downloading reverse dependencies ... downloading AlphaPart_0.9.8.tar.gz ... ok downloading BasketballAnalyzeR_0.8.0.tar.gz ... ok downloading CoSMoS_2.1.0.tar.gz ... ok downloading foreSIGHT_1.2.0.tar.gz ... ok downloading jrt_1.1.2.tar.gz ... ok downloading prevR_5.0.0.tar.gz ... ok downloading primerTree_1.0.6.tar.gz ... ok downloading QCAtools_0.2.3.tar.gz ... ok downloading reReg_1.4.7.tar.gz ... ok downloading rreg_0.2.1.tar.gz ... ok downloading atime_2025.5.24.tar.gz ... ok downloading aum_2024.6.19.tar.gz ... ok downloading binsegRcpp_2025.5.13.tar.gz ... ok downloading dartR_2.9.9.5.tar.gz ... ok downloading dartR.base_1.0.5.tar.gz ... ok downloading denvax_0.1.2.tar.gz ... ok downloading episensr_2.0.0.tar.gz ... ok downloading htsr_2.1.6.tar.gz ... ok downloading mirt_1.44.0.tar.gz ... ok downloading mlr3resampling_2025.6.23.tar.gz ... ok downloading penaltyLearning_2024.9.3.tar.gz ... ok installing dependencies ‘animint2’, ‘aplore3’, ‘atime’, ‘binsegRcpp’, ‘cmaes’, ‘cumstats’, ‘dartR.data’, ‘directlabels’, ‘editData’, ‘fastymd’, ‘fpop’, ‘ggdag’, ‘ggquiver’, ‘ggtern’, ‘grates’, ‘HardyWeinberg’, ‘hierfstat’, ‘inlinedocs’, ‘iterpc’, ‘jointseg’, ‘leaflet.minicharts’, ‘LOPART’, ‘mAr’, ‘mirtCAT’, ‘mlr3torch’, ‘mmod’, ‘nc’, ‘neuroblastoma’, ‘operators’, ‘PeakSegDisk’, ‘pedigree’, ‘penaltyLearning’, ‘plink’, ‘PopGenReport’, ‘poppr’, ‘QCA’, ‘rcorpora’, ‘re2’, ‘reda’, ‘RGN’, ‘SIBER’, ‘SNPassoc’, ‘SoilHyP’, ‘StAMPP’, ‘trapezoid’, ‘wbs’, ‘WeightedROC’ Warning: package ‘cumstats’ is not available for this version of R A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages also installing the dependencies ‘HaploSim’, ‘declared’, ‘genetics’, ‘polysat’, ‘poisbinom’, ‘acnr’ begin installing package ‘HaploSim’ begin installing package ‘declared’ begin installing package ‘genetics’ begin installing package ‘polysat’ begin installing package ‘poisbinom’ begin installing package ‘acnr’ begin installing package ‘inlinedocs’ begin installing package ‘operators’ begin installing package ‘mAr’ begin installing package ‘ggquiver’ begin installing package ‘rcorpora’ begin installing package ‘SoilHyP’ begin installing package ‘cmaes’ begin installing package ‘RGN’ begin installing package ‘reda’ begin installing package ‘re2’ begin installing package ‘binsegRcpp’ begin installing package ‘fastymd’ begin installing package ‘wbs’ begin installing package ‘fpop’ begin installing package ‘LOPART’ begin installing package ‘PeakSegDisk’ begin installing package ‘nc’ begin installing package ‘WeightedROC’ begin installing package ‘penaltyLearning’ begin installing package ‘atime’ begin installing package ‘neuroblastoma’ begin installing package ‘dartR.data’ * installing *source* package ‘WeightedROC’ ... ** this is package ‘WeightedROC’ version ‘2020.1.31’ ** package ‘WeightedROC’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (WeightedROC) begin installing package ‘StAMPP’ * installing *source* package ‘acnr’ ... ** this is package ‘acnr’ version ‘1.0.0’ ** package ‘acnr’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (acnr) begin installing package ‘ggtern’ * installing *source* package ‘mAr’ ... ** this is package ‘mAr’ version ‘1.2-0’ ** package ‘mAr’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (mAr) begin installing package ‘HardyWeinberg’ * installing *source* package ‘operators’ ... ** this is package ‘operators’ version ‘0.1-8’ ** package ‘operators’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (operators) begin installing package ‘hierfstat’ * installing *source* package ‘neuroblastoma’ ... ** this is package ‘neuroblastoma’ version ‘2023.9.3’ ** package ‘neuroblastoma’ successfully unpacked and MD5 sums checked ** using staged installation ** data ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (neuroblastoma) begin installing package ‘iterpc’ * installing *source* package ‘cmaes’ ... ** this is package ‘cmaes’ version ‘1.0-12’ ** package ‘cmaes’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cmaes) begin installing package ‘leaflet.minicharts’ * installing *source* package ‘wbs’ ... ** this is package ‘wbs’ version ‘1.4.1’ ** package ‘wbs’ 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/RtmpHpH3kh/R.INSTALL2ffbabf04775a/wbs/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c wbs.c -o wbs.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c wbs_init.c -o wbs_init.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o wbs.so wbs.o wbs_init.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpHpH3kh/R.INSTALL2ffbabf04775a/wbs/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-wbs/00new/wbs/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (wbs) begin installing package ‘mmod’ * installing *source* package ‘fastymd’ ... ** this is package ‘fastymd’ version ‘0.1.3’ ** package ‘fastymd’ 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/Rtmpu8vZIN/R.INSTALL2ffba42c5fdd9e/fastymd/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c api.c -o api.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c civil_from_days.c -o civil_from_days.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c days_from_civil.c -o days_from_civil.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c epochdays.c -o epochdays.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -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/lib -Wl,-O1 -o fastymd.so api.o civil_from_days.o days_from_civil.o epochdays.o init.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpu8vZIN/R.INSTALL2ffba42c5fdd9e/fastymd/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-fastymd/00new/fastymd/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (fastymd) begin installing package ‘SIBER’ * installing *source* package ‘nc’ ... ** this is package ‘nc’ version ‘2025.3.24’ ** package ‘nc’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (nc) begin installing package ‘ggdag’ * installing *source* package ‘HaploSim’ ... ** this is package ‘HaploSim’ version ‘1.8.4.2’ ** package ‘HaploSim’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (HaploSim) begin installing package ‘trapezoid’ * installing *source* package ‘RGN’ ... ** this is package ‘RGN’ version ‘1.0.0’ ** package ‘RGN’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ using Fortran compiler: ‘GNU Fortran (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpqdCyZP/R.INSTALL2ffba07ab0f523/RGN/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c RGN_init.c -o RGN_init.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c constantsMod.f90 -o constantsMod.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c hymod.f90 -o hymod.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c qr.f90 -o qr.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c test.f -o test.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o RGN.so RGN_init.o constantsMod.o hymod.o qr.o test.o -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpqdCyZP/R.INSTALL2ffba07ab0f523/RGN/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-RGN/00new/RGN/libs ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (RGN) begin installing package ‘aplore3’ * installing *source* package ‘atime’ ... ** this is package ‘atime’ version ‘2025.5.24’ ** package ‘atime’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (atime) begin installing package ‘editData’ * installing *source* package ‘rcorpora’ ... ** this is package ‘rcorpora’ version ‘2.0.1’ ** package ‘rcorpora’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rcorpora) begin installing package ‘plink’ * installing *source* package ‘iterpc’ ... ** this is package ‘iterpc’ version ‘0.4.2’ ** package ‘iterpc’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (iterpc) begin installing package ‘mirtCAT’ * installing *source* package ‘ggquiver’ ... ** this is package ‘ggquiver’ version ‘0.3.3’ ** package ‘ggquiver’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggquiver) begin installing package ‘animint2’ * installing *source* package ‘trapezoid’ ... ** this is package ‘trapezoid’ version ‘2.0-2’ ** package ‘trapezoid’ 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/RtmpuIpOq8/R.INSTALL2fffc26fa637dd/trapezoid/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c trapezoid.c -o trapezoid.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c trapezoif_init.c -o trapezoif_init.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o trapezoid.so trapezoid.o trapezoif_init.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpuIpOq8/R.INSTALL2fffc26fa637dd/trapezoid/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-trapezoid/00new/trapezoid/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (trapezoid) begin installing package ‘mlr3torch’ * installing *source* package ‘genetics’ ... ** this is package ‘genetics’ version ‘1.3.8.1.3’ ** package ‘genetics’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (genetics) begin installing package ‘directlabels’ * installing *source* package ‘inlinedocs’ ... ** this is package ‘inlinedocs’ version ‘2023.9.4’ ** package ‘inlinedocs’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (inlinedocs) begin installing package ‘pedigree’ * installing *source* package ‘aplore3’ ... ** this is package ‘aplore3’ version ‘0.9’ ** package ‘aplore3’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (aplore3) begin installing package ‘grates’ * installing *source* package ‘leaflet.minicharts’ ... ** this is package ‘leaflet.minicharts’ version ‘0.6.2’ ** package ‘leaflet.minicharts’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (leaflet.minicharts) begin installing package ‘jointseg’ * installing *source* package ‘declared’ ... ** this is package ‘declared’ version ‘0.25’ ** package ‘declared’ 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/Rtmp1Wyr4z/R.INSTALL2ffb562f507d2e/declared/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c declared.c -o declared.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c registerDynamicSymbol.c -o registerDynamicSymbol.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o declared.so declared.o registerDynamicSymbol.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp1Wyr4z/R.INSTALL2ffb562f507d2e/declared/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-declared/00new/declared/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (declared) begin installing package ‘QCA’ * installing *source* package ‘PeakSegDisk’ ... ** this is package ‘PeakSegDisk’ version ‘2024.10.1’ ** package ‘PeakSegDisk’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmptzAHWg/R.INSTALL2ffbb17373aca5/PeakSegDisk/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PeakSegFPOPLog.cpp -o PeakSegFPOPLog.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c funPieceListLog.cpp -o funPieceListLog.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c interface.cpp -o interface.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o PeakSegDisk.so PeakSegFPOPLog.o funPieceListLog.o interface.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmptzAHWg/R.INSTALL2ffbb17373aca5/PeakSegDisk/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-PeakSegDisk/00new/PeakSegDisk/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (PeakSegDisk) * installing *source* package ‘SoilHyP’ ... ** this is package ‘SoilHyP’ version ‘0.1.7’ ** package ‘SoilHyP’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SoilHyP) * installing *source* package ‘fpop’ ... ** this is package ‘fpop’ version ‘2019.08.26’ ** package ‘fpop’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpIsO0ob/R.INSTALL2ffbaa43768432/fpop/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c BinSeg_MultiDim.cpp -o BinSeg_MultiDim.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Call_BinSeg_MultiDim.cpp -o Call_BinSeg_MultiDim.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Heap.cpp -o Heap.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Node.cpp -o Node.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Rwrappers.cc -o Rwrappers.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c colibri.cc -o colibri.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c liste.cc -o liste.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o fpop.so BinSeg_MultiDim.o Call_BinSeg_MultiDim.o Heap.o Node.o Rwrappers.o colibri.o liste.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpIsO0ob/R.INSTALL2ffbaa43768432/fpop/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-fpop/00new/fpop/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (fpop) * installing *source* package ‘hierfstat’ ... ** this is package ‘hierfstat’ version ‘0.5-11’ ** package ‘hierfstat’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (hierfstat) * installing *source* package ‘penaltyLearning’ ... ** this is package ‘penaltyLearning’ version ‘2024.9.3’ ** package ‘penaltyLearning’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpcVKjBq/R.INSTALL2ffbb552758de6/penaltyLearning/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c interface.cpp -o interface.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c largestContinuousMinimum.cpp -o largestContinuousMinimum.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c modelSelection.cpp -o modelSelection.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c modelSelectionFwd.cpp -o modelSelectionFwd.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c modelSelectionQuadratic.cpp -o modelSelectionQuadratic.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o penaltyLearning.so interface.o largestContinuousMinimum.o modelSelection.o modelSelectionFwd.o modelSelectionQuadratic.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpcVKjBq/R.INSTALL2ffbb552758de6/penaltyLearning/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-penaltyLearning/00new/penaltyLearning/libs ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (penaltyLearning) * installing *source* package ‘editData’ ... ** this is package ‘editData’ version ‘0.1.8’ ** package ‘editData’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (editData) * installing *source* package ‘SIBER’ ... ** this is package ‘SIBER’ version ‘2.1.9’ ** package ‘SIBER’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SIBER) * installing *source* package ‘directlabels’ ... ** this is package ‘directlabels’ version ‘2025.6.24’ ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (directlabels) * installing *source* package ‘grates’ ... ** this is package ‘grates’ version ‘1.5.0’ ** package ‘grates’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (grates) * installing *source* package ‘LOPART’ ... ** this is package ‘LOPART’ version ‘2024.6.19’ ** package ‘LOPART’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpapLoLk/R.INSTALL2ffbae1567d309/LOPART/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c LOPART.cpp -o LOPART.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c interface.cpp -o interface.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o LOPART.so LOPART.o RcppExports.o interface.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpapLoLk/R.INSTALL2ffbae1567d309/LOPART/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-LOPART/00new/LOPART/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (LOPART) * installing *source* package ‘jointseg’ ... ** this is package ‘jointseg’ version ‘1.0.3’ ** package ‘jointseg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpznDdD9/R.INSTALL3001f4362f5fb5/jointseg/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Heap.cpp -o Heap.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Node.cpp -o Node.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Rwrappers.cc -o Rwrappers.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c colibri.cc -o colibri.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c liste.cc -o liste.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o jointseg.so Heap.o Node.o Rwrappers.o colibri.o init.o liste.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpznDdD9/R.INSTALL3001f4362f5fb5/jointseg/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-jointseg/00new/jointseg/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (jointseg) * installing *source* package ‘poisbinom’ ... ** this is package ‘poisbinom’ version ‘1.0.2’ ** package ‘poisbinom’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpWTJI2F/R.INSTALL2ffb734d172b40/poisbinom/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c poisbinom.cpp -o poisbinom.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o poisbinom.so RcppExports.o init.o poisbinom.o -lfftw3 -lm -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpWTJI2F/R.INSTALL2ffb734d172b40/poisbinom/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-poisbinom/00new/poisbinom/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (poisbinom) begin installing package ‘SNPassoc’ * installing *source* package ‘pedigree’ ... ** this is package ‘pedigree’ version ‘1.4.2’ ** package ‘pedigree’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpIEFqAU/R.INSTALL30016942edf082/pedigree/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Pedigree.cpp -o Pedigree.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pedigree_init.c -o pedigree_init.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o pedigree.so Pedigree.o pedigree_init.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpIEFqAU/R.INSTALL30016942edf082/pedigree/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-pedigree/00new/pedigree/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (pedigree) * installing *source* package ‘ggdag’ ... ** this is package ‘ggdag’ version ‘0.2.13’ ** package ‘ggdag’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggdag) * installing *source* package ‘StAMPP’ ... ** this is package ‘StAMPP’ version ‘1.6.3’ ** package ‘StAMPP’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (StAMPP) * installing *source* package ‘mmod’ ... ** this is package ‘mmod’ version ‘1.3.3’ ** package ‘mmod’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (mmod) begin installing package ‘PopGenReport’ * installing *source* package ‘ggtern’ ... ** this is package ‘ggtern’ version ‘3.5.0’ ** package ‘ggtern’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggtern) * installing *source* package ‘polysat’ ... ** this is package ‘polysat’ version ‘1.7-7’ ** package ‘polysat’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpNumDCQ/R.INSTALL2ffb635dfe5f6/polysat/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c deSilvaFuncs.cpp -o deSilvaFuncs.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o polysat.so RcppExports.o deSilvaFuncs.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpNumDCQ/R.INSTALL2ffb635dfe5f6/polysat/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-polysat/00new/polysat/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (polysat) begin installing package ‘poppr’ * installing *source* package ‘binsegRcpp’ ... ** this is package ‘binsegRcpp’ version ‘2025.5.13’ ** package ‘binsegRcpp’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpQ3b7If/R.INSTALL2ffb9b8946d7d/binsegRcpp/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PiecewiseFunction.cpp -o PiecewiseFunction.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c binseg.cpp -o binseg.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c cum_median.cpp -o cum_median.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c depth_first.cpp -o depth_first.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c interface.cpp -o interface.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o binsegRcpp.so PiecewiseFunction.o RcppExports.o binseg.o cum_median.o depth_first.o interface.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpQ3b7If/R.INSTALL2ffb9b8946d7d/binsegRcpp/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-binsegRcpp/00new/binsegRcpp/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (binsegRcpp) * installing *source* package ‘animint2’ ... ** this is package ‘animint2’ version ‘2025.1.28’ ** package ‘animint2’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (animint2) * installing *source* package ‘QCA’ ... ** this is package ‘QCA’ version ‘3.23’ ** package ‘QCA’ 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/RtmpVJ48ec/R.INSTALL3002941b49b2f/QCA/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c CCubes.c -o CCubes.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c QCA.c -o QCA.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c consistency.c -o consistency.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c consistent_solution.c -o consistent_solution.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c find_consistent_models.c -o find_consistent_models.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c find_models.c -o find_models.o In file included from find_models.c:29: find_models.c: In function ‘find_models’: find_models.c:73:44: warning: ‘*mintpis[0]’ may be used uninitialized [-Wmaybe-uninitialized] 73 | p_temp2 = R_Calloc(picols * mintpis[0], int); | ~~~~~~~^~~ /home/hornik/tmp/R/include/R_ext/RS.h:55:58: note: in definition of macro ‘R_Calloc’ 55 | #define R_Calloc(n, t) (t *) R_chk_calloc( (R_SIZE_T) (n), sizeof(t) ) | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c generate_matrix.c -o generate_matrix.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c registerDynamicSymbol.c -o registerDynamicSymbol.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c row_dominance.c -o row_dominance.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sort_cols.c -o sort_cols.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sort_matrix.c -o sort_matrix.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c super_rows.c -o super_rows.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c truthTable.c -o truthTable.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c utils.c -o utils.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o QCA.so CCubes.o QCA.o consistency.o consistent_solution.o find_consistent_models.o find_models.o generate_matrix.o registerDynamicSymbol.o row_dominance.o sort_cols.o sort_matrix.o super_rows.o truthTable.o utils.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpVJ48ec/R.INSTALL3002941b49b2f/QCA/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-QCA/00new/QCA/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (QCA) * installing *source* package ‘SNPassoc’ ... ** this is package ‘SNPassoc’ version ‘2.1-2’ ** package ‘SNPassoc’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SNPassoc) * installing *source* package ‘plink’ ... ** this is package ‘plink’ version ‘1.5-1’ ** package ‘plink’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (plink) * installing *source* package ‘HardyWeinberg’ ... ** this is package ‘HardyWeinberg’ version ‘1.7.8’ ** package ‘HardyWeinberg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpsdeSx6/R.INSTALL2ffe7047afb559/HardyWeinberg/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c HWxChromosomal.cpp -o HWxChromosomal.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SNPHWEX.cpp -o SNPHWEX.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c support.cpp -o support.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o HardyWeinberg.so HWxChromosomal.o RcppExports.o SNPHWEX.o support.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpsdeSx6/R.INSTALL2ffe7047afb559/HardyWeinberg/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-HardyWeinberg/00new/HardyWeinberg/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (HardyWeinberg) * installing *source* package ‘mirtCAT’ ... ** this is package ‘mirtCAT’ version ‘1.14’ ** package ‘mirtCAT’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpOP6WCq/R.INSTALL3000c32082834c/mirtCAT/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CAT_functions.cpp -o CAT_functions.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c item_functions.cpp -o item_functions.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o mirtCAT.so CAT_functions.o item_functions.o -llapack -L/home/hornik/tmp/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpOP6WCq/R.INSTALL3000c32082834c/mirtCAT/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-mirtCAT/00new/mirtCAT/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (mirtCAT) * installing *source* package ‘reda’ ... ** this is package ‘reda’ version ‘0.5.5’ ** package ‘reda’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp5kusuq/R.INSTALL2ffb93644bb596/reda/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c nonparametric_mcf.cpp -o nonparametric_mcf.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c relativeRisk.cpp -o relativeRisk.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c utils.cpp -o utils.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o reda.so RcppExports.o nonparametric_mcf.o relativeRisk.o utils.o -fopenmp -llapack -L/home/hornik/tmp/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp5kusuq/R.INSTALL2ffb93644bb596/reda/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-reda/00new/reda/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (reda) * installing *source* package ‘poppr’ ... ** this is package ‘poppr’ version ‘2.9.7’ ** package ‘poppr’ 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/Rtmp6NTBKj/R.INSTALL3005e9559a0967/poppr/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c adjust_missing.c -o adjust_missing.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bitwise_distance.c -o bitwise_distance.o bitwise_distance.c: In function ‘association_index_haploid’: bitwise_distance.c:823:7: warning: unused variable ‘only_differences’ [-Wunused-variable] 823 | int only_differences; | ^~~~~~~~~~~~~~~~ bitwise_distance.c:815:7: warning: variable ‘chr_length’ set but not used [-Wunused-but-set-variable] 815 | int chr_length; | ^~~~~~~~~~ bitwise_distance.c:808:8: warning: unused variable ‘R_chr2_1’ [-Wunused-variable] 808 | SEXP R_chr2_1; | ^~~~~~~~ bitwise_distance.c: In function ‘association_index_diploid’: bitwise_distance.c:1190:7: warning: variable ‘chr_length’ set but not used [-Wunused-but-set-variable] 1190 | int chr_length; | ^~~~~~~~~~ bitwise_distance.c:1182:8: warning: unused variable ‘R_chr2_2’ [-Wunused-variable] 1182 | SEXP R_chr2_2; | ^~~~~~~~ bitwise_distance.c:1181:8: warning: unused variable ‘R_chr2_1’ [-Wunused-variable] 1181 | SEXP R_chr2_1; | ^~~~~~~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mlg_clustering.c -o mlg_clustering.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mlg_counter.c -o mlg_counter.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c msn.c -o msn.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c omp_test.c -o omp_test.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c permut_shuffler.c -o permut_shuffler.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c poppr_distance.c -o poppr_distance.o poppr_distance.c: In function ‘bruvo_between’: poppr_distance.c:428:13: warning: variable ‘numel’ set but not used [-Wunused-but-set-variable] 428 | int numel; // Number of elements in returned matrix | ^~~~~ gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o poppr.so adjust_missing.o bitwise_distance.o init.o mlg_clustering.o mlg_counter.o msn.o omp_test.o permut_shuffler.o poppr_distance.o -fopenmp -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp6NTBKj/R.INSTALL3005e9559a0967/poppr/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-poppr/00new/poppr/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a generic function from function ‘as.genambig’ in package ‘poppr’ ** help *** installing help indices *** 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 (poppr) * installing *source* package ‘dartR.data’ ... ** this is package ‘dartR.data’ version ‘1.0.8’ ** package ‘dartR.data’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (dartR.data) * installing *source* package ‘mlr3torch’ ... ** this is package ‘mlr3torch’ version ‘0.2.1’ ** package ‘mlr3torch’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (mlr3torch) * installing *source* package ‘PopGenReport’ ... ** this is package ‘PopGenReport’ version ‘3.1’ ** package ‘PopGenReport’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (PopGenReport) * installing *source* package ‘re2’ ... ** this is package ‘re2’ version ‘0.1.4’ ** package ‘re2’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpdklWbb/R.INSTALL2ffb9841cc95a2/re2/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2google/util/rune.cc -o re2google/util/rune.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2google/util/strutil.cc -o re2google/util/strutil.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2google/re2/bitstate.cc -o re2google/re2/bitstate.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2google/re2/compile.cc -o re2google/re2/compile.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2google/re2/dfa.cc -o re2google/re2/dfa.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2google/re2/filtered_re2.cc -o re2google/re2/filtered_re2.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2google/re2/mimics_pcre.cc -o re2google/re2/mimics_pcre.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2google/re2/nfa.cc -o re2google/re2/nfa.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2google/re2/onepass.cc -o re2google/re2/onepass.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2google/re2/parse.cc -o re2google/re2/parse.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2google/re2/perl_groups.cc -o re2google/re2/perl_groups.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2google/re2/prefilter.cc -o re2google/re2/prefilter.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2google/re2/prefilter_tree.cc -o re2google/re2/prefilter_tree.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2google/re2/prog.cc -o re2google/re2/prog.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2google/re2/re2.cc -o re2google/re2/re2.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2google/re2/regexp.cc -o re2google/re2/regexp.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2google/re2/set.cc -o re2google/re2/set.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2google/re2/simplify.cc -o re2google/re2/simplify.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2google/re2/stringpiece.cc -o re2google/re2/stringpiece.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2google/re2/tostring.cc -o re2google/re2/tostring.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2google/re2/unicode_casefold.cc -o re2google/re2/unicode_casefold.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2google/re2/unicode_groups.cc -o re2google/re2/unicode_groups.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2_re2proxy.cpp -o re2_re2proxy.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2_regexp.cpp -o re2_regexp.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2_do_match.cpp -o re2_do_match.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2_locate.cpp -o re2_locate.o re2_locate.cpp: In member function ‘virtual void {anonymous}::DoLocateAll::match_found(int, re2::StringPiece&, re2::RE2Proxy::Adapter&, const re2::AllMatches&)’: re2_locate.cpp:74:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 74 | for (int row = 0; row < all_matches.size(); row++) { | ~~~~^~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2_get_options.cpp -o re2_get_options.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2_match.cpp -o re2_match.o re2_match.cpp: In member function ‘virtual void {anonymous}::DoMatchAll::match_found(int, re2::StringPiece&, re2::RE2Proxy::Adapter&, const re2::AllMatches&)’: re2_match.cpp:143:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 143 | for (int row = 0; row < all_matches.size(); row++) { | ~~~~^~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2_detect.cpp -o re2_detect.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2_match_cpp.cpp -o re2_match_cpp.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2_split.cpp -o re2_split.o re2_split.cpp: In member function ‘virtual void {anonymous}::DoSplit::match_found(int, re2::StringPiece&, re2::RE2Proxy::Adapter&, const re2::AllMatches&)’: re2_split.cpp:36:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 36 | for (; row < all_matches.size(); row++) { | ~~~~^~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2_extract_replace.cpp -o re2_extract_replace.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2_replace.cpp -o re2_replace.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2_quote_meta.cpp -o re2_quote_meta.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2_max_submatch.cpp -o re2_max_submatch.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2_capturing_group.cpp -o re2_capturing_group.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -Ire2google -DNDEBUG -include re2/re2.h -DRE2_R_BUILD -pthread -DRE2_ON_VALGRIND -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c re2_random_text.cpp -o re2_random_text.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o re2.so re2google/util/rune.o re2google/util/strutil.o re2google/re2/bitstate.o re2google/re2/compile.o re2google/re2/dfa.o re2google/re2/filtered_re2.o re2google/re2/mimics_pcre.o re2google/re2/nfa.o re2google/re2/onepass.o re2google/re2/parse.o re2google/re2/perl_groups.o re2google/re2/prefilter.o re2google/re2/prefilter_tree.o re2google/re2/prog.o re2google/re2/re2.o re2google/re2/regexp.o re2google/re2/set.o re2google/re2/simplify.o re2google/re2/stringpiece.o re2google/re2/tostring.o re2google/re2/unicode_casefold.o re2google/re2/unicode_groups.o RcppExports.o re2_re2proxy.o re2_regexp.o re2_do_match.o re2_locate.o re2_get_options.o re2_match.o re2_detect.o re2_match_cpp.o re2_split.o re2_extract_replace.o re2_replace.o re2_quote_meta.o re2_max_submatch.o re2_capturing_group.o re2_random_text.o -pthread -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpdklWbb/R.INSTALL2ffb9841cc95a2/re2/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-re2/00new/re2/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (re2) checking directlabels_2025.6.24.tar.gz ... checking AlphaPart_0.9.8.tar.gz ... checking BasketballAnalyzeR_0.8.0.tar.gz ... checking CoSMoS_2.1.0.tar.gz ... checking foreSIGHT_1.2.0.tar.gz ... checking jrt_1.1.2.tar.gz ... checking prevR_5.0.0.tar.gz ... checking primerTree_1.0.6.tar.gz ... checking QCAtools_0.2.3.tar.gz ... checking reReg_1.4.7.tar.gz ... checking rreg_0.2.1.tar.gz ... checking atime_2025.5.24.tar.gz ... checking aum_2024.6.19.tar.gz ... checking binsegRcpp_2025.5.13.tar.gz ... checking dartR_2.9.9.5.tar.gz ... checking dartR.base_1.0.5.tar.gz ... checking denvax_0.1.2.tar.gz ... checking episensr_2.0.0.tar.gz ... checking htsr_2.1.6.tar.gz ... checking mirt_1.44.0.tar.gz ... checking mlr3resampling_2025.6.23.tar.gz ... checking penaltyLearning_2024.9.3.tar.gz ... Depends: Package: directlabels Imports: grid (>= 3.0.0), quadprog Timings: user system elapsed directlabels 93.781 5.589 101.651 Results: Check status summary: NOTE OK Source packages 0 1 Reverse depends 3 18 Check results summary: directlabels ... OK rdepends_AlphaPart ... OK rdepends_atime ... OK rdepends_aum ... OK rdepends_BasketballAnalyzeR ... OK rdepends_binsegRcpp ... OK rdepends_CoSMoS ... OK rdepends_dartR.base ... OK rdepends_dartR ... OK rdepends_denvax ... OK rdepends_episensr ... OK rdepends_foreSIGHT ... OK rdepends_htsr ... OK rdepends_jrt ... NOTE * checking Rd files ... [0s/0s] NOTE rdepends_mirt ... OK rdepends_mlr3resampling ... OK rdepends_penaltyLearning ... OK rdepends_prevR ... OK rdepends_primerTree ... NOTE * checking Rd cross-references ... NOTE rdepends_QCAtools ... OK rdepends_reReg ... OK rdepends_rreg ... NOTE * checking Rd files ... [0s/0s] NOTE Check results changes: Package: denvax Check: CRAN incoming feasibility Old result: NOTE Package: mlr3resampling [Old version: 2025.3.30, New version: 2025.6.23] Check: examples Old result: ERROR New result: OK Package: mlr3resampling [Old version: 2025.3.30, New version: 2025.6.23] Check: re-building of vignette outputs Old result: ERROR New result: OK Package: QCAtools Check: CRAN incoming feasibility Old result: NOTE