* 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/Rtmp4oE6Ke/R.INSTALL3575d15cdb9a77/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/Rtmp4oE6Ke/R.INSTALL3575d15cdb9a77/ribiosUtils/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp4oE6Ke/R.INSTALL3575d15cdb9a77/ribiosUtils/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp4oE6Ke/R.INSTALL3575d15cdb9a77/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)