* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’ * 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: ‘gcc-14 (Debian 14.3.0-12) 14.3.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpurQDl5/R.INSTALL3edac41483710/ribiosUtils/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c affyfileHandler.c -o affyfileHandler.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c algutil.c -o algutil.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c alphatrans.c -o alphatrans.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c arg.c -o arg.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c array.c -o array.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c avlTree.c -o avlTree.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c binalgparser.c -o binalgparser.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bitmap.c -o bitmap.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c biurl.c -o biurl.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c blastdb.c -o blastdb.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c blastparser.c -o blastparser.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c chemutil.c -o chemutil.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c combi.c -o combi.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c eval.c -o eval.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c forest.c -o forest.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c format.c -o format.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c fuzzparser.c -o fuzzparser.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c geometry.c -o geometry.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c graphalgo.c -o graphalgo.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c graphics.c -o graphics.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hash.c -o hash.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hierclus.c -o hierclus.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hlrmisc.c -o hlrmisc.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hmmparser.c -o hmmparser.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c html.c -o html.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c htmlform.c -o htmlform.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c linestream.c -o linestream.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c lnk.c -o lnk.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c log.c -o log.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c matvec.c -o matvec.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c msfparser.c -o msfparser.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pagedesign.c -o pagedesign.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c patternmatch.c -o patternmatch.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pearsonfastaparser.c -o pearsonfastaparser.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phraplightparser.c -o phraplightparser.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c plabla.c -o plabla.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c primer3parser.c -o primer3parser.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c properties.c -o properties.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pwdecode.c -o pwdecode.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c r_endec.c -o r_endec.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c r_mmatch.c -o r_mmatch.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c r_trim.c -o r_trim.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rdbu.c -o rdbu.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c recipes.c -o recipes.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c seqautil.c -o seqautil.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sequenceAlignment.c -o sequenceAlignment.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sequtil.c -o sequtil.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c statistics.c -o statistics.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c stringlist.c -o stringlist.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c wiseparser.c -o wiseparser.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c wwwsession.c -o wwwsession.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c xmlbuilder.c -o xmlbuilder.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c xmlparser.c -o xmlparser.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -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 -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpurQDl5/R.INSTALL3edac41483710/ribiosUtils/src' make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpurQDl5/R.INSTALL3edac41483710/ribiosUtils/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpurQDl5/R.INSTALL3edac41483710/ribiosUtils/src' installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-ribiosUtils/00new/ribiosUtils/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package ‘ribiosUtils’ finding HTML links ... done allIdentical html applyTopOrIncAndNotExclFilter html asNumMatrix html assertColumnName html assertContrast html assertDesign html assertDesignContrast html bedaInfo html biomicsPstorePath2URL html bound html cbindByRownames html checkFile html chosenFew html closeLoggerConnections html columnOverlapCoefficient html compTwoVecs html corByRownames html countTokens html createDir html cumJaccardIndex html cumOverlapCoefficient html cumsumprop html cutInterval html cutreeIntoOrderedGroups html dfFactor html dfFactor2Str html equateWellLabelWidth html extname html firstUp html fixWidthStr html haltifnot html headhead html headtail html identicalMatrix html identicalMatrixValue html imatch html invertList html isDir html isError html isOdd html isRocheCompoundID html isTopOrIncAndNotExcl html jaccardIndex html keepMaxStatRow html lastChar html libordie html list2df html listOverlapCoefficient html longdf2matrix html matchColumn html matchColumnName html matrix2longdf html mergeInfreqLevelsByCumsumprop html midentical html mmatch html munion html na.false html naivePairwiseDist html ofactor html orderCutgroup html overlapCoefficient html overwriteDir html pAbsLog10Score html pQnormScore html pScore html pairwiseJaccardIndex html pairwiseOverlapDistance html percentage html print.BEDAinfo html putColsFirst html pwdecode html pwencode html qqmsg html qsystem html refactorNum html registerLog html relevels html relevelsByNamedVec html relevelsByNotNamedVec html reload html removeColumns html removeColumnsByFunc html removeColumnsWithNA html removeInvarCol html removeRowsWithNA html replaceColumnName html replaceZeroPvalue html ribiosTempdir html ribiosTempfile html ribiosUtils-package html ribiosUtils html rmat html rocheCore html rowscale html rowscale.matrix html rowscale.table html rrank html rrank.matrix html rrankInd html rsetdiff html scriptInit html setDebug html shortenRocheCompoundID html shortenStr html silencio html sortAndFilterByCumsumprop html sortByCol html sortByDimnames html strtoken html stubborngc html subsetByColumnName html summarizeRows html trim html uniqueLength html uniqueNonNA html verbose html wellIndex2position html whoami html writeLog html ** 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)