* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘BED’ ...
** this is package ‘BED’ version ‘1.6.2’
** package ‘BED’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.3.0-10) 14.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpjJhx0u/R.INSTALL16b2193afe8665/BED/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 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c extract_u_de.c -o extract_u_de.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 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c extract_u_gn.c -o extract_u_gn.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 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o
gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o BED.so extract_u_de.o extract_u_gn.o init.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpjJhx0u/R.INSTALL16b2193afe8665/BED/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpjJhx0u/R.INSTALL16b2193afe8665/BED/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpjJhx0u/R.INSTALL16b2193afe8665/BED/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-BED/00new/BED/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘BED’
finding HTML links ... done
BED html
BEIDList html
BEIDs html
beIDsToAllScopes html
bedCall html
bedImport html
beidsServer html
cacheBedCall html
cacheBedResult html
checkBeIds html
checkBedCache html
checkBedConn html
cleanDubiousXRef html
clearBedCache html
compareBedInstances html
connectToBed html
convBeIdLists html
convBeIds html
convDfBeIds html
dumpEnsCore html
dumpNcbiDb html
dumpNcbiTax html
dumpUniprotDb html
exploreBe html
exploreConvPath html
filterByBEID html
findBe html
findBeids html
firstCommonUpstreamBe html
focusOnScope.BEIDList html
focusOnScope html
forgetBedConnection html
genBePath html
genProbePath html
geneIDsToAllScopes html
getAllBeIdSources html
getBeIdConvTable html
getBeIdDescription html
getBeIdNameTable html
getBeIdNames html
getBeIdSymbolTable html
getBeIdSymbols html
getBeIdURL html
getBeIds html
getDirectOrigin html
getDirectProduct html
getEnsemblGeneIds html
getEnsemblPeptideIds html
getEnsemblTranscriptIds html
getGeneDescription html
getHomTable html
getNcbiGeneTransPep html
getOrgNames html
getRelevantIds html
getTargetedBe html
getTaxId html
getUniprot html
guessIdScope html
identicalScopes html
is.BEIDList html
largestBeSource html
listBe html
listBeIdSources html
listDBAttributes html
listOrganisms html
listPlatforms html
loadBE html
loadBENames html
loadBESymbols html
loadBEVersion html
loadBeAttribute html
loadBedModel html
loadBedOtherIndexes html
loadBedResult html
loadCodesFor html
loadCorrespondsTo html
loadHistory html
loadIsAssociatedTo html
loadIsExpressedAs html
loadIsHomologOf html
loadIsTranslatedIn html
loadLuceneIndexes html
loadNCBIEntrezGOFunctions html
loadNcbiTax html
loadOrganisms html
loadPlf html
loadProbes html
lsBedCache html
lsBedConnections html
metadata-set html
metadata html
registerBEDB html
scope html
scopes html
searchBeid html
searchId html
setBedVersion html
showBedDataModel html
*** copying figures
** building package indices
** installing vignettes
** 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 (BED)