Open HenrikBengtsson opened 9 months ago
After implementing RUNPATH scans (#37) via make check, only 3 software tools came up;
make check
15/103: blast Makefile:18: warning: overriding recipe for target '/wynton/home/cbi/shared/software/CBI/blast-2.14.1/bin/blastx' ../utils.mk:212: warning: ignoring old recipe for target '/wynton/home/cbi/shared/software/CBI/blast-2.14.1/bin/blastx' *** RUNPATH checks ... 050.rpath.bats ✗ Does not use RUNPATH (from function `fail' in file /wynton/home/cbi/shared/software/CBI/bats-support-0.3.0/src/error.bash, line 40, in test file /wynton/home/cbi/hb/repositories/CBI-software/CBI/.incl/tests/050.rpath.bats, line 39) `fail "[${MODULE_NAME}/${MODULE_VERSION}] Detected ${#rpath_files[@]} binaries ($(sed -E "s|${PREFIX}/||g" <<< "${rpath_files[*]}") ) with RUNPATH dependencies: [n=${#rpath_deps[@]}] ${rpath_deps[*]}"' failed Scanning 28 executables under /wynton/home/cbi/shared/software/CBI/blast-2.14.1 [blast/2.14.1] Detected 24 binaries (bin/blastdb_aliastool bin/blastdbcheck bin/blastdbcmd bin/blast_formatter bin/blast_formatter_vd b bin/blastn bin/blastn_vdb bin/blastp bin/blast_vdb_cmd bin/blastx bin/convert2blastmask bin/deltablast bin/dustmasker bin/makeblastdb bin/makembindex bin/makeprofiledb bin/psiblast bin/rpsblast bin/rpstblastn bin/segmasker bin/tblastn bin/tblastn_vdb bin/tblastx bin/win dowmasker) with RUNPATH dependencies: [n=6] /netopt/ncbi_tools64/lzo-2.05/lib64 /netopt/ncbi_tools64/zstd-1.5.2/GCC481-ReleaseMT64/lib64 /opt/ncbi/64/lzo-2.05/lib64 /opt/ncbi/64/zstd-1.5.2/GCC481-ReleaseMT64/lib64 /opt/ncbi/gcc/7.3.0/lib64/ /opt/ncbi/gcc/7.3.0/lib/gcc/x86 _64-redhat-linux-gnu/7.3.0/ 1 test, 1 failure
29/103: cutadapt Makefile:23: warning: overriding recipe for target '/wynton/home/cbi/shared/software/CBI/_centos7/cutadapt-4.4/bin/cutadapt' ../utils.mk:212: warning: ignoring old recipe for target '/wynton/home/cbi/shared/software/CBI/_centos7/cutadapt-4.4/bin/cutadapt' *** RUNPATH checks ... 050.rpath.bats ✗ Does not use RUNPATH (from function `fail' in file /wynton/home/cbi/shared/software/CBI/bats-support-0.3.0/src/error.bash, line 40, in test file /wynton/home/cbi/hb/repositories/CBI-software/CBI/.incl/tests/050.rpath.bats, line 39) `fail "[${MODULE_NAME}/${MODULE_VERSION}] Detected ${#rpath_files[@]} binaries ($(sed -E "s|${PREFIX}/||g" <<< "${rpath_files[*]}") ) with RUNPATH dependencies: [n=${#rpath_deps[@]}] ${rpath_deps[*]}"' failed Scanning 7 executables under /wynton/home/cbi/shared/software/CBI/_centos7/cutadapt-4.4 [cutadapt/4.4] Detected 3 binaries (venv/bin/python venv/bin/python3 venv/bin/python3.8) with RUNPATH dependencies: [n=1] /opt/rh/rh- python38/root/usr/lib64 1 test, 1 failure
62/103: oraclejdk Makefile:19: warning: overriding recipe for target '/wynton/home/cbi/shared/software/CBI/_centos7/oraclejdk-17.0.8/bin/java' ../utils.mk:212: warning: ignoring old recipe for target '/wynton/home/cbi/shared/software/CBI/_centos7/oraclejdk-17.0.8/bin/java' *** RUNPATH checks ... 050.rpath.bats ✗ Does not use RUNPATH (from function `fail' in file /wynton/home/cbi/shared/software/CBI/bats-support-0.3.0/src/error.bash, line 40, in test file /wynton/home/cbi/hb/repositories/CBI-software/CBI/.incl/tests/050.rpath.bats, line 39) `fail "[${MODULE_NAME}/${MODULE_VERSION}] Detected ${#rpath_files[@]} binaries ($(sed -E "s|${PREFIX}/||g" <<< "${rpath_files[*]}") ) with RUNPATH dependencies: [n=${#rpath_deps[@]}] ${rpath_deps[*]}"' failed Scanning 30 executables under /wynton/home/cbi/shared/software/CBI/_centos7/oraclejdk-17.0.8 [oraclejdk/17.0.8] Detected 28 binaries (bin/jar bin/jarsigner bin/java bin/javac bin/javadoc bin/javap bin/jcmd bin/jconsole bin/jdb bin/jdeprscan bin/jdeps bin/jfr bin/jhsdb bin/jimage bin/jinfo bin/jlink bin/jmap bin/jmod bin/jpackage bin/jps bin/jrunscript bin/jshe ll bin/jstack bin/jstat bin/jstatd bin/keytool bin/rmiregistry bin/serialver) with RUNPATH dependencies: [n=2] $ORIGIN $ORIGIN/../lib 1 test, 1 failure
After implementing RUNPATH scans (#37) via
make check, only 3 software tools came up;blast
cutadapt
oraclejdk