downloading reverse dependencies ... downloading lancor_0.1.2.tar.gz ... ok downloading nlts_1.0-2.tar.gz ... ok downloading stops_1.8-2.tar.gz ... ok downloading bullseye_0.1.1.tar.gz ... ok downloading Hmisc_5.2-2.tar.gz ... ok installing dependencies ‘acepack’, ‘cmaes’, ‘cordillera’, ‘DendSer’, ‘DiceOptim’, ‘htm2txt’, ‘linkspotter’, ‘openintro’, ‘pomp’, ‘qreport’, ‘safer’, ‘scagnostics’, ‘smacofx’, ‘sparkline’ also installing the dependencies ‘GeneralizedUmatrix’, ‘ProjectionBasedClustering’, ‘rAmCharts’, ‘airports’, ‘cherryblossom’, ‘usdata’ begin installing package ‘GeneralizedUmatrix’ begin installing package ‘rAmCharts’ begin installing package ‘airports’ begin installing package ‘cherryblossom’ begin installing package ‘usdata’ begin installing package ‘acepack’ begin installing package ‘cmaes’ begin installing package ‘cordillera’ begin installing package ‘DiceOptim’ begin installing package ‘pomp’ begin installing package ‘scagnostics’ begin installing package ‘DendSer’ begin installing package ‘qreport’ begin installing package ‘sparkline’ begin installing package ‘safer’ begin installing package ‘htm2txt’ * 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) * installing *source* package ‘htm2txt’ ... ** this is package ‘htm2txt’ version ‘2.2.2’ ** package ‘htm2txt’ 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 (htm2txt) * installing *source* package ‘safer’ ... ** this is package ‘safer’ version ‘0.2.1’ ** package ‘safer’ 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 (safer) * installing *source* package ‘cordillera’ ... ** this is package ‘cordillera’ version ‘1.0-3’ ** package ‘cordillera’ 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 (cordillera) * installing *source* package ‘cherryblossom’ ... ** this is package ‘cherryblossom’ version ‘0.1.0’ ** package ‘cherryblossom’ 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 (cherryblossom) * installing *source* package ‘airports’ ... ** this is package ‘airports’ version ‘0.1.0’ ** package ‘airports’ 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 (airports) * installing *source* package ‘sparkline’ ... ** this is package ‘sparkline’ version ‘2.0’ ** package ‘sparkline’ 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 (sparkline) * installing *source* package ‘scagnostics’ ... ** this is package ‘scagnostics’ version ‘0.2-6’ ** package ‘scagnostics’ 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 (scagnostics) * installing *source* package ‘DendSer’ ... ** this is package ‘DendSer’ version ‘1.0.2’ ** package ‘DendSer’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-12) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmphkPPeW/R.INSTALL396312770d147c/DendSer/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c DendSer_init.c -o DendSer_init.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c carct.c -o carct.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cbar.c -o cbar.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c clpl.c -o clpl.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cpl.c -o cpl.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o DendSer.so DendSer_init.o carct.o cbar.o clpl.o cpl.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmphkPPeW/R.INSTALL396312770d147c/DendSer/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-DendSer/00new/DendSer/libs ** R ** demo ** byte-compile and prepare package for lazy loading Warning in seriation::set_criterion_method("dist", "BAR", criterion_method_dist_BAR, : Entry with name ‘BAR’ already exists! Modifying entry. ** 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 (DendSer) * installing *source* package ‘acepack’ ... ** this is package ‘acepack’ version ‘1.5.1’ ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-12) 14.2.0’ using Fortran compiler: ‘GNU Fortran (Debian 14.2.0-12) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp0EbLjD/R.INSTALL3962fb650af2f6/acepack/src' gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c acedata.f90 -o acedata.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c acemod.f90 -o acemod.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c bakfit.f90 -o bakfit.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c calcmu.f90 -o calcmu.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c ctsub.f90 -o ctsub.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c favas.f90 -o favas.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/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 gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c mace.f90 -o mace.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c model.f90 -o model.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c montne.f90 -o montne.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c rlsmo.f90 -o rlsmo.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c scail.f90 -o scail.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c smooth.f90 -o smooth.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c smothr.f90 -o smothr.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c sort.f90 -o sort.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c supersmoother.f90 -o supersmoother.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c supsmu.f90 -o supsmu.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o acepack.so acedata.o acemod.o bakfit.o calcmu.o ctsub.o favas.o init.o mace.o model.o montne.o rlsmo.o scail.o smooth.o smothr.o sort.o supersmoother.o supsmu.o -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp0EbLjD/R.INSTALL3962fb650af2f6/acepack/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-acepack/00new/acepack/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 (acepack) * installing *source* package ‘usdata’ ... ** this is package ‘usdata’ version ‘0.3.1’ ** package ‘usdata’ 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 (usdata) begin installing package ‘openintro’ * installing *source* package ‘DiceOptim’ ... ** this is package ‘DiceOptim’ version ‘2.1.1’ ** package ‘DiceOptim’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-12) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpsS5a3w/R.INSTALL39630478c020e9/DiceOptim/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c davies.c -o davies.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c packagename_init.c -o packagename_init.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o DiceOptim.so davies.o packagename_init.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpsS5a3w/R.INSTALL39630478c020e9/DiceOptim/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-DiceOptim/00new/DiceOptim/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 (DiceOptim) * installing *source* package ‘qreport’ ... ** this is package ‘qreport’ version ‘1.0-1’ ** package ‘qreport’ 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 (qreport) * installing *source* package ‘rAmCharts’ ... ** this is package ‘rAmCharts’ version ‘2.1.16’ ** package ‘rAmCharts’ 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 (rAmCharts) begin installing package ‘linkspotter’ * installing *source* package ‘linkspotter’ ... ** this is package ‘linkspotter’ version ‘1.3.0’ ** package ‘linkspotter’ 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 (linkspotter) * installing *source* package ‘pomp’ ... ** this is package ‘pomp’ version ‘6.1’ ** package ‘pomp’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-12) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpbLBwum/R.INSTALL3963084324b5f8/pomp/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bspline.c -o bspline.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dinit.c -o dinit.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c distributions.c -o distributions.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dmeasure.c -o dmeasure.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dprior.c -o dprior.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dprocess.c -o dprocess.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c emeasure.c -o emeasure.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c euler.c -o euler.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c gompertz.c -o gompertz.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/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 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c logmeanexp.c -o logmeanexp.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c lookup_table.c -o lookup_table.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mif2.c -o mif2.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ou2.c -o ou2.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c partrans.c -o partrans.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pfilter.c -o pfilter.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pomp_fun.c -o pomp_fun.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c probe.c -o probe.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c probe_acf.c -o probe_acf.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c probe_marginal.c -o probe_marginal.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c probe_nlar.c -o probe_nlar.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c resample.c -o resample.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rinit.c -o rinit.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rmeasure.c -o rmeasure.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rprior.c -o rprior.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rprocess.c -o rprocess.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c simulate.c -o simulate.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c skeleton.c -o skeleton.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sobolseq.c -o sobolseq.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ssa.c -o ssa.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c synth_lik.c -o synth_lik.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c trajectory.c -o trajectory.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c transformations.c -o transformations.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c userdata.c -o userdata.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c vmeasure.c -o vmeasure.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c wpfilter.c -o wpfilter.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o pomp.so bspline.o dinit.o distributions.o dmeasure.o dprior.o dprocess.o emeasure.o euler.o gompertz.o init.o logmeanexp.o lookup_table.o mif2.o ou2.o partrans.o pfilter.o pomp_fun.o probe.o probe_acf.o probe_marginal.o probe_nlar.o resample.o rinit.o rmeasure.o rprior.o rprocess.o simulate.o skeleton.o sobolseq.o ssa.o synth_lik.o trajectory.o transformations.o userdata.o vmeasure.o wpfilter.o -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpbLBwum/R.INSTALL3963084324b5f8/pomp/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-pomp/00new/pomp/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 (pomp) * installing *source* package ‘GeneralizedUmatrix’ ... ** this is package ‘GeneralizedUmatrix’ version ‘1.2.6’ ** package ‘GeneralizedUmatrix’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-12) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpIBoHdW/R.INSTALL396300368e318f/GeneralizedUmatrix/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c Delta3DWeightsC.cpp -o Delta3DWeightsC.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c addRowWiseC.cpp -o addRowWiseC.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c trainstepC.cpp -o trainstepC.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c trainstepC2.cpp -o trainstepC2.o In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppParallel/include/tbb/tbb.h:32, from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppParallel/include/RcppParallel/TBB.h:10, from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppParallel/include/RcppParallel.h:24, from trainstepC2.cpp:2: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic& tbb::internal::as_atomic(T&) [with T = long unsigned int]’: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here 251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id); | ~~~~~~~~~^~~~~~~~~~~~~~~~ /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘long unsigned int’ to ‘tbb::atomic&’ does not use ‘constexpr tbb::atomic::atomic(long unsigned int)’ [-Wcast-user-defined] 544 | return (atomic&)t; | ^~~~~~~~~~~~~ /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]’: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here 291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL ) | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘tbb::interface5::internal::hash_map_base::bucket*’ to ‘tbb::atomic&’ does not use ‘constexpr tbb::atomic::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]’ [-Wcast-user-defined] 544 | return (atomic&)t; | ^~~~~~~~~~~~~ g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o GeneralizedUmatrix.so Delta3DWeightsC.o RcppExports.o addRowWiseC.o trainstepC.o trainstepC2.o -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpIBoHdW/R.INSTALL396300368e318f/GeneralizedUmatrix/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-GeneralizedUmatrix/00new/GeneralizedUmatrix/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 (GeneralizedUmatrix) begin installing package ‘ProjectionBasedClustering’ * installing *source* package ‘openintro’ ... ** this is package ‘openintro’ version ‘2.5.0’ ** package ‘openintro’ 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 (openintro) * installing *source* package ‘ProjectionBasedClustering’ ... ** this is package ‘ProjectionBasedClustering’ version ‘1.2.2’ ** package ‘ProjectionBasedClustering’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-12) 14.2.0’ using C++17 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpBbS4B6/R.INSTALL3967b81a533071/ProjectionBasedClustering/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c DijkstraSSSP.cpp -o DijkstraSSSP.o DijkstraSSSP.cpp: In function ‘Rcpp::NumericVector DijkstraSSSP(Rcpp::NumericMatrix, Rcpp::NumericMatrix, int)’: DijkstraSSSP.cpp:38:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 38 | for(int i=0;i::run(double*, int, int, double*, int, double, double, int, int, int, int, bool, int, double, double, double*, bool, double) [with treeT = SplitTree; double (* dist_fn)(const DataPoint&, const DataPoint&) = euclidean_distance]’, inlined from ‘Rcpp::NumericMatrix opt_multicore_tnse_cpp(Rcpp::NumericMatrix, int, double, int, int, double, int, double, double, int, double, int)’ at tsne.cpp:653:23: tsne.cpp:186:17: warning: ‘error_rc_prev’ may be used uninitialized [-Wmaybe-uninitialized] 186 | if (error_rc < error_rc_prev && iter > auto_iter_buffer_ee) { | ^~ tsne.cpp: In function ‘Rcpp::NumericMatrix opt_multicore_tnse_cpp(Rcpp::NumericMatrix, int, double, int, int, double, int, double, double, int, double, int)’: tsne.cpp:159:12: note: ‘error_rc_prev’ was declared here 159 | double error_rc_prev; // to store previous iteration's error rate of change in auto_iter mode | ^~~~~~~~~~~~~ In member function ‘double TSNE::computeGradient(int*, int*, double*, double*, int, int, double*, double, bool) [with treeT = SplitTree; double (* dist_fn)(const DataPoint&, const DataPoint&) = euclidean_distance]’, inlined from ‘void TSNE::run(double*, int, int, double*, int, double, double, int, int, int, int, bool, int, double, double, double*, bool, double) [with treeT = SplitTree; double (* dist_fn)(const DataPoint&, const DataPoint&) = euclidean_distance]’ at tsne.cpp:180:39, inlined from ‘Rcpp::NumericMatrix opt_multicore_tnse_cpp(Rcpp::NumericMatrix, int, double, int, int, double, int, double, double, int, double, int)’ at tsne.cpp:653:23: tsne.cpp:271:13: warning: ‘need_eval_error_algo’ may be used uninitialized [-Wmaybe-uninitialized] 271 | #pragma omp parallel for reduction(+:P_i_sum,C) | ^~~ tsne.cpp: In function ‘Rcpp::NumericMatrix opt_multicore_tnse_cpp(Rcpp::NumericMatrix, int, double, int, int, double, int, double, double, int, double, int)’: tsne.cpp:169:14: note: ‘need_eval_error_algo’ was declared here 169 | bool need_eval_error_algo, need_eval_error_verbose = false; | ^~~~~~~~~~~~~~~~~~~~ In member function ‘void TSNE::run(double*, int, int, double*, int, double, double, int, int, int, int, bool, int, double, double, double*, bool, double) [with treeT = SplitTree; double (* dist_fn)(const DataPoint&, const DataPoint&) = euclidean_distance_squared]’, inlined from ‘Rcpp::NumericMatrix opt_multicore_tnse_cpp(Rcpp::NumericMatrix, int, double, int, int, double, int, double, double, int, double, int)’ at tsne.cpp:649:23: tsne.cpp:186:17: warning: ‘error_rc_prev’ may be used uninitialized [-Wmaybe-uninitialized] 186 | if (error_rc < error_rc_prev && iter > auto_iter_buffer_ee) { | ^~ tsne.cpp: In function ‘Rcpp::NumericMatrix opt_multicore_tnse_cpp(Rcpp::NumericMatrix, int, double, int, int, double, int, double, double, int, double, int)’: tsne.cpp:159:12: note: ‘error_rc_prev’ was declared here 159 | double error_rc_prev; // to store previous iteration's error rate of change in auto_iter mode | ^~~~~~~~~~~~~ In member function ‘double TSNE::computeGradient(int*, int*, double*, double*, int, int, double*, double, bool) [with treeT = SplitTree; double (* dist_fn)(const DataPoint&, const DataPoint&) = euclidean_distance_squared]’, inlined from ‘void TSNE::run(double*, int, int, double*, int, double, double, int, int, int, int, bool, int, double, double, double*, bool, double) [with treeT = SplitTree; double (* dist_fn)(const DataPoint&, const DataPoint&) = euclidean_distance_squared]’ at tsne.cpp:180:39, inlined from ‘Rcpp::NumericMatrix opt_multicore_tnse_cpp(Rcpp::NumericMatrix, int, double, int, int, double, int, double, double, int, double, int)’ at tsne.cpp:649:23: tsne.cpp:271:13: warning: ‘need_eval_error_algo’ may be used uninitialized [-Wmaybe-uninitialized] 271 | #pragma omp parallel for reduction(+:P_i_sum,C) | ^~~ tsne.cpp: In function ‘Rcpp::NumericMatrix opt_multicore_tnse_cpp(Rcpp::NumericMatrix, int, double, int, int, double, int, double, double, int, double, int)’: tsne.cpp:169:14: note: ‘need_eval_error_algo’ was declared here 169 | bool need_eval_error_algo, need_eval_error_verbose = false; | ^~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o ProjectionBasedClustering.so DijkstraSSSP.o NeRV.o RcppExports.o c_measure.o calculatedistancematrix.o conjugategradientopt.o conttrust.o datamatrix.o dataset.o distancematrix.o dynamicdouble.o euclidean.o euclideansquared.o exception.o goldensectionsearch.o inputprobentropy.o klmeasure.o klrank.o nervcostfunction.o nervoptstrat.o nervprobability.o randomdatagenerator.o rankmatrix.o recorder.o splittree.o tsne.o -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpBbS4B6/R.INSTALL3967b81a533071/ProjectionBasedClustering/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-ProjectionBasedClustering/00new/ProjectionBasedClustering/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 (ProjectionBasedClustering) begin installing package ‘smacofx’ * installing *source* package ‘smacofx’ ... ** this is package ‘smacofx’ version ‘1.6-1’ ** package ‘smacofx’ 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 ** 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 (smacofx) checking acepack_1.5.1.tar.gz ... checking lancor_0.1.2.tar.gz ... checking nlts_1.0-2.tar.gz ... checking stops_1.8-2.tar.gz ... checking bullseye_0.1.1.tar.gz ... checking Hmisc_5.2-2.tar.gz ... Depends: Timings: user system elapsed acepack 17.473 3.49 23.494 Results: Check status summary: NOTE OK Source packages 1 0 Reverse depends 1 4 Check results summary: acepack ... NOTE * checking CRAN incoming feasibility ... [5s/7s] NOTE rdepends_bullseye ... OK rdepends_Hmisc ... NOTE * checking R code for possible problems ... [64s/64s] NOTE rdepends_lancor ... OK rdepends_nlts ... OK rdepends_stops ... OK