* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘batchtools’ ...
** this is package ‘batchtools’ version ‘0.9.17’
** package ‘batchtools’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpmjSEzy/R.INSTALL2a8f8475178b56/batchtools/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 binpack.c -o binpack.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 count_not_missing.c -o count_not_missing.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 fill_gaps.c -o fill_gaps.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 -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 lpt.c -o lpt.o
gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o batchtools.so binpack.o count_not_missing.o fill_gaps.o init.o lpt.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpmjSEzy/R.INSTALL2a8f8475178b56/batchtools/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpmjSEzy/R.INSTALL2a8f8475178b56/batchtools/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpmjSEzy/R.INSTALL2a8f8475178b56/batchtools/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-batchtools/00new/batchtools/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘batchtools’
finding HTML links ... done
JobCollection html
JobExperiment html
JobNames html
JoinTables html
Rd warning: JoinTables.Rd:51: missing link ‘data.table’
Tags html
Worker html
Rd warning: Worker.Rd:8: missing link ‘R6Class’
addAlgorithm html
addExperiments html
Rd warning: addExperiments.Rd:40: missing link ‘data.table’
addProblem html
assertRegistry html
batchExport html
batchMap html
Rd warning: batchMap.Rd:42: missing link ‘data.table’
batchMapResults html
Rd warning: batchMapResults.Rd:41: missing link ‘data.table’
batchReduce html
Rd warning: batchReduce.Rd:36: missing link ‘data.table’
batchtools-package html
btlapply html
cfBrewTemplate html
cfHandleUnknownSubmitError html
cfKillJob html
cfReadBrewTemplate html
chunk html
clearRegistry html
doJobCollection html
estimateRuntimes html
Rd warning: estimateRuntimes.Rd:13: missing link ‘data.table’
Rd warning: estimateRuntimes.Rd:33: missing link ‘data.table’
execJob html
findConfFile html
findJobs html
Rd warning: findJobs.Rd:102: missing link ‘data.table’
findTemplateFile html
getDefaultRegistry html
getErrorMessages html
Rd warning: getErrorMessages.Rd:29: missing link ‘data.table’
getJobTable html
Rd warning: getJobTable.Rd:33: missing link ‘data.table’
getStatus html
grepLogs html
Rd warning: grepLogs.Rd:36: missing link ‘data.table’
killJobs html
Rd warning: killJobs.Rd:21: missing link ‘data.table’
loadRegistry html
loadResult html
makeClusterFunctions html
makeClusterFunctionsDocker html
makeClusterFunctionsInteractive html
makeClusterFunctionsLSF html
makeClusterFunctionsMulticore html
makeClusterFunctionsOpenLava html
makeClusterFunctionsSGE html
makeClusterFunctionsSSH html
makeClusterFunctionsSlurm html
makeClusterFunctionsSocket html
makeClusterFunctionsTORQUE html
makeExperimentRegistry html
makeRegistry html
makeSubmitJobResult html
reduceResults html
reduceResultsList html
removeExperiments html
Rd warning: removeExperiments.Rd:21: missing link ‘data.table’
removeRegistry html
resetJobs html
Rd warning: resetJobs.Rd:21: missing link ‘data.table’
runHook html
Rd warning: runHook.Rd:41: missing link ‘data.table’
runOSCommand html
saveRegistry html
showLog html
submitJobs html
Rd warning: submitJobs.Rd:41: missing link ‘data.table’
summarizeExperiments html
Rd warning: summarizeExperiments.Rd:28: missing link ‘data.table’
sweepRegistry html
syncRegistry html
testJob html
unwrap html
Rd warning: unwrap.Rd:28: missing link ‘data.table’
waitForJobs html
** 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 (batchtools)