Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Compile issues - version dependencies? #284

Open
Neato-Nick opened this issue Dec 4, 2023 · 9 comments
Open

Compile issues - version dependencies? #284

Neato-Nick opened this issue Dec 4, 2023 · 9 comments

Comments

@Neato-Nick
Copy link

Neato-Nick commented Dec 4, 2023 •
edited
Loading

Hi, I've gotten various compilation issues as I've tried various installs of root, htslib, and samtools available on my HPC. Exactly which versions are required for install?

I've tried samtools 1.9 and 1.13. In both cases, I linked the samtools src dir that also contained an htslib* sub-dir contained libhts.a.
I'm using root 6.10 and have run thisroot.sh. echo $ROOTSYS indicated this worked. I've tried gcc 4.94, 8.3, and 12.3.1.

Lastly, here is my OS info:

$ cat /etc/os-release
NAME="Red Hat Enterprise Linux Server"
VERSION="7.9 (Maipo)"
ID="rhel"
ID_LIKE="fedora"
VARIANT="Server"
VARIANT_ID="server"
VERSION_ID="7.9"
PRETTY_NAME="Red Hat Enterprise Linux Server 7.9 (Maipo)"

When I compile, I get this error

$ make OMP=no
Compiling with NO parallel support
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\"  -o cnvnator obj/cnvnator.o obj/EXOnator.o obj/IO.o obj/Visualizer.o obj/HisMaker.o obj/AliParser.o obj/FastaParser.o obj/VcfParser.o obj/Genotyper.o obj/Interval.o obj/Genome.o samtools/libbam.a samtools/htslib-1.9/libhts.a -lz -lbz2 -lcurl -llzma -lreadline -L/gpfs/runtime/opt/root/6.10/lib      -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore
/usr/bin/ld: samtools/htslib-1.9/libhts.a(thread_pool.o): undefined reference to symbol 'pthread_mutexattr_settype@@GLIBC_2.2.5'
//usr/lib64/libpthread.so.0: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make: *** [cnvnator] Error 1

Following #15 (comment) I edited the Makefile with -lpthread and I got a new error. It's the same whether or not I compile with OMP

First with just make I got errors related to libcrypto:

/usr/bin/ld: samtools/htslib-1.13/libhts.a(hfile_s3.o): undefined reference to symbol 'EVP_sha256@@libcrypto.so.10'

So I did the alternate compilation suggested:

$ make LIBS="-lcrypto"
Compiling with parallel (OpenMP) support
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -o cnvnator obj/cnvnator.o obj/EXOnator.o obj/IO.o obj/Visualizer.o obj/HisMaker.o obj/AliParser.o obj/FastaParser.o obj/VcfParser.o obj/Genotyper.o obj/Interval.o obj/Genome.o samtools/libbam.a samtools/htslib-1.13/libhts.a -lcrypto -lz -lbz2 -lcurl -llzma -lreadline -L/gpfs/runtime/opt/root/6.10/lib      -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore
obj/IO.o: In function `IO::treeName(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) [clone .constprop.114]':
IO.cpp:(.text+0xd9): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x170): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/IO.o: In function `IO::treeName(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
IO.cpp:(.text+0x279): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x310): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/IO.o: In function `IO::IO(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
IO.cpp:(.text+0xc85): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/IO.o: In function `IO::signalName(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int)':
IO.cpp:(.text+0x1a96): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x1ae9): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x1ccb): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x1d1e): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x26c1): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x2a5c): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x2aaf): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x2ba7): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x2bfa): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x2cb6): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x2d09): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x2d6d): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x2dc0): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x2ef4): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x2f47): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x3027): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x307a): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x30de): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x3131): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x3195): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x31e8): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x324c): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x329f): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x3303): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x3356): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x33ba): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x340d): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x3471): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x34c4): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x3528): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x357b): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x35df): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x3632): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x36a8): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x36fb): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x37e4): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x3837): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x38c2): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x3915): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x39a0): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x39f3): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x3a7e): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x3ad1): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x3b5c): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x3baf): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x3c3a): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x3c8d): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x3d18): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x3d6b): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/IO.o: In function `IO::newSignalTH1(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int, int, double, double)':
IO.cpp:(.text+0x6120): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x626f): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/IO.o: In function `IO::newSignalTH2(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int, int, double, double, int, double, double)':
IO.cpp:(.text+0x64b8): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
IO.cpp:(.text+0x662a): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/Visualizer.o: In function `Visualizer::parseRegionOption(TString, TString&, int&, int&, TString&)':
Visualizer.cpp:(.text+0x58ea): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
Visualizer.cpp:(.text+0x59d1): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
Visualizer.cpp:(.text+0x5a45): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/Visualizer.o: In function `Visualizer::generateView(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, TVirtualPad*)':
Visualizer.cpp:(.text+0x61c8): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
Visualizer.cpp:(.text+0x6629): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
Visualizer.cpp:(.text+0x6dbe): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/Visualizer.o:Visualizer.cpp:(.text+0x739e): more undefined references to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' follow
obj/HisMaker.o: In function `HisMaker::generateView(TString, int, int, bool, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)':
HisMaker.cpp:(.text+0x164b3): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
HisMaker.cpp:(.text+0x165b9): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/HisMaker.o: In function `HisMaker::genotype(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int, bool, bool)':
HisMaker.cpp:(.text+0x16e30): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/HisMaker.o: In function `HisMaker::printRegion(TString, int, int, bool, bool)':
HisMaker.cpp:(.text+0x173c2): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
HisMaker.cpp:(.text+0x17ce8): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/HisMaker.o: In function `HisMaker::produceHistogramsNew(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)':
HisMaker.cpp:(.text+0x1a3ef): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/HisMaker.o: In function `HisMaker::mergeTrees(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)':
HisMaker.cpp:(.text+0x1be09): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/HisMaker.o: In function `HisMaker::eval(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int, bool, bool)':
HisMaker.cpp:(.text+0x2032a): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/HisMaker.o: In function `HisMaker::partition(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int, bool, bool, bool, bool, int)':
HisMaker.cpp:(.text+0x23f72): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
HisMaker.cpp:(.text+0x24332): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/HisMaker.o: In function `HisMaker::partition2D(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int, bool, bool, bool, bool, int)':
HisMaker.cpp:(.text+0x25182): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
HisMaker.cpp:(.text+0x25201): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
HisMaker.cpp:(.text+0x25699): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/HisMaker.o:HisMaker.cpp:(.text+0x28397): more undefined references to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' follow
obj/HisMaker.o: In function `HisMaker::generateViewBAF(TString, int, int, bool, bool)':
HisMaker.cpp:(.text+0x2b031): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/HisMaker.o: In function `HisMaker::generateView(bool, bool)':
HisMaker.cpp:(.text+0x2bcda): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
HisMaker.cpp:(.text+0x2c812): undefined reference to `TString::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/HisMaker.o: In function `HisMaker::view(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int, bool, bool)':
HisMaker.cpp:(.text+0x2d60a): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/HisMaker.o: In function `HisMaker::produceHistograms(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int, bool)':
HisMaker.cpp:(.text+0x30997): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
HisMaker.cpp:(.text+0x309d6): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
HisMaker.cpp:(.text+0x30a1e): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
HisMaker.cpp:(.text+0x30a8e): undefined reference to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
obj/HisMaker.o:HisMaker.cpp:(.text+0x30bd3): more undefined references to `TString::TString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' follow
collect2: error: ld returned 1 exit status
make: *** [cnvnator] Error 1
@Neato-Nick
Copy link
Author

Neato-Nick commented Dec 4, 2023 •
edited
Loading

I see the README says to use the latest release of samtools. I did that (samtools 1.18) and get a different error. I got the above by using samtools 1.9, which I found worked from a thread from a few years ago #180

Here's the error using samtools 1.18

(base) [ncauldro@node1324 src]$ make LIBS="-lcrypto"
Compiling with parallel (OpenMP) support
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.18 -Isamtools/htslib-1.18/htslib -c cnvnator.cpp -o obj/cnvnator.o
In file included from cnvnator.cpp:14:0:
AliParser.hh:18:3: error: ‘samfile_t’ does not name a type
   samfile_t   *file;
   ^
AliParser.hh:19:3: error: ‘bam_index_t’ does not name a type
   bam_index_t *index;
   ^
AliParser.hh: In member function ‘std::string AliParser::getQueryName()’:
AliParser.hh:98:69: error: ‘bam1_qname’ was not declared in this scope
   inline string getQueryName() { return (record) ? bam1_qname(record) : ""; }
                                                                     ^
make: *** [obj/cnvnator.o] Error 1

@abyzov
Copy link
Member

abyzov commented Dec 5, 2023 via email

@Neato-Nick
Copy link
Author

Neato-Nick commented Dec 5, 2023 •
edited
Loading

Hi, I checked that header file in samtools/htslib 1.18 and found:
samfile_t - NOT described
bam_index_t - NOT described
bam1_t - is described

in the file CNVnator_v0.4.1/src/samtools/htslib-1.18/htslib/sam.h
(samtools dir is symlinked from my install dir of samtools 1.18)

@Neato-Nick
Copy link
Author

Neato-Nick commented Dec 5, 2023 •
edited
Loading

With samtools 1.9 I get this error. It's much cleaner than the stack I posted in OP for some reason. I chose v1.9 here because it was the "current release" at the time the current version of cnvnator was released.

$ source /path/to/root/6.10/bin/thisroot.sh
$ samtools/samtools --version
samtools 1.9
Using htslib 1.9
Copyright (C) 2018 Genome Research Ltd.
$
$ # Compile with all defaults
$ make
Compiling with parallel (OpenMP) support
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -o cnvnator obj/cnvnator.o obj/EXOnator.o obj/IO.o obj/Visualizer.o obj/HisMaker.o obj/AliParser.o obj/FastaParser.o obj/VcfParser.o obj/Genotyper.o obj/Interval.o obj/Genome.o samtools/libbam.a samtools/htslib-1.9/libhts.a -lz -lbz2 -lcurl -llzma -lreadline -L/gpfs/runtime/opt/root/6.10/lib      -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore
/usr/bin/ld: samtools/htslib-1.9/libhts.a(hfile_s3.o): undefined reference to symbol 'HMAC@@libcrypto.so.10'
//usr/lib64/libcrypto.so.10: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make: *** [cnvnator] Error 1
$
$ # libcrypto error, modified configuration as per cnvnator readme
$ make LIBS="-lcrypto"
Compiling with parallel (OpenMP) support
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -o cnvnator obj/cnvnator.o obj/EXOnator.o obj/IO.o obj/Visualizer.o obj/HisMaker.o obj/AliParser.o obj/FastaParser.o obj/VcfParser.o obj/Genotyper.o obj/Interval.o obj/Genome.o samtools/libbam.a samtools/htslib-1.9/libhts.a -lcrypto -lz -lbz2 -lcurl -llzma -lreadline -L/gpfs/runtime/opt/root/6.10/lib      -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore
/gpfs/runtime/opt/root/6.10/lib/libCore.so: undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)@GLIBCXX_3.4.20'
/gpfs/runtime/opt/root/6.10/lib/libCore.so: undefined reference to `__cxa_throw_bad_array_new_length@CXXABI_1.3.8'
collect2: error: ld returned 1 exit status
make: *** [cnvnator] Error 1
$
$ # try compile without multi-threading
$ make LIBS="-lcrypto" OMP=no
Compiling with NO parallel support
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\"  -o cnvnator obj/cnvnator.o obj/EXOnator.o obj/IO.o obj/Visualizer.o obj/HisMaker.o obj/AliParser.o obj/FastaParser.o obj/VcfParser.o obj/Genotyper.o obj/Interval.o obj/Genome.o samtools/libbam.a samtools/htslib-1.9/libhts.a -lcrypto -lz -lbz2 -lcurl -llzma -lreadline -L/gpfs/runtime/opt/root/6.10/lib      -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore
obj/HisMaker.o: In function `calcLevelsInner(double const*, double const*, bool const*, int, int, double*, double const*, double const*) [clone ._omp_fn.0]':
HisMaker.cpp:(.text+0x2bb): undefined reference to `omp_get_num_threads'
HisMaker.cpp:(.text+0x2c3): undefined reference to `omp_get_thread_num'
HisMaker.cpp:(.text+0x577): undefined reference to `GOMP_barrier'
obj/HisMaker.o: In function `calcLevelsInner(double const*, double const*, bool const*, int, int, double*, double const*, double const*)':
HisMaker.cpp:(.text+0x9293): undefined reference to `GOMP_parallel_start'
HisMaker.cpp:(.text+0x92a5): undefined reference to `GOMP_parallel_end'
/gpfs/runtime/opt/root/6.10/lib/libCore.so: undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)@GLIBCXX_3.4.20'
/gpfs/runtime/opt/root/6.10/lib/libCore.so: undefined reference to `__cxa_throw_bad_array_new_length@CXXABI_1.3.8'
collect2: error: ld returned 1 exit status
make: *** [cnvnator] Error 1

@abyzov
Copy link
Member

abyzov commented Dec 5, 2023 via email

@Neato-Nick
Copy link
Author

Just tried a few combos preceded by make clean and did not have luck. Looks like the error could be stemming from root. What versions are compatible?

(base) [ncauldro@node1317 src]$ make clean
Compiling with parallel (OpenMP) support
rm -fr obj cnvnator
(base) [ncauldro@node1317 src]$ make
Compiling with parallel (OpenMP) support
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c cnvnator.cpp -o obj/cnvnator.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c EXOnator.cpp -o obj/EXOnator.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c IO.cpp -o obj/IO.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c Visualizer.cpp -o obj/Visualizer.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c HisMaker.cpp -o obj/HisMaker.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c AliParser.cpp -o obj/AliParser.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c FastaParser.cpp -o obj/FastaParser.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c VcfParser.cpp -o obj/VcfParser.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c Genotyper.cpp -o obj/Genotyper.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c Interval.cpp -o obj/Interval.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c Genome.cpp -o obj/Genome.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -o cnvnator obj/cnvnator.o obj/EXOnator.o obj/IO.o obj/Visualizer.o obj/HisMaker.o obj/AliParser.o obj/FastaParser.o obj/VcfParser.o obj/Genotyper.o obj/Interval.o obj/Genome.o samtools/libbam.a samtools/htslib-1.9/libhts.a -lz -lbz2 -lcurl -llzma -lreadline -L/gpfs/runtime/opt/root/6.10/lib      -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore
/usr/bin/ld: samtools/htslib-1.9/libhts.a(hfile_s3.o): undefined reference to symbol 'HMAC@@libcrypto.so.10'
//usr/lib64/libcrypto.so.10: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make: *** [cnvnator] Error 1

(base) [ncauldro@node1317 src]$ make clean
Compiling with parallel (OpenMP) support
rm -fr obj cnvnator
(base) [ncauldro@node1317 src]$ make LIBS="-lcrypto"
Compiling with parallel (OpenMP) support
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c cnvnator.cpp -o obj/cnvnator.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c EXOnator.cpp -o obj/EXOnator.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c IO.cpp -o obj/IO.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c Visualizer.cpp -o obj/Visualizer.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c HisMaker.cpp -o obj/HisMaker.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c AliParser.cpp -o obj/AliParser.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c FastaParser.cpp -o obj/FastaParser.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c VcfParser.cpp -o obj/VcfParser.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c Genotyper.cpp -o obj/Genotyper.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c Interval.cpp -o obj/Interval.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c Genome.cpp -o obj/Genome.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -o cnvnator obj/cnvnator.o obj/EXOnator.o obj/IO.o obj/Visualizer.o obj/HisMaker.o obj/AliParser.o obj/FastaParser.o obj/VcfParser.o obj/Genotyper.o obj/Interval.o obj/Genome.o samtools/libbam.a samtools/htslib-1.9/libhts.a -lcrypto -lz -lbz2 -lcurl -llzma -lreadline -L/gpfs/runtime/opt/root/6.10/lib      -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore
/gpfs/runtime/opt/root/6.10/lib/libCore.so: undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)@GLIBCXX_3.4.20'
/gpfs/runtime/opt/root/6.10/lib/libCore.so: undefined reference to `__cxa_throw_bad_array_new_length@CXXABI_1.3.8'
collect2: error: ld returned 1 exit status
make: *** [cnvnator] Error 1

(base) [ncauldro@node1317 src]$ make clean
Compiling with parallel (OpenMP) support
rm -fr obj cnvnator
(base) [ncauldro@node1317 src]$ make LIBS="-lcrypto" OMP=no
Compiling with NO parallel support
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\"  -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c cnvnator.cpp -o obj/cnvnator.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\"  -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c EXOnator.cpp -o obj/EXOnator.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\"  -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c IO.cpp -o obj/IO.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\"  -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c Visualizer.cpp -o obj/Visualizer.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\"  -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c HisMaker.cpp -o obj/HisMaker.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\"  -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c AliParser.cpp -o obj/AliParser.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\"  -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c FastaParser.cpp -o obj/FastaParser.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\"  -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c VcfParser.cpp -o obj/VcfParser.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\"  -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c Genotyper.cpp -o obj/Genotyper.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\"  -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c Interval.cpp -o obj/Interval.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\"  -I/gpfs/runtime/opt/root/6.10/include      -Isamtools -Isamtools/htslib-1.9 -Isamtools/htslib-1.9/htslib -c Genome.cpp -o obj/Genome.o
g++ -O3 -std=c++11 -lpthread -DCNVNATOR_VERSION=\"v0.4.1\"  -o cnvnator obj/cnvnator.o obj/EXOnator.o obj/IO.o obj/Visualizer.o obj/HisMaker.o obj/AliParser.o obj/FastaParser.o obj/VcfParser.o obj/Genotyper.o obj/Interval.o obj/Genome.o samtools/libbam.a samtools/htslib-1.9/libhts.a -lcrypto -lz -lbz2 -lcurl -llzma -lreadline -L/gpfs/runtime/opt/root/6.10/lib      -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore
/gpfs/runtime/opt/root/6.10/lib/libCore.so: undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)@GLIBCXX_3.4.20'
/gpfs/runtime/opt/root/6.10/lib/libCore.so: undefined reference to `__cxa_throw_bad_array_new_length@CXXABI_1.3.8'
collect2: error: ld returned 1 exit status
make: *** [cnvnator] Error 1

@yangliu2009
Copy link

I got the same sam_file error for version 1.9 and 1.16 of samtools/htslib:
AliParser.hh:18:3: error: ?samfile_t? does not name a type; did you mean ?samFile??

The version 1.18 of htslib also doesn't have definition for samfile_t, but still samFile: https://github.com/samtools/htslib/blob/1.18/htslib/sam.h

@abyzov
Copy link
Member

abyzov commented Dec 15, 2023 via email

@yangliu2009
Copy link

I was able to install cnvnator (commit ae7f64f, PR #260 ) with samtools 1.12. Thanks.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@Neato-Nick @abyzov @yangliu2009