* installing *source* package ‘ribiosUtils’ ... ** this is package ‘ribiosUtils’ version ‘1.7.7’ ** package ‘ribiosUtils’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘clang version 21.1.8’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/ribiosUtils/src' /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c affyfileHandler.c -o affyfileHandler.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c algutil.c -o algutil.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c alphatrans.c -o alphatrans.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c arg.c -o arg.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c array.c -o array.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c avlTree.c -o avlTree.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c binalgparser.c -o binalgparser.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c bitmap.c -o bitmap.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c biurl.c -o biurl.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c blastdb.c -o blastdb.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c blastparser.c -o blastparser.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c chemutil.c -o chemutil.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c combi.c -o combi.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c eval.c -o eval.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c forest.c -o forest.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c format.c -o format.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c fuzzparser.c -o fuzzparser.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c geometry.c -o geometry.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c graphalgo.c -o graphalgo.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c graphics.c -o graphics.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c hash.c -o hash.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c hierclus.c -o hierclus.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c hlrmisc.c -o hlrmisc.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c hmmparser.c -o hmmparser.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c html.c -o html.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c htmlform.c -o htmlform.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c init.c -o init.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c linestream.c -o linestream.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c lnk.c -o lnk.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c log.c -o log.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c matvec.c -o matvec.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c msfparser.c -o msfparser.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c pagedesign.c -o pagedesign.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c patternmatch.c -o patternmatch.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c pearsonfastaparser.c -o pearsonfastaparser.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phraplightparser.c -o phraplightparser.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c plabla.c -o plabla.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c primer3parser.c -o primer3parser.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c properties.c -o properties.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c pwdecode.c -o pwdecode.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c r_endec.c -o r_endec.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c r_mmatch.c -o r_mmatch.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c r_trim.c -o r_trim.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c rdbu.c -o rdbu.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c recipes.c -o recipes.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c seqautil.c -o seqautil.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c sequenceAlignment.c -o sequenceAlignment.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c sequtil.c -o sequtil.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c statistics.c -o statistics.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c stringlist.c -o stringlist.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c wiseparser.c -o wiseparser.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c wwwsession.c -o wwwsession.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c xmlbuilder.c -o xmlbuilder.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c xmlparser.c -o xmlparser.o /usr/local/clang21/bin/clang -std=gnu23 -shared -L/usr/local/clang/lib64 -L/usr/local/clang21/lib -L/usr/local/clang21/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -o ribiosUtils.so affyfileHandler.o algutil.o alphatrans.o arg.o array.o avlTree.o binalgparser.o bitmap.o biurl.o blastdb.o blastparser.o chemutil.o combi.o eval.o forest.o format.o fuzzparser.o geometry.o graphalgo.o graphics.o hash.o hierclus.o hlrmisc.o hmmparser.o html.o htmlform.o init.o linestream.o lnk.o log.o matvec.o msfparser.o pagedesign.o patternmatch.o pearsonfastaparser.o phraplightparser.o plabla.o primer3parser.o properties.o pwdecode.o r_endec.o r_mmatch.o r_trim.o rdbu.o recipes.o seqautil.o sequenceAlignment.o sequtil.o statistics.o stringlist.o wiseparser.o wwwsession.o xmlbuilder.o xmlparser.o make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/ribiosUtils/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/ribiosUtils/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/ribiosUtils/src' installing to /data/gannet/ripley/R/packages/tests-clang/ribiosUtils.Rcheck/00LOCK-ribiosUtils/00new/ribiosUtils/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ribiosUtils)