dev-lang/icc defines the environmental variable LIB which the plink makefile uses. plink needs to be compiled with LIB="" emerge plink in order to compile properly if icc is installed. Reproducible: Always Steps to Reproduce: 1. emerge icc 2. emerge plink 3. Actual Results: g++ -O2 -pipe -O3 -I. -DUNIX -DSKIP -DWITH_R_PLUGINS -DWITH_ZLIB -o plink plink.o options.o input.o binput.o tinput.o genome.o helper.o stats.o filters.o locus.o multi.o crandom.o cluster.o mds.o output.o informative.o assoc.o epi.o prephap.o phase.o trio.o tdt.o sharing.o genepi.o sets.o perm.o mh.o genedrop.o gxe.o merge.o hotel.o multiple.o haploCC.o haploTDT.o poo.o webcheck.o qfam.o linear.o bmerge.o parse.o mishap.o legacy.o homozyg.o segment.o model.o logistic.o glm.o dcdflib.o elf.o dfam.o fisher.o linput.o sockets.o lookup.o proxy.o pdriver.o haploQTL.o haplohelper.o haplowindow.o genogroup.o nonfounderphasing.o clumpld.o genoerr.o em.o impute.o metaem.o profile.o nlist.o whap.o simul.o gvar.o cnv.o step.o greport.o flip.o qualscores.o cnvqt.o cfamily.o setscreen.o idhelp.o tag.o hapglm.o lookup2.o blox.o zed.o dosage.o annot.o metaanal.o r.o Rconnection.o zfstream.o /opt/intel/Compiler/11.1/072/ipp//lib -ldl -lcrypt -lz g++: /opt/intel/Compiler/11.1/072/ipp//lib: No such file or directory For some reason I have not been able to determine, the package.env mechanism does not for the workaround given.
I cannot reporduce this. Please reporten if it still is valid.
plink is now at plink-1.07-r1 in ~amd64, and still fails for me: # echo $LIB ${IPPROOT}/lib # grep plink /etc/portage/package.env sci-biology/plink nolibenv.conf # more /etc/portage/env/nolibenv.conf LIB="" # emerge -1 plink ... x86_64-pc-linux-gnu-g++ -Wl,-z,now -O2 -pipe -I. -DUNIX -DSKIP -DWITH_ZLIB -DWITH_LAPACK -o plink plink.o options.o input.o binput.o tinput.o genome.o helper.o stats.o filters.o locus.o multi.o crandom.o cluster.o mds.o output.o informative.o assoc.o epi.o prephap.o phase.o trio.o tdt.o sharing.o genepi.o sets.o perm.o mh.o genedrop.o gxe.o merge.o hotel.o multiple.o haploCC.o haploTDT.o poo.o webcheck.o qfam.o linear.o bmerge.o parse.o mishap.o legacy.o homozyg.o segment.o model.o logistic.o glm.o dcdflib.o elf.o dfam.o fisher.o linput.o sockets.o lookup.o proxy.o pdriver.o haploQTL.o haplohelper.o haplowindow.o genogroup.o nonfounderphasing.o clumpld.o genoerr.o em.o impute.o metaem.o profile.o nlist.o whap.o simul.o gvar.o cnv.o step.o greport.o flip.o qualscores.o cnvqt.o cfamily.o setscreen.o idhelp.o tag.o hapglm.o lookup2.o blox.o zed.o dosage.o annot.o metaanal.o zfstream.o lapackf.o /opt/intel/Compiler/11.1/072/ipp//lib -lz `pkg-config --libs lapack` x86_64-pc-linux-gnu-g++: /opt/intel/Compiler/11.1/072/ipp//lib: No such file or directory make: *** [plink] Error 1 emake failed * ERROR: sci-biology/plink-1.07-r1 failed: * (no error message) * * Call stack: * ebuild.sh, line 56: Called src_compile * environment, line 2487: Called die * The specific snippet of code: * emake CXX_UNIX=$(tc-getCXX) || die * * If you need support, post the output of 'emerge --info =sci-biology/plink-1.07-r1', * the complete build log and the output of 'emerge -pqv =sci-biology/plink-1.07-r1'. * The complete build log is located at '/var/tmp/portage/sci-biology/plink-1.07-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/plink-1.07-r1/temp/environment'. * S: '/var/tmp/portage/sci-biology/plink-1.07-r1/work/plink-1.07-src' >>> Failed to emerge sci-biology/plink-1.07-r1, Log file: >>> '/var/tmp/portage/sci-biology/plink-1.07-r1/temp/build.log' * Messages for package sci-biology/plink-1.07-r1: * ERROR: sci-biology/plink-1.07-r1 failed: ... yet # LIB="" emerge -1 plink works for me.
All ebuilds in the tree do not set $LIB anymore.
