downloading reverse dependencies ... downloading aihuman_1.0.1.tar.gz ... ok downloading chillR_0.76.tar.gz ... ok downloading CIMTx_1.2.0.tar.gz ... ok downloading DImodelsVis_1.0.3.tar.gz ... ok downloading ForIT_2.5.0.tar.gz ... ok downloading gaussplotR_0.2.5.tar.gz ... ok downloading injurytools_1.0.3.tar.gz ... ok downloading klovan_0.1.0.tar.gz ... ok downloading loewesadditivity_0.1.0.tar.gz ... ok downloading Markovchart_2.1.5.tar.gz ... ok downloading mosaicCalc_0.6.4.tar.gz ... ok downloading nimblewomble_0.1.0.tar.gz ... ok downloading OVtool_1.0.3.tar.gz ... ok downloading paths_0.1.1.tar.gz ... ok downloading senseweight_0.0.1.tar.gz ... ok downloading SOMbrero_1.4.4.tar.gz ... ok downloading survSens_1.1.0.tar.gz ... ok downloading TPMplt_0.1.7.tar.gz ... ok downloading voluModel_0.2.3.tar.gz ... ok downloading vprr_0.2.3.tar.gz ... ok downloading ICvectorfields_0.1.2.tar.gz ... ok downloading igrf_2.0.tar.gz ... ok downloading pcpr_1.0.0.tar.gz ... ok downloading plotthis_0.7.4.tar.gz ... ok downloading SensIAT_0.2.0.tar.gz ... ok installing dependencies ‘calculus’, ‘clustree’, ‘cmocean’, ‘DImodels’, ‘DImodelsMulti’, ‘ecmwfr’, ‘gglogger’, ‘ggmanh’, ‘ggupset’, ‘ggVennDiagram’, ‘iNEXT’, ‘kriging’, ‘ManifoldOptim’, ‘MAVE’, ‘metR’, ‘modEvA’, ‘ncf’, ‘OptimalCutpoints’, ‘orthogonalsplinebasis’, ‘PieGlyph’, ‘plotwidgets’, ‘rangeBuilder’, ‘rcdo’, ‘RGeostats’, ‘RMAWGEN’, ‘tmle’, ‘varhandle’, ‘VBTree’ Warning: package ‘RGeostats’ 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 ‘hnp’, ‘SeqArray’, ‘pals’ begin installing package ‘SeqArray’ begin installing package ‘hnp’ begin installing package ‘pals’ begin installing package ‘kriging’ begin installing package ‘rcdo’ begin installing package ‘ecmwfr’ begin installing package ‘RMAWGEN’ begin installing package ‘tmle’ begin installing package ‘PieGlyph’ begin installing package ‘plotwidgets’ begin installing package ‘calculus’ begin installing package ‘varhandle’ begin installing package ‘VBTree’ begin installing package ‘modEvA’ begin installing package ‘cmocean’ begin installing package ‘rangeBuilder’ begin installing package ‘ncf’ begin installing package ‘clustree’ begin installing package ‘gglogger’ begin installing package ‘ggVennDiagram’ begin installing package ‘ggupset’ begin installing package ‘iNEXT’ begin installing package ‘OptimalCutpoints’ begin installing package ‘MAVE’ begin installing package ‘orthogonalsplinebasis’ begin installing package ‘ManifoldOptim’ begin installing package ‘metR’ * installing *source* package ‘cmocean’ ... ** this is package ‘cmocean’ version ‘0.3-2’ ** package ‘cmocean’ 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 (cmocean) * installing *source* package ‘varhandle’ ... ** this is package ‘varhandle’ version ‘2.0.6’ ** package ‘varhandle’ 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 (varhandle) * installing *source* package ‘kriging’ ... ** this is package ‘kriging’ version ‘1.2’ ** package ‘kriging’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-1) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp6AlQqC/R.INSTALL213128524febb0/kriging/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c kriging.c -o kriging.o kriging.c: In function ‘krigpred’: kriging.c:136:13: warning: unused variable ‘k’ [-Wunused-variable] 136 | int i, j, k; | ^ gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o kriging.so kriging.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp6AlQqC/R.INSTALL213128524febb0/kriging/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-kriging/00new/kriging/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 (kriging) * installing *source* package ‘plotwidgets’ ... ** this is package ‘plotwidgets’ version ‘0.5.1’ ** package ‘plotwidgets’ 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 (plotwidgets) * installing *source* package ‘VBTree’ ... ** this is package ‘VBTree’ version ‘0.1.1’ ** package ‘VBTree’ 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 (VBTree) * installing *source* package ‘orthogonalsplinebasis’ ... ** this is package ‘orthogonalsplinebasis’ version ‘0.1.7’ ** package ‘orthogonalsplinebasis’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘integrate’ in package ‘orthogonalsplinebasis’ ** 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 (orthogonalsplinebasis) * installing *source* package ‘hnp’ ... ** this is package ‘hnp’ version ‘1.2-7’ ** package ‘hnp’ 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 (hnp) begin installing package ‘DImodels’ * installing *source* package ‘pals’ ... ** this is package ‘pals’ version ‘1.10’ ** package ‘pals’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** 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 (pals) * installing *source* package ‘ecmwfr’ ... ** this is package ‘ecmwfr’ version ‘2.0.3’ ** package ‘ecmwfr’ 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 (ecmwfr) * installing *source* package ‘ncf’ ... ** this is package ‘ncf’ version ‘1.3-2’ ** package ‘ncf’ 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 (ncf) * installing *source* package ‘OptimalCutpoints’ ... ** this is package ‘OptimalCutpoints’ version ‘1.1-5’ ** package ‘OptimalCutpoints’ 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 (OptimalCutpoints) * installing *source* package ‘gglogger’ ... ** this is package ‘gglogger’ version ‘0.1.6’ ** package ‘gglogger’ 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 (gglogger) * installing *source* package ‘ggupset’ ... ** this is package ‘ggupset’ version ‘0.4.1’ ** package ‘ggupset’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (ggupset) * installing *source* package ‘ggVennDiagram’ ... ** this is package ‘ggVennDiagram’ version ‘1.5.4’ ** package ‘ggVennDiagram’ 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 (ggVennDiagram) * installing *source* package ‘PieGlyph’ ... ** this is package ‘PieGlyph’ version ‘1.1.0’ ** package ‘PieGlyph’ 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 (PieGlyph) * installing *source* package ‘clustree’ ... ** this is package ‘clustree’ version ‘0.5.1’ ** package ‘clustree’ 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 (clustree) * installing *source* package ‘rcdo’ ... ** this is package ‘rcdo’ version ‘0.3.0’ ** package ‘rcdo’ 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 (rcdo) * installing *source* package ‘RMAWGEN’ ... ** this is package ‘RMAWGEN’ version ‘1.3.9.3’ ** package ‘RMAWGEN’ 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 (RMAWGEN) * installing *source* package ‘tmle’ ... ** this is package ‘tmle’ version ‘2.1.1’ ** package ‘tmle’ 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 (tmle) * installing *source* package ‘rangeBuilder’ ... ** this is package ‘rangeBuilder’ version ‘2.2’ ** package ‘rangeBuilder’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-1) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpBoqIN8/R.INSTALL21315634ef04a4/rangeBuilder/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/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++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/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 rangeBuilderRcpp.cpp -o rangeBuilderRcpp.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o rangeBuilder.so RcppExports.o rangeBuilderRcpp.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpBoqIN8/R.INSTALL21315634ef04a4/rangeBuilder/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-rangeBuilder/00new/rangeBuilder/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 (rangeBuilder) * installing *source* package ‘metR’ ... ** this is package ‘metR’ version ‘0.18.2’ ** 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 (metR) * installing *source* package ‘DImodels’ ... ** this is package ‘DImodels’ version ‘1.3.3’ ** package ‘DImodels’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** 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 (DImodels) begin installing package ‘DImodelsMulti’ * installing *source* package ‘iNEXT’ ... ** this is package ‘iNEXT’ version ‘3.0.2’ ** package ‘iNEXT’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-1) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmplQfC6Y/R.INSTALL2131717e17e509/iNEXT/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/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++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/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 subfuns.cpp -o subfuns.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o iNEXT.so RcppExports.o subfuns.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmplQfC6Y/R.INSTALL2131717e17e509/iNEXT/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-iNEXT/00new/iNEXT/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 (iNEXT) * installing *source* package ‘calculus’ ... ** this is package ‘calculus’ version ‘1.1.0’ ** package ‘calculus’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-1) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpUYUxke/R.INSTALL21314d6e21a6a2/calculus/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/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++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/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 calculus.cpp -o calculus.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o calculus.so RcppExports.o calculus.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpUYUxke/R.INSTALL21314d6e21a6a2/calculus/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-calculus/00new/calculus/libs ** 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 ** 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 (calculus) * installing *source* package ‘DImodelsMulti’ ... ** this is package ‘DImodelsMulti’ version ‘1.2.0’ ** package ‘DImodelsMulti’ 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 (DImodelsMulti) * installing *source* package ‘modEvA’ ... ** this is package ‘modEvA’ version ‘3.39’ ** package ‘modEvA’ 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 ** 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 (modEvA) * installing *source* package ‘SeqArray’ ... ** this is package ‘SeqArray’ version ‘1.48.2’ ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-1) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-1) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpDYFgrz/R.INSTALL213119312e6575/SeqArray/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ConvToGDS.cpp -o ConvToGDS.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c FileMerge.cpp -o FileMerge.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c GetData.cpp -o GetData.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Index.cpp -o Index.o Index.cpp: In member function ‘void SeqArray::CProgress::ShowProgress()’: Index.cpp:1273:66: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1273 | if (R_Process_StatusFName.size() < *R_Process_Count) return; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c LinkSNPRelate.cpp -o LinkSNPRelate.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Methods.cpp -o Methods.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_SeqArray.c -o R_SeqArray.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ReadBySample.cpp -o ReadBySample.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ReadByUnit.cpp -o ReadByUnit.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ReadByVariant.cpp -o ReadByVariant.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SeqArray.cpp -o SeqArray.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pkg_test.cpp -o pkg_test.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c samtools_ext.c -o samtools_ext.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c vectorization.cpp -o vectorization.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o SeqArray.so ConvGDS2VCF.o ConvToGDS.o ConvVCF2GDS.o FileMerge.o GetData.o Index.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByUnit.o ReadByVariant.o SeqArray.o pkg_test.o samtools_ext.o vectorization.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpDYFgrz/R.INSTALL213119312e6575/SeqArray/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-SeqArray/00new/SeqArray/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 (SeqArray) begin installing package ‘ggmanh’ * installing *source* package ‘MAVE’ ... ** this is package ‘MAVE’ version ‘1.3.12’ ** package ‘MAVE’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-1) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpzLxm2H/R.INSTALL21316d65630959/MAVE/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/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 CVfast_R.cpp -o CVfast_R.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo.h:29, from CVfast_R.cpp:4: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/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 MAVEfast.cpp -o MAVEfast.o MAVEfast.cpp: In function ‘void MAVEfast(emxArray_real_T*, const emxArray_real_T*, emxArray_char_T*, double, double, emxArray_real_T*, emxArray_real_T*, emxArray_real_T*, emxArray_real_T*, emxArray_real_T*)’: MAVEfast.cpp:2285:10: warning: ‘di_data$’ may be used uninitialized [-Wmaybe-uninitialized] 2285 | br = di_data[0]; | ~~~^~~~~~~~~~~~ MAVEfast.cpp:989:7: note: ‘di_data$’ was declared here 989 | int di_data[1]; | ^~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/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 MAVEfast_R.cpp -o MAVEfast_R.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo.h:29, from MAVEfast_R.cpp:9: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ MAVEfast_R.cpp: In function ‘Rcpp::List MAVEfastCpp(Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::CharacterVector, double, double)’: MAVEfast_R.cpp:47:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 47 | for(int i=0;i