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ComparativeGenomicsToolkit / hal

Hierarchical Alignment Format
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make: *** [../rules.mk:32: ../bin/halApiTests] Error 1 #142

Open Boer223 opened 4 years ago

Boer223 commented 4 years ago

Hi,

When I building hal in the hal/ directory, it occurs the following error:

h5c++  -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc/ -Ihdf5_impl -Immap_impl -I tests -o ../bin/halApiTests ../objs/api/tests/allTests.o ../objs/api/tests/halAlignmentInstanceTest.o ../objs/api/tests/halAlignmentTest.o ../objs/api/tests/halBottomSegmentTest.o ../objs/api/tests/halColumnIteratorTest.o ../objs/api/tests/halGappedSegmentIteratorTest.o ../objs/api/tests/halGenomeTest.o ../objs/api/tests/halMappedSegmentTest.o ../objs/api/tests/halMetaDataTest.o ../objs/api/tests/halRandomData.o ../objs/api/tests/halRearrangementTest.o ../objs/api/tests/halSequenceTest.o ../objs/api/tests/halTopSegmentTest.o ../objs/api/tests/halValidateTest.o  ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
g++: error: /scr/home/buildbot/buildbot/kituo-slave/hdf518-StdRelease-code-centos7/build/autotools/hdf5/lib/libhdf5_hl_cpp.a: No such file or directory
g++: error: /scr/home/buildbot/buildbot/kituo-slave/hdf518-StdRelease-code-centos7/build/autotools/hdf5/lib/libhdf5_cpp.a: No such file or directory
g++: error: /scr/home/buildbot/buildbot/kituo-slave/hdf518-StdRelease-code-centos7/build/autotools/hdf5/lib/libhdf5_hl.a: No such file or directory
g++: error: /scr/home/buildbot/buildbot/kituo-slave/hdf518-StdRelease-code-centos7/build/autotools/hdf5/lib/libhdf5.a: No such file or directory
make: *** [../rules.mk:32: ../bin/halApiTests] Error 1

So, how to solve this error? Thank you in advance!

diekhans commented 4 years ago

The last person who had this incorrectly set their environment so one of the variables include a new line. Please check or attached output of env command.

XiaoboCui notifications@github.com writes:

Hi,

When I building hal in the hal/ directory, it occurs the following error:

h5c++  -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc/ -Ihdf5_impl -Immap_impl -I tests -o ../bin/halApiTests ../objs/api/tests/allTests.o ../objs/api/tests/halAlignmentInstanceTest.o ../objs/api/tests/halAlignmentTest.o ../objs/api/tests/halBottomSegmentTest.o ../objs/api/tests/halColumnIteratorTest.o ../objs/api/tests/halGappedSegmentIteratorTest.o ../objs/api/tests/halGenomeTest.o ../objs/api/tests/halMappedSegmentTest.o ../objs/api/tests/halMetaDataTest.o ../objs/api/tests/halRandomData.o ../objs/api/tests/halRearrangementTest.o ../objs/api/tests/halSequenceTest.o ../objs/api/tests/halTopSegmentTest.o ../objs/api/tests/halValidateTest.o  ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
g++: error: /scr/home/buildbot/buildbot/kituo-slave/hdf518-StdRelease-code-centos7/build/autotools/hdf5/lib/libhdf5_hl_cpp.a: No such file or directory
g++: error: /scr/home/buildbot/buildbot/kituo-slave/hdf518-StdRelease-code-centos7/build/autotools/hdf5/lib/libhdf5_cpp.a: No such file or directory
g++: error: /scr/home/buildbot/buildbot/kituo-slave/hdf518-StdRelease-code-centos7/build/autotools/hdf5/lib/libhdf5_hl.a: No such file or directory
g++: error: /scr/home/buildbot/buildbot/kituo-slave/hdf518-StdRelease-code-centos7/build/autotools/hdf5/lib/libhdf5.a: No such file or directory
make: *** [../rules.mk:32: ../bin/halApiTests] Error 1

So, how to solve this error? Thank you in advance!

-- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/hal/issues/142 Hi,

When I building hal in the hal/ directory, it occurs the following error:

h5c++ -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc/ -Ihdf5_impl -Immap_impl -I tests -o ../bin/halApiTests ../objs/api/tests/allTests.o ../objs/api/tests/halAlignmentInstanceTest.o ../objs/api/tests/halAlignmentTest.o ../objs/api/tests/halBottomSegmentTest.o ../objs/api/tests/halColumnIteratorTest.o ../objs/api/tests/halGappedSegmentIteratorTest.o ../objs/api/tests/halGenomeTest.o ../objs/api/tests/halMappedSegmentTest.o ../objs/api/tests/halMetaDataTest.o ../objs/api/tests/halRandomData.o ../objs/api/tests/halRearrangementTest.o ../objs/api/tests/halSequenceTest.o ../objs/api/tests/halTopSegmentTest.o ../objs/api/tests/halValidateTest.o ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a g++: error: /scr/home/buildbot/buildbot/kituo-slave/hdf518-StdRelease-code-centos7/build/autotools/hdf5/lib/libhdf5_hl_cpp.a: No such file or directory g++: error: /scr/home/buildbot/buildbot/kituo-slave/hdf518-StdRelease-code-centos7/build/autotools/hdf5/lib/libhdf5_cpp.a: No such file or directory g++: error: /scr/home/buildbot/buildbot/kituo-slave/hdf518-StdRelease-code-centos7/build/autotools/hdf5/lib/libhdf5_hl.a: No such file or directory g++: error: /scr/home/buildbot/buildbot/kituo-slave/hdf518-StdRelease-code-centos7/build/autotools/hdf5/lib/libhdf5.a: No such file or directory make: *** [../rules.mk:32: ../bin/halApiTests] Error 1

So, how to solve this error? Thank you in advance!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.*

Boer223 commented 4 years ago

My env is:

CPLUS_INCLUDE_PATH=/home/cuixb/tools/biosoft/conda3/include:
MANPATH=/opt/gridview//pbs/dispatcher/share/man:/opt/gridview/clusquota//man:
XDG_SESSION_ID=826197
HOSTNAME=admin
EGNEP=/home/cuixb/tools/biosoft/egnep-1.5.1
HDF5_INCLUDE=/home/cuixb/tools/biosoft/hdf5/include
DIAMOND_PATH=/home/cuixb/tools/biosoft/conda3/envs/braker/bin
TERM=xterm-256color
SHELL=/bin/bash
HISTSIZE=1000
SSH_CLIENT=10.71.6.3 9429 22
PERL5LIB=/usr/lib/perl5/site_perl:/home/cuixb/perl5/lib/perl5::/home/cuixb/tools/biosoft/hupan/lib/:/home/cuixb/tools/biosoft/EUPAN/lib/:/home/cuixb/tools/biosoft/conda3/lib/5.26.2/:/home/cuixb/tools/biosoft/conda3/lib/site_perl/5.26.2/
ALN_TAB=/home/cuixb/tools/biosoft/conda3/envs/braker/share/spaln/table
QTDIR=/usr/lib64/qt-3.3
QTINC=/usr/lib64/qt-3.3/include
PERL_MB_OPT=--install_base /home/cuixb/perl5
SSH_TTY=/dev/pts/0
CLUSCONF_HOME=/opt/gridview/clusconf
QT_GRAPHICSSYSTEM_CHECKED=1
USER=cuixb
GENEMARK_PATH=/home/cuixb/tools/biosoft/genemark_et
LD_LIBRARY_PATH=/public/software/lib:/opt/gridview//pbs/dispatcher/lib::/usr/local/lib64:/usr/local/lib:/home/cuixb/tools/biosoft/hupan/lib/:/home/cuixb/tools/biosoft/EUPAN/lib/:/home/cuixb/tools/biosoft/hdf5/lib
LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:
AUGUSTUS_SCRIPTS_PATH=/home/cuixb/tools/biosoft/conda3/envs/braker/bin
PYTHON3_PATH=/home/cuixb/tools/biosoft/conda3/envs/braker/bin
CDBTOOLS_PATH=/home/cuixb/tools/biosoft/conda3/envs/braker/bin
NFSCONF=/opt/gridview/clusconf/etc/nfs.cfg
MAIL=/var/spool/mail/cuixb
PATH=/home/cuixb/tools/biosoft/cactus-bin-v1.0.0/bin:/home/cuixb/tools/biosoft/hdf5/bin:/home/cuixb/tools/biosoft/ppsPCP-1.0/bin:/home/cuixb/tools/biosoft/hupan/bin:/home/cuixb/tools/biosoft/EUPAN/bin:/home/cuixb/tools/biosoft/conda3/bin:/public/software/bin:/usr/lib64/qt-3.3/bin:/home/cuixb/perl5/bin:/opt/gridview//pbs/dispatcher-sched/bin:/opt/gridview//pbs/dispatcher-sched/sbin:/opt/gridview//pbs/dispatcher/bin/lsf_cmd:/opt/gridview//pbs/dispatcher/bin:/opt/gridview//pbs/dispatcher/sbin:/opt/gridview/clusquota//bin:/opt/gridview/clusquota//sbin:/opt/gridview/clusconf/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/home/cuixb/tools/biosoft/RepeatMasker:/home/cuixb/tools/biosoft/RepeatModeler:/home/cuixb/.aspera/connect/bin:/home/cuixb/tools/biosoft/genemark_et:/home/cuixb/tools/biosoft/bedtools2/bin:/home/cuixb/tools/biosoft/blat-v36:/home/cuixb/tools/biosoft/cufflinks-2.2.1:/home/cuixb/tools/biosoft/GRIDSS:/home/cuixb/tools/biosoft/samtools-1.10:/home/cuixb/tools/biosoft/bwa-0.7.17:/home/cuixb/tools/biosoft/R:/home/cuixb/tools/biosoft/snpEff:/home/cuixb/tools/sysoft:/home/cuixb/tools/biosoft/FREEC-11.5:/home/cuixb/tools/biosoft/bcftools:/home/cuixb/tools/biosoft/delly-0.7.7:/home/cuixb/tools/biosoft/fastx_toolkit/bin:/home/cuixb/tools/biosoft/seqkit-0.12.1:/home/cuixb/tools/sysoft/cmake-3.17.2-Linux-x86_64/bin:/home/cuixb/tools/biosoft/sratoolkit/bin:/public/software/mpi/mpich/3.2/gnu/bin:/home/cuixb/tools/biosoft/maker/bin:/home/cuixb/tools/biosoft/gmap/bin:/home/cuixb/tools/biosoft/cactus-bin-v1.0.0/bin:/home/cuixb/tools/biosoft/cactus-bin-v1.0.0/venv/bin:/home/cuixb/tools/biosoft/MCScanX:/home/cuixb/tools/biosoft/MCScanX/downstream_analyses:/home/cuixb/tools/biosoft/ncbi-blast-2.10.1+/bin:/home/cuixb/tools/biosoft/smartie-sv/bin:/home/cuixb/tools/biosoft/svmu-0.3:/home/cuixb/tools/biosoft/lastz-1.04.03/bin:/home/cuixb/tools/biosoft/SURVIVOR-1.0.6/Debug:/home/cuixb/tools/biosoft/last-1066/src:/home/cuixb/tools/biosoft/last-1066/scripts:/home/cuixb/tools/biosoft/Picky-0.2.a/src:/home/cuixb/tools/biosoft/mafft-7.470/bin:/home/cuixb/tools/biosoft/bioawk-1.0:/home/cuixb/tools/biosoft/vcftools_0.1.13/bin:/home/cuixb/.local/bin:/home/cuixb/bin
C_INCLUDE_PATH=/home/cuixb/tools/biosoft/conda3/include:
PWD=/home/cuixb/tools/biosoft
IPMICONF=/opt/gridview/clusconf/etc/ipmi.cfg
LANG=en_US.UTF-8
KDEDIRS=/usr
AUTOCLUSCONF=/opt/gridview/clusconf/etc/autoconf.cfg
GRIDVIEW_HOME=/opt/gridview/
PERLLIB=/usr/lib/perl5/site_perl:
HDF5_LIB=/home/cuixb/tools/biosoft/hdf5/lib
HISTCONTROL=ignoredups
SHLVL=1
HOME=/home/cuixb
SENTIEON_LICENSE=admin:8990
ALIGNMENT_TOOL_PATH=/home/cuixb/tools/biosoft/conda3/envs/braker/bin
AUGUSTUS_CONFIG_PATH=/home/cuixb/tools/biosoft/conda3/envs/braker/config
PERL_LOCAL_LIB_ROOT=:/home/cuixb/perl5
ALN_DBS=/home/cuixb/tools/biosoft/conda3/envs/braker/share/spaln/seqdb
LOGNAME=cuixb
QTLIB=/usr/lib64/qt-3.3/lib
STARTWAITTIME=300
SSH_CONNECTION=10.71.6.3 9429 10.71.6.248 22
PKG_CONFIG_PATH=:/home/cuixb/tools/sysoft/jansson-2.12
LESSOPEN=||/usr/bin/lesspipe.sh %s
BLAST_PATH=/home/cuixb/tools/biosoft/conda3/envs/braker/bin
XDG_RUNTIME_DIR=/run/user/1017
QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins
EUGENEDIR=/home/cuixb/tools/biosoft/eugene-4.2a/
PERL_MM_OPT=INSTALL_BASE=/home/cuixb/perl5
_=/usr/bin/env
OLDPWD=/home/cuixb/tools/biosoft/sonLib
diekhans commented 4 years ago

It looks like hdf5 is not installed correctly. The h5c++ commands adds the locations of the library files.

XiaoboCui notifications@github.com writes:

Hi,

When I building hal in the hal/ directory, it occurs the following error:


h5c++  -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc/ -Ihdf5_impl -Immap_impl -I tests -o ../bin/halApiTests ../objs/api/tests/allTests.o ../objs/api/tests/halAlignmentInstanceTest.o ../objs/api/tests/halAlignmentTest.o ../objs/api/tests/halBottomSegmentTest.o ../objs/api/tests/halColumnIteratorTest.o ../objs/api/tests/halGappedSegmentIteratorTest.o ../objs/api/tests/halGenomeTest.o ../objs/api/tests/halMappedSegmentTest.o ../objs/api/tests/halMetaDataTest.o ../objs/api/tests/halRandomData.o ../objs/api/tests/halRearrangementTest.o ../objs/api/tests/halSequenceTest.o ../objs/api/tests/halTopSegmentTest.o ../objs/api/tests/halValidateTest.o  ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a
g++: error: /scr/home/buildbot/buildbot/kituo-slave/hdf518-StdRelease-code-centos7/build/autotools/hdf5/lib/libhdf5_hl_cpp.a: No such file or directory
g++: error: /scr/home/buildbot/buildbot/kituo-slave/hdf518-StdRelease-code-centos7/build/autotools/hdf5/lib/libhdf5_cpp.a: No such file or directory
g++: error: /scr/home/buildbot/buildbot/kituo-slave/hdf518-StdRelease-code-centos7/build/autotools/hdf5/lib/libhdf5_hl.a: No such file or directory
g++: error: /scr/home/buildbot/buildbot/kituo-slave/hdf518-StdRelease-code-centos7/build/autotools/hdf5/lib/libhdf5.a: No such file or directory
make: *** [../rules.mk:32: ../bin/halApiTests] Error 1
wjdavis90 commented 3 years ago

Hi Chipcui, I'm getting the same (or at least similar) error. Did you get this resolved?