installation fails undefined reference to BamTools functions
wiraki opened this issue · comments
Hello,
I am trying to install whamg with
git clone --recursive https://github.com/zeeev/wham.git; cd wham; make
I have seen a couple of other issues referring to similar problems but I couldn't fix it myself. Here is the part that raises the error:
g++ -fstack-protector-all -Wall -DVERSION=\"v1.7.0-311-g4e8c-dirty\" -std=c++0x -Wno-sign-compare -O3 -Isrc/lib -Isrc/bamtools/include -Isrc/bamtools/src -Isrc/ -Isrc/fastahack -Isrc/Complete-Striped-Smith-Waterman-Library/src/ src/bin/whamg.cpp src/bamtools/lib/libbamtools.a src/obj/entropy.o src/obj/read_pileup.o src/obj/split.o src/obj/readPileUp.o src/obj/flag.o src/fastahack/Fasta.o src/Complete-Striped-Smith-Waterman-Library/src/ssw_cpp.o src/Complete-Striped-Smith-Waterman-Library/src/ssw.o -o bin/whamg -fopenmp -lz -lm
src/bin/whamg.cpp: In function ‘void findPairs(std::vector<node*>&, breakpoint*, std::map<int, std::map<int, breakpoint*> >&)’:
src/bin/whamg.cpp:1706:9: warning: variable ‘lmax’ set but not used [-Wunused-but-set-variable]
int lmax = 0;
^
src/bin/whamg.cpp:1707:9: warning: variable ‘rmax’ set but not used [-Wunused-but-set-variable]
int rmax = 0;
^
src/bin/whamg.cpp:1709:9: warning: variable ‘edsn’ set but not used [-Wunused-but-set-variable]
int edsn = 0;
^
/tmp/cc2QE5uH.o: In function `bool BamTools::BamAlignment::GetTag<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&) const [clone .part.22]':
whamg.cpp:(.text+0x73): undefined reference to `BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char*&, unsigned int const&, unsigned int&) const'
/tmp/cc2QE5uH.o: In function `loadBam(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)':
whamg.cpp:(.text+0x5cf3): undefined reference to `BamTools::BamReader::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
whamg.cpp:(.text+0x6745): undefined reference to `BamTools::BamReader::OpenIndex(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/tmp/cc2QE5uH.o: In function `gatherBamStats(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)':
whamg.cpp:(.text+0x9b2b): undefined reference to `BamTools::BamReader::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
whamg.cpp:(.text+0x9c37): undefined reference to `BamTools::BamReader::OpenIndex(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/tmp/cc2QE5uH.o: In function `runRegion(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, int, std::vector<BamTools::RefData, std::allocator<BamTools::RefData> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)':
whamg.cpp:(.text+0xd33e): undefined reference to `BamTools::BamReader::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
whamg.cpp:(.text+0xd438): undefined reference to `BamTools::BamReader::OpenIndex(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/tmp/cc2QE5uH.o: In function `main':
whamg.cpp:(.text.startup+0xf4): undefined reference to `BamTools::BamMultiReader::Open(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)'
src/obj/readPileUp.o: In function `readPileUp::processPileup(long*)':
readPileUp.cpp:(.text+0x28b4): undefined reference to `BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char*&, unsigned int const&, unsigned int&) const'
collect2: error: ld returned 1 exit status
make: *** [bin/whamg] Error 1
Would appreciate some help :)
Hi @mpauper,
What system are you using? Do you have a newer version of bamtools in your path?
Hi @zeeev ,
Thanks for the prompt reply!
I am on a CentOS 7.4 system.
I do not have any other bamtools in my path.
cmake version 3.12.1
gcc version 5.1.0
Hello,
I am not sure that this is the correct way to do it but here is what I tried:
> cd src/bamtools/
> git pull
You are not currently on a branch. Please specify which
branch you want to merge with. See git-pull(1) for details.
> git checkout master
Previous HEAD position was 2d7685d... Clarified documentation on BamReader::GetNextAlignmentCore
Switched to branch 'master'
> git pull
Already up-to-date.
> cd ../..
> make
I still have the same error, however.
Old thread, but I wanted to note that I had similar issues and was able to resolve them by using an older version of Cmake and gcc. I switched from Cmake 3.16 and gcc 7.1 to Cmake 3.5.1 and gcc 4.8.5 and the compilation worked.
Hi Shawn, Did you try updating the checkout of bamtools prior to the build, like I suggested? Did that solve the problem? If so, I will just update the bamtools checkout. —Zev
…
On Aug 20, 2018, at 2:41 PM, Shawn Rynearson @.***> wrote: @zeeev https://github.com/zeeev I think this is related to the issue <#47> I opened. Possibility related to the bamtools build in your makefile. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#49 (comment)>, or mute the thread https://github.com/notifications/unsubscribe-auth/AAnxIRSrZVlsIv5mrjSiWYi2-su4AR-5ks5uSy0jgaJpZM4V_upl.
Hi, @zeeev I have the same problem as #47 and I have read about the other problem #47, and the solution you proposed. But I'm not sure I understand what do you mean by "go into the bamtools submodule, in whamg, prior to building and then update the branch?" Could you give more detailed instructions about it and I will try it immediately.
Many thanks.
I tried to change LBAMTOOLS=src/bamtools/lib/libbamtools.a to LBAMTOOLS=src/bamtools/build/src/api/libbamtools.a
It works. Though I'm not sure if it also because I made other changes to my environment.
Quentin