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bcgsc / orca

:whale: Genomics Research Container Architecture
http://www.bcgsc.ca/services/orca
GNU General Public License v3.0
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discovardenovo #19

Open tmozgach opened 7 years ago

tmozgach commented 7 years ago 
==> Installing homebrew/science/discovardenovo
==> Downloading ftp://ftp.broadinstitute.org/pub/crd/DiscovarDeNovo/latest_source_code/discovardenovo-52488.tar.gz
######################################################################## 100.0%
==> ./configure --disable-silent-rules --prefix=/home/linuxbrew/.linuxbrew/Cellar/discovardenovo/52488
==> make install
Last 15 lines from /home/linuxbrew/.cache/Homebrew/Logs/discovardenovo/02.make:
make[1]: *** [CrossOut] Error 1
make[1]: *** Waiting for unfinished jobs....
libDiscovarDeNovo.a(GapToyCore.o): In function `GapToyCore(int, char**)':
/tmp/discovardenovo-20170816-914-1loskbi/discovardenovo-52488/src/paths/long/large/GapToyCore.cc:625: undefined reference to `digraphE<BaseVec>::O(int) const'
libDiscovarDeNovo.a(FinalFiles.o): In function `FinalFiles(HyperBasevector const&, vec<int, std::allocator<int> > const&, MasterVec<ReadPath> const&, vec<FeudalString<char, std::char_traits<char> >, std::allocator<FeudalString<char, std::char_traits<char> > > > const&, vec<long, std::allocator<long> > const&, FeudalString<char, std::char_traits<char> > const&, FeudalString<char, std::char_traits<char> > const&, int, int, unsigned char, FeudalString<char, std::char_traits<char> > const&, unsigned char const&, FeudalString<char, std::char_traits<char> > const&, std::map<FeudalString<char, std::char_traits<char> >, GapToyResults, std::less<FeudalString<char, std::char_traits<char> > >, std::allocator<std::pair<FeudalString<char, std::char_traits<char> > const, GapToyResults> > >&, FeudalString<char, std::char_traits<char> > const&, FeudalString<char, std::char_traits<char> > const&, vec<int, std::allocator<int> > const&, MasterVec<BaseVec> const&, unsigned char)':
/tmp/discovardenovo-20170816-914-1loskbi/discovardenovo-52488/src/paths/long/large/FinalFiles.cc:249: undefined reference to `digraphE<BaseVec>::O(int) const'
libDiscovarDeNovo.a(Improve60.o): In function `Improve60(HyperBasevector&, vec<int, std::allocator<int> >&, MasterVec<ReadPath>&, MasterVec<BaseVec> const&, MasterVec<PQVecA<MempoolAllocator<unsigned char> > > const&, unsigned char) [clone ._omp_fn.0]':
/tmp/discovardenovo-20170816-914-1loskbi/discovardenovo-52488/src/paths/long/large/Improve60.cc:92: undefined reference to `digraphE<BaseVec>::O(int) const'
/tmp/discovardenovo-20170816-914-1loskbi/discovardenovo-52488/src/paths/long/large/Improve60.cc:94: undefined reference to `digraphE<BaseVec>::O(int) const'
/tmp/discovardenovo-20170816-914-1loskbi/discovardenovo-52488/src/paths/long/large/Improve60.cc:68: undefined reference to `digraphE<BaseVec>::O(int) const'
libDiscovarDeNovo.a(Improve60.o):/tmp/discovardenovo-20170816-914-1loskbi/discovardenovo-52488/src/paths/long/large/Improve60.cc:68: more undefined references to `digraphE<BaseVec>::O(int) const' follow
collect2: error: ld returned 1 exit status
make[1]: *** [DiscovarDeNovo] Error 1
make[1]: Leaving directory `/tmp/discovardenovo-20170816-914-1loskbi/discovardenovo-52488/src'
make: *** [install-recursive] Error 1
sjackman commented 7 years ago

Please report the output of…

brew install discovardenovo
brew gist-logs discovardenovo
tmozgach commented 7 years ago

@sjackman 

==> Installing discovardenovo from homebrew/science
==> Installing dependencies for homebrew/science/discovardenovo: jemalloc
==> Installing homebrew/science/discovardenovo dependency: jemalloc
==> Downloading https://linuxbrew.bintray.com/bottles/jemalloc-5.0.1.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring jemalloc-5.0.1.x86_64_linux.bottle.tar.gz
🍺  /home/linuxbrew/.linuxbrew/Cellar/jemalloc/5.0.1: 16 files, 37.5MB
==> Installing homebrew/science/discovardenovo
==> Downloading ftp://ftp.broadinstitute.org/pub/crd/DiscovarDeNovo/latest_source_code/discovardenovo-52488.tar.gz
######################################################################## 100.0%
==> ./configure --disable-silent-rules --prefix=/home/linuxbrew/.linuxbrew/Cellar/discovardenovo/52488
==> make install
Last 15 lines from /home/linuxbrew/.cache/Homebrew/Logs/discovardenovo/02.make:
make[1]: *** [CrossOut] Error 1
make[1]: *** Waiting for unfinished jobs....
libDiscovarDeNovo.a(GapToyCore.o): In function `GapToyCore(int, char**)':
/tmp/discovardenovo-20170817-1013-3zupua/discovardenovo-52488/src/paths/long/large/GapToyCore.cc:625: undefined reference to `digraphE<BaseVec>::O(int) const'
libDiscovarDeNovo.a(FinalFiles.o): In function `FinalFiles(HyperBasevector const&, vec<int, std::allocator<int> > const&, MasterVec<ReadPath> const&, vec<FeudalString<char, std::char_traits<char> >, std::allocator<FeudalString<char, std::char_traits<char> > > > const&, vec<long, std::allocator<long> > const&, FeudalString<char, std::char_traits<char> > const&, FeudalString<char, std::char_traits<char> > const&, int, int, unsigned char, FeudalString<char, std::char_traits<char> > const&, unsigned char const&, FeudalString<char, std::char_traits<char> > const&, std::map<FeudalString<char, std::char_traits<char> >, GapToyResults, std::less<FeudalString<char, std::char_traits<char> > >, std::allocator<std::pair<FeudalString<char, std::char_traits<char> > const, GapToyResults> > >&, FeudalString<char, std::char_traits<char> > const&, FeudalString<char, std::char_traits<char> > const&, vec<int, std::allocator<int> > const&, MasterVec<BaseVec> const&, unsigned char)':
/tmp/discovardenovo-20170817-1013-3zupua/discovardenovo-52488/src/paths/long/large/FinalFiles.cc:249: undefined reference to `digraphE<BaseVec>::O(int) const'
libDiscovarDeNovo.a(Improve60.o): In function `Improve60(HyperBasevector&, vec<int, std::allocator<int> >&, MasterVec<ReadPath>&, MasterVec<BaseVec> const&, MasterVec<PQVecA<MempoolAllocator<unsigned char> > > const&, unsigned char) [clone ._omp_fn.0]':
/tmp/discovardenovo-20170817-1013-3zupua/discovardenovo-52488/src/paths/long/large/Improve60.cc:92: undefined reference to `digraphE<BaseVec>::O(int) const'
/tmp/discovardenovo-20170817-1013-3zupua/discovardenovo-52488/src/paths/long/large/Improve60.cc:94: undefined reference to `digraphE<BaseVec>::O(int) const'
/tmp/discovardenovo-20170817-1013-3zupua/discovardenovo-52488/src/paths/long/large/Improve60.cc:68: undefined reference to `digraphE<BaseVec>::O(int) const'
libDiscovarDeNovo.a(Improve60.o):/tmp/discovardenovo-20170817-1013-3zupua/discovardenovo-52488/src/paths/long/large/Improve60.cc:68: more undefined references to `digraphE<BaseVec>::O(int) const' follow
collect2: error: ld returned 1 exit status
make[1]: *** [DiscovarDeNovo] Error 1
make[1]: Leaving directory `/tmp/discovardenovo-20170817-1013-3zupua/discovardenovo-52488/src'
make: *** [install-recursive] Error 1

READ THIS: https://github.com/Linuxbrew/brew/blob/master/docs/Troubleshooting.md#troubleshooting
Please do not report this issue to Homebrew/brew or Homebrew/core, which support macOS only.

https://gist.github.com/05a2d84e9265b7da0e8ab31be12281d7

sjackman commented 7 years ago 
/bin/bash ../libtool --tag=CXX   --mode=link g++-4.8 -pthread -fopenmp -fpermissive -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -ggdb -DNDEBUG   -o DiscovarDeNovo DiscovarDeNovo.o libDiscovarDeNovo.a -lz -ljemalloc  
libtool: link: g++-4.8 -pthread -fopenmp -fpermissive -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -ggdb -DNDEBUG -o DiscovarDeNovo DiscovarDeNovo.o  libDiscovarDeNovo.a -lz -ljemalloc -pthread
libDiscovarDeNovo.a(FinalFiles.o): In function `FinalFiles(HyperBasevector const&, vec<int, std::allocator<int> > const&, MasterVec<ReadPath> const&, vec<FeudalString<char, std::char_traits<char> >, std::allocator<FeudalString<char, std::char_traits<char> > > > const&, vec<long, std::allocator<long> > const&, FeudalString<char, std::char_traits<char> > const&, FeudalString<char, std::char_traits<char> > const&, int, int, unsigned char, FeudalString<char, std::char_traits<char> > const&, unsigned char const&, FeudalString<char, std::char_traits<char> > const&, std::map<FeudalString<char, std::char_traits<char> >, GapToyResults, std::less<FeudalString<char, std::char_traits<char> > >, std::allocator<std::pair<FeudalString<char, std::char_traits<char> > const, GapToyResults> > >&, FeudalString<char, std::char_traits<char> > const&, FeudalString<char, std::char_traits<char> > const&, vec<int, std::allocator<int> > const&, MasterVec<BaseVec> const&, unsigned char)':
/tmp/discovardenovo-20170817-1013-3zupua/discovardenovo-52488/src/paths/long/large/FinalFiles.cc:249: undefined reference to `digraphE<BaseVec>::O(int) const'
collect2: error: ld returned 1 exit status
make[1]: *** [CrossOut] Error 1

https://gist.github.com/anonymous/05a2d84e9265b7da0e8ab31be12281d7#file-02-make-L336

sjackman commented 7 years ago

This is a bit of a shot in the dark, but can you try…

# Fix error: undefined reference to `digraphE<BaseVec>::O(int) const'
depends_on "binutils" => :build unless OS.mac?
tmozgach commented 7 years ago

@sjackman didn't solve a problem. Got a the same error.

sjackman commented 7 years ago

We may have to drop discovardenovo if we're unable to find a fix.

tmozgach commented 7 years ago

https://github.com/Homebrew/homebrew-science/issues/6147

sjackman commented 7 years ago

I did manage to compile discovardenovo once with GCC 4.9:

/gsc/btl/linuxbrew/Cellar/discovardenovo/52488/INSTALL_RECEIPT.json

I can't unfortunately tell you what I did to get it to compile. =/