downloading reverse dependencies ‘autoTS’, ‘climwin’, ‘exdex’, ‘fasstr’, ‘fastTS’, ‘gwid’, ‘heatwaveR’, ‘highfrequency’, ‘ICSClust’, ‘ICtest’, ‘IDF’, ‘irg’, ‘lacunaritycovariance’, ‘mem’, ‘oddstream’, ‘PAMmisc’, ‘planr’, ‘sentometrics’, ‘Signac’, ‘trendseries’, ‘tsensembler’, ‘tsfeatures’, ‘TSS.RESTREND’, ‘TwoRegression’, ‘ChemoSpec2D’, ‘dvmisc’, ‘recipes’ trying URL 'file:///data/Repositories/CRAN/src/contrib/autoTS_0.9.11.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/climwin_1.2.33.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/exdex_1.2.4.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/fasstr_0.5.3.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/fastTS_1.0.3.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/gwid_0.3.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/heatwaveR_0.5.5.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/highfrequency_1.0.3.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/ICSClust_0.1.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/ICtest_0.3-6.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/IDF_2.1.3.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/irg_0.1.6.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/lacunaritycovariance_1.1-9.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/mem_2.19.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/oddstream_0.5.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/PAMmisc_1.12.7.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/planr_0.6.3.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/sentometrics_1.0.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/Signac_1.16.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/trendseries_1.1.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/tsensembler_0.1.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/tsfeatures_1.1.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/TSS.RESTREND_0.3.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/TwoRegression_1.1.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/ChemoSpec2D_0.5.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/dvmisc_1.1.4.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/recipes_1.3.1.tar.gz' installing dependencies ‘bfast’, ‘biovizBase’, ‘ChemoSpecUtils’, ‘chromVAR’, ‘fICA’, ‘FKF’, ‘ggseqlogo’, ‘hpfilter’, ‘mblm’, ‘Mcomp’, ‘MCS’, ‘mFilter’, ‘monmlp’, ‘motifmatchr’, ‘MuMIn’, ‘mvtsplot’, ‘nlme’, ‘otrimle’, ‘PamBinaries’, ‘PAutilities’, ‘RcppRoll’, ‘reactablefmtr’, ‘readJDX’, ‘rerddap’, ‘rpart’, ‘sparkline’, ‘tab’, ‘tclust’, ‘TFBSTools’, ‘tidyhydat’, ‘tidync’, ‘tsbox’, ‘wrswoR’, ‘zyp’ Warning: packages ‘reactablefmtr’, ‘chromVAR’ are not available for this version of R Versions of these packages 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 ‘PairedData’, ‘DirichletMultinomial’, ‘seqLogo’, ‘TFMPvalue’, ‘strucchangeRcpp’, ‘equivalence’ begin installing package ‘PairedData’ begin installing package ‘DirichletMultinomial’ begin installing package ‘seqLogo’ begin installing package ‘TFMPvalue’ begin installing package ‘strucchangeRcpp’ begin installing package ‘tidyhydat’ begin installing package ‘zyp’ begin installing package ‘rerddap’ begin installing package ‘tidync’ begin installing package ‘FKF’ begin installing package ‘otrimle’ begin installing package ‘tclust’ begin installing package ‘mvtsplot’ begin installing package ‘fICA’ begin installing package ‘PamBinaries’ begin installing package ‘sparkline’ begin installing package ‘MCS’ begin installing package ‘ggseqlogo’ begin installing package ‘rpart’ begin installing package ‘wrswoR’ begin installing package ‘hpfilter’ begin installing package ‘mFilter’ begin installing package ‘tsbox’ begin installing package ‘monmlp’ begin installing package ‘nlme’ begin installing package ‘mblm’ begin installing package ‘ChemoSpecUtils’ begin installing package ‘readJDX’ * installing *source* package ‘mblm’ ... ** this is package ‘mblm’ version ‘0.12.1’ ** package ‘mblm’ 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 (mblm) begin installing package ‘tab’ * installing *source* package ‘mvtsplot’ ... ** this is package ‘mvtsplot’ version ‘1.0-5’ ** package ‘mvtsplot’ 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 (mvtsplot) begin installing package ‘RcppRoll’ * installing *source* package ‘zyp’ ... ** this is package ‘zyp’ version ‘0.11-1’ ** package ‘zyp’ 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 (zyp) * installing *source* package ‘monmlp’ ... ** this is package ‘monmlp’ version ‘1.1.5-1’ ** package ‘monmlp’ 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 (monmlp) * 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 ‘MCS’ ... ** this is package ‘MCS’ version ‘0.2.0’ ** package ‘MCS’ 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 (MCS) * installing *source* package ‘mFilter’ ... ** this is package ‘mFilter’ version ‘0.1-5’ ** package ‘mFilter’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** 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 (mFilter) * installing *source* package ‘FKF’ ... ** this is package ‘FKF’ version ‘0.2.6’ ** package ‘FKF’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-15) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp5Or24b/R.INSTALLa4ed449509d30/FKF/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 fkflib.c -o fkflib.o 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 init.c -o init.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o FKF.so fkflib.o init.o -llapack -L/home/hornik/tmp/R-d-gcc-15/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp5Or24b/R.INSTALLa4ed449509d30/FKF/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-FKF/00new/FKF/libs ** R ** demo ** 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 (FKF) * installing *source* package ‘seqLogo’ ... ** this is package ‘seqLogo’ version ‘1.77.0’ ** 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 (seqLogo) * installing *source* package ‘otrimle’ ... ** this is package ‘otrimle’ version ‘2.0’ ** package ‘otrimle’ 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 (otrimle) * installing *source* package ‘readJDX’ ... ** this is package ‘readJDX’ version ‘0.6.4’ ** package ‘readJDX’ 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 (readJDX) * installing *source* package ‘tidync’ ... ** this is package ‘tidync’ version ‘0.4.0’ ** package ‘tidync’ 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 (tidync) * installing *source* package ‘tidyhydat’ ... ** this is package ‘tidyhydat’ version ‘1.0.0’ ** package ‘tidyhydat’ 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 (tidyhydat) * installing *source* package ‘rerddap’ ... ** this is package ‘rerddap’ version ‘1.2.3’ ** package ‘rerddap’ 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 (rerddap) * installing *source* package ‘hpfilter’ ... ** this is package ‘hpfilter’ version ‘1.0.2’ ** package ‘hpfilter’ 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 (hpfilter) * installing *source* package ‘ggseqlogo’ ... ** this is package ‘ggseqlogo’ version ‘0.2.2’ ** package ‘ggseqlogo’ 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 (ggseqlogo) * installing *source* package ‘tsbox’ ... ** this is package ‘tsbox’ version ‘0.4.2’ ** package ‘tsbox’ 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 (tsbox) * installing *source* package ‘PairedData’ ... ** this is package ‘PairedData’ version ‘1.1.1’ ** package ‘PairedData’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘summary’ in package ‘PairedData’ ** 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 (PairedData) begin installing package ‘equivalence’ * installing *source* package ‘PamBinaries’ ... ** this is package ‘PamBinaries’ version ‘1.9.3’ ** package ‘PamBinaries’ 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 (PamBinaries) * installing *source* package ‘rpart’ ... ** this is package ‘rpart’ version ‘4.1.27’ ** package ‘rpart’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-15) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpcn40do/R.INSTALLa4f0b592f9d87/rpart/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 anova.c -o anova.o 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 anovapred.c -o anovapred.o 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 branch.c -o branch.o 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 bsplit.c -o bsplit.o 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 choose_surg.c -o choose_surg.o 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 fix_cp.c -o fix_cp.o 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 free_tree.c -o free_tree.o 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 gini.c -o gini.o 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 graycode.c -o graycode.o 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 init.c -o init.o 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 insert_split.c -o insert_split.o 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 make_cp_list.c -o make_cp_list.o 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 make_cp_table.c -o make_cp_table.o 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 mysort.c -o mysort.o 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 nodesplit.c -o nodesplit.o 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 partition.c -o partition.o 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 poisson.c -o poisson.o 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 pred_rpart.c -o pred_rpart.o 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 print_tree.c -o print_tree.o 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 rpart.c -o rpart.o 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 rpart_callback.c -o rpart_callback.o 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 rpartexp.c -o rpartexp.o 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 rpartexp2.c -o rpartexp2.o 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 rpcountup.c -o rpcountup.o 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 rpmatrix.c -o rpmatrix.o 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 rundown.c -o rundown.o 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 rundown2.c -o rundown2.o 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 surrogate.c -o surrogate.o 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 usersplit.c -o usersplit.o 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 xpred.c -o xpred.o 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 xval.c -o xval.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o rpart.so anova.o anovapred.o branch.o bsplit.o choose_surg.o fix_cp.o free_tree.o gini.o graycode.o init.o insert_split.o make_cp_list.o make_cp_table.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o print_tree.o rpart.o rpart_callback.o rpartexp.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o surrogate.o usersplit.o xpred.o xval.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpcn40do/R.INSTALLa4f0b592f9d87/rpart/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-rpart/00new/rpart/libs ** 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 ** 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 (rpart) begin installing package ‘biovizBase’ * installing *source* package ‘ChemoSpecUtils’ ... ** this is package ‘ChemoSpecUtils’ version ‘1.0.5’ ** package ‘ChemoSpecUtils’ 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 (ChemoSpecUtils) * installing *source* package ‘DirichletMultinomial’ ... ** this is package ‘DirichletMultinomial’ version ‘1.53.0’ ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-15) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpxZCDhp/R.INSTALLa4eb85dc47ba5/DirichletMultinomial/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 `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_DirichletMultinomial.c -o R_init_DirichletMultinomial.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dirichlet_fit.c -o dirichlet_fit.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dirichlet_fit_main.c -o dirichlet_fit_main.o dirichlet_fit_main.c: In function ‘hessian’: dirichlet_fit_main.c:391:34: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] 391 | adCJK0[j] += adPi[i] * n ? gsl_sf_psi(adAlpha[j] + n) : dPsiAlpha; | ~~~~~~~~^~~ dirichlet_fit_main.c:393:33: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] 393 | adCJK[j] += adPi[i] * n ? gsl_sf_psi_1(adAlpha[j] + n): dPsi1Alpha; | ~~~~~~~~^~~ gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o DirichletMultinomial.so R_init_DirichletMultinomial.o dirichlet_fit.o dirichlet_fit_main.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpxZCDhp/R.INSTALLa4eb85dc47ba5/DirichletMultinomial/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-DirichletMultinomial/00new/DirichletMultinomial/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 (DirichletMultinomial) * installing *source* package ‘TFMPvalue’ ... ** this is package ‘TFMPvalue’ version ‘1.0.0’ ** package ‘TFMPvalue’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-15) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-15) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpawlPh1/R.INSTALLa4ec54c1e4980/TFMPvalue/src' g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/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 ArgumentException.cpp -o ArgumentException.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/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 FileException.cpp -o FileException.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/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 Matrix.cpp -o Matrix.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/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 ParseException.cpp -o ParseException.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/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 TFMMain.cpp -o TFMMain.o TFMMain.cpp: In function ‘SEXPREC* pv2sc(SEXP, SEXP, SEXP, SEXP)’: TFMMain.cpp:159:8: warning: unused variable ‘sortColumns’ [-Wunused-variable] 159 | bool sortColumns = false; | ^~~~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/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 TFMPvalue_init.c -o TFMPvalue_init.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/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 TFMpvalue.cpp -o TFMpvalue.o TFMpvalue.cpp: In function ‘void testLazyDistrib(Matrix, double, double)’: TFMpvalue.cpp:119:13: warning: unused variable ‘totalSize’ [-Wunused-variable] 119 | qlonglong totalSize = 0; | ^~~~~~~~~ TFMpvalue.cpp:120:13: warning: unused variable ‘totalOp’ [-Wunused-variable] 120 | qlonglong totalOp = 0; | ^~~~~~~ TFMpvalue.cpp: In function ‘void testFastPvalue(Matrix, double, double)’: TFMpvalue.cpp:185:13: warning: unused variable ‘totalSize’ [-Wunused-variable] 185 | qlonglong totalSize = 0; | ^~~~~~~~~ TFMpvalue.cpp:186:13: warning: unused variable ‘totalOp’ [-Wunused-variable] 186 | qlonglong totalOp = 0; | ^~~~~~~ TFMpvalue.cpp:190:10: warning: unused variable ‘pvalue’ [-Wunused-variable] 190 | double pvalue = m.fastPvalue(&m,(qlonglong)(score * m.granularity + m.offset)); | ^~~~~~ g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o TFMPvalue.so ArgumentException.o FileException.o Matrix.o ParseException.o TFMMain.o TFMPvalue_init.o TFMpvalue.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpawlPh1/R.INSTALLa4ec54c1e4980/TFMPvalue/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-TFMPvalue/00new/TFMPvalue/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 (TFMPvalue) begin installing package ‘TFBSTools’ * installing *source* package ‘wrswoR’ ... ** this is package ‘wrswoR’ version ‘1.2.0’ ** package ‘wrswoR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-15) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpUzQ7mf/R.INSTALLa4f0a40412ca0/wrswoR/src' g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/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++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/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 sample_int_crank.cpp -o sample_int_crank.o 'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o wrswoR.so RcppExports.o sample_int_crank.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR 'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpUzQ7mf/R.INSTALLa4f0a40412ca0/wrswoR/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-wrswoR/00new/wrswoR/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 (wrswoR) * installing *source* package ‘equivalence’ ... ** this is package ‘equivalence’ version ‘0.8.2’ ** package ‘equivalence’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-15) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp9DDcVM/R.INSTALLa5466369b9cba/equivalence/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 equivalence_init.c -o equivalence_init.o 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 sumU.c -o sumU.o 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 sumW.c -o sumW.o 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 sumXXY.c -o sumXXY.o 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 sumXYY.c -o sumXYY.o 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 sumq.c -o sumq.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o equivalence.so equivalence_init.o sumU.o sumW.o sumXXY.o sumXYY.o sumq.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp9DDcVM/R.INSTALLa5466369b9cba/equivalence/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-equivalence/00new/equivalence/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 (equivalence) begin installing package ‘PAutilities’ * installing *source* package ‘tab’ ... ** this is package ‘tab’ version ‘5.1.1’ ** package ‘tab’ 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 (tab) * installing *source* package ‘RcppRoll’ ... ** this is package ‘RcppRoll’ version ‘0.3.2’ ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-15) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp0sOdWO/R.INSTALLa51a35e1289f/RcppRoll/src' g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/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++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/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 RcppRoll.cpp -o RcppRoll.o g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o RcppRoll.so RcppExports.o RcppRoll.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp0sOdWO/R.INSTALLa51a35e1289f/RcppRoll/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-RcppRoll/00new/RcppRoll/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 (RcppRoll) * installing *source* package ‘nlme’ ... ** this is package ‘nlme’ version ‘3.1-169’ ** package ‘nlme’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-15) 15.2.0’ using Fortran compiler: ‘GNU Fortran (Debian 15.2.0-15) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpNCwoJW/R.INSTALLa4f2122df5fd4/nlme/src' gfortran-15 -fpic -g -O2 -Wall -pedantic -mtune=native -c chol.f -o chol.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c corStruct.c -o corStruct.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c gnls.c -o gnls.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c matrix.c -o matrix.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c nlOptimizer.c -o nlOptimizer.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c nlme.c -o nlme.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c nlmefit.c -o nlmefit.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pdMat.c -o pdMat.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pythag.c -o pythag.o gfortran-15 -fpic -g -O2 -Wall -pedantic -mtune=native -c rs.f -o rs.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o pythag.o rs.o -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpNCwoJW/R.INSTALLa4f2122df5fd4/nlme/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-nlme/00new/nlme/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 (nlme) begin installing package ‘Mcomp’ begin installing package ‘MuMIn’ * installing *source* package ‘fICA’ ... ** this is package ‘fICA’ version ‘1.1-3’ ** package ‘fICA’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-15) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-15) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpyh8n3f/R.INSTALLa4ee951e48e60/fICA/src' g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 fica.cpp -o fica.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/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 'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o fICA.so fica.o init.o -llapack -L/home/hornik/tmp/R-d-gcc-15/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-15/lib -lR 'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpyh8n3f/R.INSTALLa4ee951e48e60/fICA/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-fICA/00new/fICA/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 (fICA) * installing *source* package ‘Mcomp’ ... ** this is package ‘Mcomp’ version ‘2.8’ ** package ‘Mcomp’ 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 (Mcomp) * installing *source* package ‘PAutilities’ ... ** this is package ‘PAutilities’ version ‘1.3.0’ ** package ‘PAutilities’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-15) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpuUHlvT/R.INSTALLa56254a81de12/PAutilities/src' g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/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++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/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 get_indices.cpp -o get_indices.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/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 rolling_groups.cpp -o rolling_groups.o g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o PAutilities.so RcppExports.o get_indices.o rolling_groups.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpuUHlvT/R.INSTALLa56254a81de12/PAutilities/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-PAutilities/00new/PAutilities/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 (PAutilities) * installing *source* package ‘MuMIn’ ... ** this is package ‘MuMIn’ version ‘1.48.19’ ** package ‘MuMIn’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** demo ** 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 (MuMIn) * installing *source* package ‘biovizBase’ ... ** this is package ‘biovizBase’ version ‘1.59.0’ ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-15) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp0Hy9tG/R.INSTALLa54f7248cf912/biovizBase/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 R_init_biovizBase.c -o R_init_biovizBase.o 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 bin_offsets.c -o bin_offsets.o bin_offsets.c: In function ‘scan_bam_bin_offsets’: bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of ‘strncmp’ differ in signedness [-Wpointer-sign] 57 | if (strncmp(b, "BAI\1", 4)) | ^ | | | Rbyte * {aka unsigned char *} In file included from /home/hornik/tmp/R-d-gcc-15/include/R_ext/RS.h:34, from /home/hornik/tmp/R-d-gcc-15/include/Rdefines.h:38, from bin_offsets.h:1, from bin_offsets.c:3: /usr/include/string.h:159:33: note: expected ‘const char *’ but argument is of type ‘Rbyte *’ {aka ‘unsigned char *’} 159 | extern int strncmp (const char *__s1, const char *__s2, size_t __n) | ~~~~~~~~~~~~^~~~ gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o biovizBase.so R_init_biovizBase.o bin_offsets.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp0Hy9tG/R.INSTALLa54f7248cf912/biovizBase/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-biovizBase/00new/biovizBase/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 (biovizBase) * installing *source* package ‘tclust’ ... ** this is package ‘tclust’ version ‘2.1-2’ ** package ‘tclust’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-15) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmphFtlHE/R.INSTALLa4f054d4858b7/tclust/src' g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 rlg.cpp -o rlg.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 tclust.cpp -o tclust.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 tkmeans.cpp -o tkmeans.o g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o tclust.so RcppExports.o rlg.o tclust.o tkmeans.o -fopenmp -llapack -L/home/hornik/tmp/R-d-gcc-15/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmphFtlHE/R.INSTALLa4f054d4858b7/tclust/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-tclust/00new/tclust/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 (tclust) * installing *source* package ‘TFBSTools’ ... ** this is package ‘TFBSTools’ version ‘1.49.0’ ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-15) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpwtcm5q/R.INSTALLa55e9392fad0a/TFBSTools/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 matrixAlignerDynamic.c -o matrixAlignerDynamic.o matrixAlignerDynamic.c: In function ‘score’: matrixAlignerDynamic.c:235:22: warning: ‘best_pntr’ may be used uninitialized [-Wmaybe-uninitialized] 235 | while (current_pntr->father != NULL){ // while the father of the current pointer exists, walk through the best posible alignment | ~~~~~~~~~~~~^~~~~~~~ matrixAlignerDynamic.c:115:17: note: ‘best_pntr’ was declared here 115 | struct entry *best_pntr; // pointer to the best entry so far | ^~~~~~~~~ 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 R_init_TFBSTools.c -o R_init_TFBSTools.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o TFBSTools.so matrixAlignerDynamic.o R_init_TFBSTools.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpwtcm5q/R.INSTALLa55e9392fad0a/TFBSTools/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-TFBSTools/00new/TFBSTools/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘seqLogo’ in package ‘TFBSTools’ Creating a new generic function for ‘pattern’ in package ‘TFBSTools’ Creating a generic function for ‘colSums’ from package ‘base’ in package ‘TFBSTools’ Creating a generic function for ‘rowSums’ from package ‘base’ in package ‘TFBSTools’ ** 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 (TFBSTools) begin installing package ‘motifmatchr’ * installing *source* package ‘strucchangeRcpp’ ... ** this is package ‘strucchangeRcpp’ version ‘1.5-4-1.0.1’ ** package ‘strucchangeRcpp’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-15) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-15) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpPyA8cG/R.INSTALLa4ed66a216156/strucchangeRcpp/src' g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 breakpoints.cpp -o breakpoints.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 efp.cpp -o efp.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 fstats.cpp -o fstats.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 recresid.cpp -o recresid.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 rootmatrix.cpp -o rootmatrix.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c strucchange_functions.c -o strucchange_functions.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c strucchange_init.c -o strucchange_init.o g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o strucchangeRcpp.so RcppExports.o breakpoints.o efp.o fstats.o recresid.o rootmatrix.o strucchange_functions.o strucchange_init.o -llapack -L/home/hornik/tmp/R-d-gcc-15/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpPyA8cG/R.INSTALLa4ed66a216156/strucchangeRcpp/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-strucchangeRcpp/00new/strucchangeRcpp/libs ** R ** data *** moving datasets to lazyload DB ** demo ** 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 (strucchangeRcpp) begin installing package ‘bfast’ * installing *source* package ‘bfast’ ... ** this is package ‘bfast’ version ‘1.7.1’ ** package ‘bfast’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-15) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp1RjBw1/R.INSTALLa58c569b99b62/bfast/src' g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/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++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/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 bfastts.cpp -o bfastts.o g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o bfast.so RcppExports.o bfastts.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp1RjBw1/R.INSTALLa58c569b99b62/bfast/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-bfast/00new/bfast/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 (bfast) Warning: SystemRequirements specified C++11: support has been removed * installing *source* package ‘motifmatchr’ ... ** this is package ‘motifmatchr’ version ‘1.33.0’ ** using staged installation ** libs specified C++11 using C++ compiler: ‘g++-15 (Debian 15.2.0-15) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp1ITejx/R.INSTALLa587f2e9cf93f/motifmatchr/src' g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 r_interface.cpp -o r_interface.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 MOODS/scanner.cpp -o MOODS/scanner.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 MOODS/motif_h.cpp -o MOODS/motif_h.o MOODS/motif_h.cpp: In member function ‘std::vector MOODS::scan::MotifH::expected_scores(const std::vector&)’: MOODS/motif_h.cpp:26:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 26 | for (int i = 0; i < cols; ++i){ | ~~^~~~~~ MOODS/motif_h.cpp:27:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 27 | for (int j = 0; j < rows; ++j){ | ~~^~~~~~ MOODS/motif_h.cpp: In member function ‘virtual std::pair MOODS::scan::MotifH::check_hit(const std::string&, const std::vector&, std::size_t, double)’: MOODS/motif_h.cpp:256:25: warning: suggest parentheses around arithmetic in operand of ‘^’ [-Wparentheses] 256 | CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]]; | ~~~~~^~~~~~~~~~~~~~~~~ g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 MOODS/motif_0.cpp -o MOODS/motif_0.o MOODS/motif_0.cpp: In function ‘std::vector MOODS::scan::expected_differences(const score_matrix&, const std::vector&)’: MOODS/motif_0.cpp:28:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 28 | for (int i = 0; i < m; ++i) | ~~^~~ MOODS/motif_0.cpp:31:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 31 | for (int j = 0; j < a; ++j) | ~~^~~ MOODS/motif_0.cpp:38:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 38 | for (int j = 0; j < a; ++j) | ~~^~~ MOODS/motif_0.cpp: In function ‘unsigned int MOODS::scan::window_position(const std::vector&, unsigned int, unsigned int)’: MOODS/motif_0.cpp:64:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 64 | for (int i = 0; i < m - l; ++i) | ~~^~~~~~~ MOODS/motif_0.cpp: In function ‘std::vector MOODS::scan::compute_lookahead_order(const std::vector&, unsigned int, unsigned int, unsigned int)’: MOODS/motif_0.cpp:96:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 96 | for (int i = 0; i < window_pos; ++i) | ~~^~~~~~~~~~~~ MOODS/motif_0.cpp:100:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 100 | for (int i = window_pos+l; i < m; ++i) | ~~^~~ g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 MOODS/moods_tools.cpp -o MOODS/moods_tools.o MOODS/moods_tools.cpp: In function ‘double MOODS::tools::threshold_from_p(const score_matrix&, const std::vector&, const double&)’: MOODS/moods_tools.cpp:155:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 155 | for (size_t i = 0; i < n; ++i) | ~~^~~ MOODS/moods_tools.cpp:157:30: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 157 | for (size_t j = 0; j < a; ++j) | ~~^~~ MOODS/moods_tools.cpp:168:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 168 | for (size_t i = 0; i < n; ++i) | ~~^~~ MOODS/moods_tools.cpp:172:30: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 172 | for (size_t j = 1; j < a; ++j) | ~~^~~ MOODS/moods_tools.cpp:190:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 190 | for (size_t j = 0; j < a; ++j) | ~~^~~ MOODS/moods_tools.cpp:193:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 193 | for (size_t i = 1; i < n; ++i) | ~~^~~ MOODS/moods_tools.cpp:195:30: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 195 | for (size_t j = 0; j < a; ++j) | ~~^~~ MOODS/moods_tools.cpp: In function ‘score_matrix MOODS::tools::log_odds(const std::vector >&, const std::vector >&, const std::vector&, double, std::size_t)’: MOODS/moods_tools.cpp:320:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 320 | for (size_t PCODE = 0; PCODE < 1 << (SHIFT * r); ++PCODE ){ | ~~~~~~^~~~~~~~~~~~~~~~~~ MOODS/moods_tools.cpp:328:46: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 328 | for (size_t SCODE = 0; SCODE < 1 << (SHIFT * (q - r - 1)); ++SCODE){ | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ MOODS/moods_tools.cpp: In function ‘double MOODS::tools::threshold_from_p(const score_matrix&, const std::vector&, const double&, std::size_t)’: MOODS/moods_tools.cpp:454:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 454 | for (size_t i = 0; i < cols; ++i) | ~~^~~~~~ MOODS/moods_tools.cpp:456:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 456 | for (size_t CODE = 0; CODE < rows; ++CODE) | ~~~~~^~~~~~ MOODS/moods_tools.cpp:468:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 468 | for (size_t i = 0; i < cols; ++i) | ~~^~~~~~ MOODS/moods_tools.cpp:472:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 472 | for (size_t CODE = 1; CODE < rows; ++CODE) | ~~~~~^~~~~~ MOODS/moods_tools.cpp:489:32: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 489 | for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE){ | ~~~~~^~~~~~~~~~~~~~~~~~~~ MOODS/moods_tools.cpp:500:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 500 | for (size_t i = 1; i < cols; ++i) | ~~^~~~~~ MOODS/moods_tools.cpp:503:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 503 | for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE) | ~~~~~^~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 MOODS/moods_scan.cpp -o MOODS/moods_scan.o MOODS/moods_scan.cpp: In function ‘std::vector > MOODS::scan::scan_best_hits_dna(const std::string&, const std::vector > >&, std::size_t, int, unsigned int, std::size_t, std::size_t)’: MOODS/moods_scan.cpp:97:14: warning: unused variable ‘done’ [-Wunused-variable] 97 | bool done = 0; | ^~~~ MOODS/moods_scan.cpp: In function ‘std::vector MOODS::scan::naive_scan_dna(const std::string&, score_matrix, double, std::size_t)’: MOODS/moods_scan.cpp:252:33: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses] 252 | CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]]; | ~~~~~^~~~~~~~~~~~~~~~~ g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 MOODS/moods_parsers.cpp -o MOODS/moods_parsers.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 MOODS/moods_misc.cpp -o MOODS/moods_misc.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I./MOODS/ -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/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 MOODS/match_types.cpp -o MOODS/match_types.o g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o motifmatchr.so ./RcppExports.o ./r_interface.o ./MOODS/scanner.o ./MOODS/motif_h.o ./MOODS/motif_0.o ./MOODS/moods_tools.o ./MOODS/moods_scan.o ./MOODS/moods_parsers.o ./MOODS/moods_misc.o ./MOODS/match_types.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp1ITejx/R.INSTALLa587f2e9cf93f/motifmatchr/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-motifmatchr/00new/motifmatchr/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 (motifmatchr) checking RcppRoll_0.3.2.tar.gz ... checking autoTS_0.9.11.tar.gz ... checking climwin_1.2.33.tar.gz ... checking exdex_1.2.4.tar.gz ... checking fasstr_0.5.3.tar.gz ... checking fastTS_1.0.3.tar.gz ... checking gwid_0.3.0.tar.gz ... checking heatwaveR_0.5.5.tar.gz ... checking highfrequency_1.0.3.tar.gz ... checking ICSClust_0.1.1.tar.gz ... checking ICtest_0.3-6.tar.gz ... checking IDF_2.1.3.tar.gz ... checking irg_0.1.6.tar.gz ... checking lacunaritycovariance_1.1-9.tar.gz ... checking mem_2.19.tar.gz ... checking oddstream_0.5.0.tar.gz ... checking PAMmisc_1.12.7.tar.gz ... checking planr_0.6.3.tar.gz ... checking sentometrics_1.0.1.tar.gz ... checking Signac_1.16.0.tar.gz ... checking trendseries_1.1.0.tar.gz ... checking tsensembler_0.1.0.tar.gz ... checking tsfeatures_1.1.1.tar.gz ... checking TSS.RESTREND_0.3.1.tar.gz ... checking TwoRegression_1.1.1.tar.gz ... checking ChemoSpec2D_0.5.1.tar.gz ... checking dvmisc_1.1.4.tar.gz ... checking recipes_1.3.1.tar.gz ... Depends: Package: RcppRoll Depends: R (>= 2.15.1) Imports: Rcpp LinkingTo: Rcpp Timings: user system elapsed RcppRoll 53.759 4.499 59.123 Results: Check status summary: ERROR NOTE OK Source packages 0 0 1 Reverse depends 1 2 24 Check results summary: RcppRoll ... OK rdepends_autoTS ... OK rdepends_ChemoSpec2D ... OK rdepends_climwin ... OK rdepends_dvmisc ... OK rdepends_exdex ... OK rdepends_fasstr ... OK rdepends_fastTS ... OK rdepends_gwid ... NOTE * checking DESCRIPTION meta-information ... NOTE rdepends_heatwaveR ... OK rdepends_highfrequency ... OK rdepends_ICSClust ... OK rdepends_ICtest ... OK rdepends_IDF ... OK rdepends_irg ... OK rdepends_lacunaritycovariance ... OK rdepends_mem ... OK rdepends_oddstream ... OK rdepends_PAMmisc ... OK rdepends_planr ... ERROR * checking re-building of vignette outputs ... [7s/7s] ERROR rdepends_recipes ... OK rdepends_sentometrics ... OK rdepends_Signac ... NOTE * checking Rd cross-references ... NOTE rdepends_trendseries ... OK rdepends_tsensembler ... OK rdepends_tsfeatures ... OK rdepends_TSS.RESTREND ... OK rdepends_TwoRegression ... OK Check results changes: Package: autoTS Check: CRAN incoming feasibility Old result: NOTE Package: dvmisc Check: CRAN incoming feasibility Old result: NOTE Package: tsensembler Check: CRAN incoming feasibility Old result: NOTE Package: TSS.RESTREND Check: CRAN incoming feasibility Old result: NOTE