O2 -Wall -Wextra -Wswitch-default -Wno-strict-aliasing -pthread -D_GIT_VERSION="\"4.0.6\"" -D_MACHTYPE="\"x86_64\""  -c -o liblobstr_a-EntropyDetection.o `test -f 'EntropyDetection.cpp' || echo './'`EntropyDetection.cpp
common.cpp: In function ‘bool fexists(const char*)’:
common.cpp:195:10: error: cannot convert ‘std::ifstream {aka std::basic_ifstream<char>}’ to ‘bool’ in return
   return ifile;
          ^
Makefile:1958: recipe for target 'liblobstr_a-common.o' failed
make[2]: *** [liblobstr_a-common.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory '/tmp/lobstr-20170831-4088-1ol7xyc/lobSTR-4.0.6/src'
Makefile:441: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/tmp/lobstr-20170831-4088-1ol7xyc/lobSTR-4.0.6'
Makefile:373: recipe for target 'all' failed
make: *** [all] Error 2

sjackman added a commit to sjackman/lobstr-code that referenced this issue Sep 2, 2017
@sjackman
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sjackman commented Sep 2, 2017

I've opened PR #89 to hopefully address this issue.

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