installation fault

[flapa86]

Hi, I have this error

fatal: Not a git repository (or any of the parent directories): .git
make -C /opt/install-bin/rvtests-master/src release
fatal: Not a git repository (or any of the parent directories): .git
.....

/bin/ld: cannot find -lpthread
/bin/ld: cannot find -lstdc++
/bin/ld: cannot find -lm
/bin/ld: cannot find -lpthread
/bin/ld: cannot find -lc
collect2: error: ld returned 1 exit status
make[1]: *** [/opt/install-bin/rvtests-master/executable/rvtest] Error 1
make[1]: Leaving directory `/opt/install-bin/rvtests-master/src'
make: *** [release] Error 2

[zhanxw]

Which system did you use? More information will be helpful.

…

On Tue, Nov 17, 2020 at 10:25 AM flapa86 ***@***.***> wrote: Hi, I have this error make[1]: Entering directory /opt/install-bin/rvtests-master/src' g++ -o /opt/install-bin/rvtests-master/executable/rvtest Main.o DataConsolidator.o ModelFitter.o TabixUtil.o ModelManager.o ModelParser.o Model.o GenotypeExtractor.o VCFGenotypeExtractor.o BGenGenotypeExtractor.o KGGGenotypeExtractor.o DataLoader.o GenotypeCounter.o SingleDummy.o -O2 -DNDEBUG -D__STDC_LIMIT_MACROS -std=c++0x -Wall -Wno-unused-function -fopenmp -DGIT_VERSION="\"Unknown\"" -D_USE_KNETFILE -static /opt/install-bin/rvtests-master/regression/lib-regression.a /opt/install-bin/rvtests-master/libVcf/lib-vcf.a /opt/install-bin/rvtests-master/libBgen/lib-bgen.a /opt/install-bin/rvtests-master/base/lib-base.a /opt/install-bin/rvtests-master/libsrc/lib-goncalo.a /opt/install-bin/rvtests-master/third/samtools/bcftools/libbcf.a /opt/install-bin/rvtests-master/third/samtools/libbam.a /opt/install-bin/rvtests-master/third/tabix/libtabix.a /opt/install-bin/rvtests-master/third/pcre/lib/libpcreposix.a /opt/install-bin/rvtests-master/third/pcre/lib/libpcre.a /opt/install-bin/rvtests-master/third/gsl/lib/libgsl.a /opt/install-bin/rvtests-master/third/zlib/libz.a /opt/install-bin/rvtests-master/third/bzip2/libbz2.a /opt/install-bin/rvtests-master/third/nlopt/lib/libnlopt.a /opt/install-bin/rvtests-master/third/sqlite/lib/libsqlite3.a /opt/install-bin/rvtests-master/third/zstd/lib/libzstd.a /opt/install-bin/rvtests-master/third/cnpy/libcnpy.a -lm -lpthread /bin/ld: cannot find -lpthread /bin/ld: cannot find -lstdc++ /bin/ld: cannot find -lm /bin/ld: cannot find -lpthread /bin/ld: cannot find -lc collect2: error: ld returned 1 exit status make[1]: *** [/opt/install-bin/rvtests-master/executable/rvtest] Error 1 make[1]: Leaving directory /opt/install-bin/rvtests-master/src' make: *** [release] Error 2 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#114>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABGRCDSJGERZ2F5HUBTFE3SQKPX3ANCNFSM4TYZMHUA> .

[flapa86]

Linux 3.10.0-1062.9.1.el7.x86_64 (RedHat system)

[longqh3]

@flapa86
Hi, I also encountered this issue which can be solved via install/upgrade required packages.
Try yum install glibc-static to solve "-lm", "-lc" missing and yum install libstdc++-static to solve "-lstdc++" missing. After installation, the "-lpthread" missing was solved naturally.

Ref:
cannot find -lc and -lm in g++ linux
Matlab Kalman /usr/bin/ld: cannot find -lstdc++.

[longqh3]

@zhanxw
After solving the dependency issue, I also encountered an "internal" error which required your help. The error log was listed behind.

fatal: Not a git repository (or any parent up to mount point /sdb1)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
make -C /sdb1/tools/lqh/rvtests-master/src release
fatal: Not a git repository (or any parent up to mount point /sdb1)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
make[1]: Entering directory `/sdb1/tools/lqh/rvtests-master/src'
make[1]: Nothing to be done for `release'.
make[1]: Leaving directory `/sdb1/tools/lqh/rvtests-master/src'
make -C /sdb1/tools/lqh/rvtests-master/vcfUtils release
fatal: Not a git repository (or any parent up to mount point /sdb1)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
make[1]: Entering directory `/sdb1/tools/lqh/rvtests-master/vcfUtils'
make[1]: *** No rule to make target `createBCF2Index.cpp', needed by `../executable/createBCF2Index'.  Stop.
make[1]: Leaving directory `/sdb1/tools/lqh/rvtests-master/vcfUtils'
make: *** [release] Error 2

I used your latest source codes (directly downloaded from github main-page) to conduct make process. Any help would be appreciated.