* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘Signac’ ...
** package ‘Signac’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
make[1]: Entering directory '/tmp/RtmpKSMfrL/R.INSTALL3a1347469ed5e0/Signac/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c filter.cpp -o filter.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c group.cpp -o group.o
group.cpp: In function ‘SEXPREC* groupCommand(std::string, Rcpp::Nullable<Rcpp::Vector<16> >, std::size_t, bool)’:
group.cpp:40:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
40 | for (size_t i=0; i<whitelist_cells.size(); i++) {
| ~^~~~~~~~~~~~~~~~~~~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c split.cpp -o split.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c validate.cpp -o validate.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o Signac.so RcppExports.o filter.o group.o split.o validate.o -lz -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpKSMfrL/R.INSTALL3a1347469ed5e0/Signac/src'
make[1]: Entering directory '/tmp/RtmpKSMfrL/R.INSTALL3a1347469ed5e0/Signac/src'
make[1]: Leaving directory '/tmp/RtmpKSMfrL/R.INSTALL3a1347469ed5e0/Signac/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Signac/00new/Signac/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘Signac’
finding HTML links ... done
AccessiblePeaks html
AddChromatinModule html
AddMotifs html
AggregateTiles html
AlleleFreq html
Annotation html
AnnotationPlot html
AverageCounts html
BigwigTrack html
BinarizeCounts html
CallPeaks html
Cells-set html
Cells html
CellsPerGroup html
ChromatinAssay-class html
ClosestFeature html
ClusterClonotypes html
CombineTracks html
ConnectionsToLinks html
ConvertMotifID html
CountFragments html
CountsInRegion html
CoverageBrowser html
CoveragePlot html
CreateChromatinAssay html
CreateFragmentObject html
CreateMotifMatrix html
CreateMotifObject html
DensityScatter html
DepthCor html
DownsampleFeatures html
ExpressionPlot html
Extend html
FRiP html
FeatureMatrix html
FilterCells html
FindClonotypes html
FindMotifs html
FindTopFeatures html
Footprint html
FractionCountsInRegion html
Fragment-class html
FragmentHistogram html
Fragments html
GRangesToString html
GeneActivity html
GenomeBinMatrix html
GetCellsInRegion html
GetFootprintData html
GetFragmentData html
GetGRangesFromEnsDb html
GetIntersectingFeatures html
GetLinkedGenes html
GetLinkedPeaks html
GetMotifData html
GetTSSPositions html
IdentifyVariants html
InsertionBias html
IntersectMatrix html
Jaccard html
LinkPeaks html
LinkPlot html
Links html
LookupGeneCoords html
MatchRegionStats html
Motif-class html
MotifCounts html
MotifPlot html
Motifs html
NucleosomeSignal html
PeakPlot html
PlotFootprint html
ReadMGATK html
RegionHeatmap html
RegionMatrix html
RegionPlot html
RegionStats html
RunChromVAR html
RunSVD html
RunTFIDF html
SetMotifData html
Signac-package html
SplitFragments html
StringToGRanges html
SubsetMatrix html
TSSEnrichment html
TSSPlot html
TilePlot html
UnifyPeaks html
UpdatePath html
ValidateCells html
ValidateFragments html
ValidateHash html
VariantPlot html
as.ChromatinAssay html
atac_small html
blacklist_ce10 html
blacklist_ce11 html
blacklist_dm3 html
blacklist_dm6 html
blacklist_hg19 html
blacklist_hg38 html
blacklist_hg38_unified html
blacklist_mm10 html
corSparse html
coverage-ChromatinAssay-method html
findOverlaps-methods html
granges-methods html
head.Fragment html
inter-range-methods html
finding level-2 HTML links ... done
nearest-methods html
reexports html
REDIRECT:topic Previous alias or file overwritten by alias: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Signac/00new/Signac/help/Cells.html
seqinfo-methods html
subset.Fragment html
subset.Motif html
theme_browser html
*** copying figures
** 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 (Signac)