downloading reverse dependencies ... downloading biomartr_1.0.7.tar.gz ... ok downloading codez_1.0.0.tar.gz ... ok downloading EcotoneFinder_0.2.3.tar.gz ... ok downloading EnvNJ_0.1.3.tar.gz ... ok downloading GRelevance_1.0.tar.gz ... ok downloading iSubGen_1.0.1.tar.gz ... ok downloading jenga_1.3.0.tar.gz ... ok downloading motif_0.6.4.tar.gz ... ok downloading mSigTools_1.0.7.tar.gz ... ok downloading naive_1.2.3.tar.gz ... ok downloading noisyr_1.0.0.tar.gz ... ok downloading regional_0.4.4.tar.gz ... ok downloading segen_1.1.0.tar.gz ... ok downloading SemNeT_1.4.4.tar.gz ... ok downloading spooky_1.4.0.tar.gz ... ok downloading supercells_1.0.0.tar.gz ... ok downloading tetragon_1.3.0.tar.gz ... ok downloading mmb_0.13.3.tar.gz ... ok downloading priorsense_1.0.4.tar.gz ... ok downloading Rfast_2.1.0.tar.gz ... ok installing dependencies ‘bio3d’, ‘cmdstanr’, ‘comat’, ‘ConsensusClusterPlus’, ‘cosmicsig’, ‘ICAMS’, ‘iwmm’, ‘NetworkToolbox’, ‘philentropy’, ‘Rmisc’, ‘SemNetCleaner’, ‘SemNetDictionaries’, ‘spreadr’, ‘supercells’, ‘vegclust’ Warning: packages ‘cmdstanr’, ‘iwmm’ 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 ‘IsingFit’, ‘searcher’, ‘easycsv’, ‘editData’ begin installing package ‘IsingFit’ begin installing package ‘searcher’ begin installing package ‘editData’ begin installing package ‘easycsv’ begin installing package ‘Rmisc’ begin installing package ‘vegclust’ begin installing package ‘bio3d’ begin installing package ‘comat’ begin installing package ‘ConsensusClusterPlus’ begin installing package ‘cosmicsig’ begin installing package ‘ICAMS’ begin installing package ‘spreadr’ begin installing package ‘philentropy’ * installing *source* package ‘searcher’ ... ** package ‘searcher’ 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 (searcher) * installing *source* package ‘easycsv’ ... ** package ‘easycsv’ 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 (easycsv) begin installing package ‘SemNetDictionaries’ * installing *source* package ‘cosmicsig’ ... ** package ‘cosmicsig’ 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 (cosmicsig) * installing *source* package ‘Rmisc’ ... ** package ‘Rmisc’ 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 (Rmisc) * installing *source* package ‘ConsensusClusterPlus’ ... ** package ‘ConsensusClusterPlus’ 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 (ConsensusClusterPlus) * installing *source* package ‘editData’ ... ** package ‘editData’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (editData) * installing *source* package ‘SemNetDictionaries’ ... ** package ‘SemNetDictionaries’ 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 (SemNetDictionaries) begin installing package ‘SemNetCleaner’ * installing *source* package ‘vegclust’ ... ** package ‘vegclust’ 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 (vegclust) * installing *source* package ‘IsingFit’ ... ** package ‘IsingFit’ 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 (IsingFit) begin installing package ‘NetworkToolbox’ * installing *source* package ‘spreadr’ ... ** package ‘spreadr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpYUK4dJ/R.INSTALL63ad25df29501/spreadr/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 -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c create_mat_t.cpp -o create_mat_t.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o spreadr.so RcppExports.o create_mat_t.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpYUK4dJ/R.INSTALL63ad25df29501/spreadr/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-spreadr/00new/spreadr/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 (spreadr) * installing *source* package ‘SemNetCleaner’ ... ** package ‘SemNetCleaner’ 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 (SemNetCleaner) * installing *source* package ‘NetworkToolbox’ ... ** package ‘NetworkToolbox’ 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 (NetworkToolbox) * installing *source* package ‘philentropy’ ... ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpLLzFGL/R.INSTALL63ad46ecc5c67/philentropy/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I../src -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_PHILENTROPY -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -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 -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../src -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_PHILENTROPY -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -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 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c dist_matrix.cpp -o dist_matrix.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o philentropy.so RcppExports.o dist_matrix.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpLLzFGL/R.INSTALL63ad46ecc5c67/philentropy/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-philentropy/00new/philentropy/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (philentropy) begin installing package ‘supercells’ * installing *source* package ‘supercells’ ... ** package ‘supercells’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpKNPF0P/R.INSTALL63d9e52de4f73/supercells/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/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c calc_stats.cpp -o calc_stats.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/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c cpp11.cpp -o cpp11.o In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11.hpp:3, from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/declarations.hpp:13, from cpp11.cpp:5: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:11:9: warning: "R_NO_REMAP" redefined 11 | #define R_NO_REMAP | ^~~~~~~~~~ : note: this is the location of the previous definition 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/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c create_connectivity.cpp -o create_connectivity.o In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/matrix.hpp:6, from slic.h:2, from create_connectivity.cpp:1: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:11:9: warning: "R_NO_REMAP" redefined 11 | #define R_NO_REMAP | ^~~~~~~~~~ : note: this is the location of the previous definition 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/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c distances.cpp -o distances.o In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11.hpp:3, from distances.h:1, from distances.cpp:1: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:11:9: warning: "R_NO_REMAP" redefined 11 | #define R_NO_REMAP | ^~~~~~~~~~ : note: this is the location of the previous definition In file included from distances.cpp:2: dtw/include/DTW.hpp: In function ‘double DTW::p_norm(std::vector, std::vector, double)’: dtw/include/DTW.hpp:50:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 50 | for (int i = 0; i < a.size() ; i++) { | ~~^~~~~~~~~~ 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/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c generate_superpixels.cpp -o generate_superpixels.o In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/matrix.hpp:6, from slic.h:2, from generate_superpixels.cpp:1: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:11:9: warning: "R_NO_REMAP" redefined 11 | #define R_NO_REMAP | ^~~~~~~~~~ : note: this is the location of the previous definition 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/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c private_functions.cpp -o private_functions.o In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/matrix.hpp:6, from slic.h:2, from private_functions.cpp:1: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:11:9: warning: "R_NO_REMAP" redefined 11 | #define R_NO_REMAP | ^~~~~~~~~~ : note: this is the location of the previous definition 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/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c run_slic.cpp -o run_slic.o In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/matrix.hpp:6, from slic.h:2, from run_slic.cpp:1: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:11:9: warning: "R_NO_REMAP" redefined 11 | #define R_NO_REMAP | ^~~~~~~~~~ : note: this is the location of the previous definition 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/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c writers.cpp -o writers.o In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/matrix.hpp:6, from slic.h:2, from writers.cpp:1: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:11:9: warning: "R_NO_REMAP" redefined 11 | #define R_NO_REMAP | ^~~~~~~~~~ : note: this is the location of the previous definition g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o supercells.so calc_stats.o cpp11.o create_connectivity.o distances.o generate_superpixels.o private_functions.o run_slic.o writers.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpKNPF0P/R.INSTALL63d9e52de4f73/supercells/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-supercells/00new/supercells/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** 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 (supercells) * installing *source* package ‘ICAMS’ ... ** package ‘ICAMS’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ICAMS) * installing *source* package ‘bio3d’ ... ** package ‘bio3d’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp2bhq5E/R.INSTALL63ac61678f742/bio3d/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -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 -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. -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 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c gzstream.cpp -o gzstream.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -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 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -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 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c read_cif.cpp -o read_cif.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -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 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c read_crd.cpp -o read_crd.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -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 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c read_pdb.cpp -o read_pdb.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -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 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c read_prmtop.cpp -o read_prmtop.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -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 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c utils.cpp -o utils.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o bio3d.so RcppExports.o gzstream.o init.o read_cif.o read_crd.o read_pdb.o read_prmtop.o utils.o -lz -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp2bhq5E/R.INSTALL63ac61678f742/bio3d/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-bio3d/00new/bio3d/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 (bio3d) * installing *source* package ‘comat’ ... ** package ‘comat’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpwrQEDQ/R.INSTALL63ace24ae1d3b/comat/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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c create_neighborhood.cpp -o create_neighborhood.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c get_class_index_map.cpp -o get_class_index_map.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c get_entropy.cpp -o get_entropy.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c get_normalized.cpp -o get_normalized.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c get_unique_values.cpp -o get_unique_values.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c it_metrics.cpp -o it_metrics.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c rcpp_get_cocoma.cpp -o rcpp_get_cocoma.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c rcpp_get_coma.cpp -o rcpp_get_coma.o rcpp_get_coma.cpp: In function ‘Rcpp::IntegerMatrix rcpp_get_coma_internal(const Rcpp::IntegerMatrix&, arma::imat, std::vector >)’: rcpp_get_coma.cpp:54:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 54 | neig_col < ncols && | ~~~~~~~~~^~~~~~~ rcpp_get_coma.cpp:55:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 55 | neig_row < nrows) { | ~~~~~~~~~^~~~~~~ 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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c rcpp_get_incoma.cpp -o rcpp_get_incoma.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c rcpp_get_vec.cpp -o rcpp_get_vec.o rcpp_get_vec.cpp: In function ‘Rcpp::NumericVector rcpp_get_incove(Rcpp::List, bool, bool, std::string)’: rcpp_get_vec.cpp:104:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 104 | for (std::size_t i = 0; i < x_len; ++i){ | ~~^~~~~~~ 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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c rcpp_get_wecoma.cpp -o rcpp_get_wecoma.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c triangular_index.cpp -o triangular_index.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o comat.so RcppExports.o create_neighborhood.o get_class_index_map.o get_entropy.o get_normalized.o get_unique_values.o it_metrics.o rcpp_get_cocoma.o rcpp_get_coma.o rcpp_get_incoma.o rcpp_get_vec.o rcpp_get_wecoma.o triangular_index.o -fopenmp -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/RtmpwrQEDQ/R.INSTALL63ace24ae1d3b/comat/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-comat/00new/comat/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** 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 (comat) checking philentropy_0.9.0.tar.gz ... checking biomartr_1.0.7.tar.gz ... checking codez_1.0.0.tar.gz ... checking EcotoneFinder_0.2.3.tar.gz ... checking EnvNJ_0.1.3.tar.gz ... checking GRelevance_1.0.tar.gz ... checking iSubGen_1.0.1.tar.gz ... checking jenga_1.3.0.tar.gz ... checking motif_0.6.4.tar.gz ... checking mSigTools_1.0.7.tar.gz ... checking naive_1.2.3.tar.gz ... checking noisyr_1.0.0.tar.gz ... checking regional_0.4.4.tar.gz ... checking segen_1.1.0.tar.gz ... checking SemNeT_1.4.4.tar.gz ... checking spooky_1.4.0.tar.gz ... checking supercells_1.0.0.tar.gz ... checking tetragon_1.3.0.tar.gz ... checking mmb_0.13.3.tar.gz ... checking priorsense_1.0.4.tar.gz ... checking Rfast_2.1.0.tar.gz ... Depends: Package: philentropy Depends: R (>= 3.1.2) Imports: Rcpp, KernSmooth, poorman LinkingTo: Rcpp Timings: user system elapsed philentropy 55.686 5.902 65.307 Results: Check status summary: NOTE OK Source packages 0 1 Reverse depends 3 17 Check results summary: philentropy ... OK rdepends_biomartr ... OK rdepends_codez ... OK rdepends_EcotoneFinder ... OK rdepends_EnvNJ ... NOTE * checking Rd files ... [0s/0s] NOTE rdepends_GRelevance ... OK rdepends_iSubGen ... OK rdepends_jenga ... OK rdepends_mmb ... OK rdepends_motif ... OK rdepends_mSigTools ... OK rdepends_naive ... OK rdepends_noisyr ... OK rdepends_priorsense ... OK rdepends_regional ... OK rdepends_Rfast ... NOTE * checking Rd cross-references ... NOTE * checking compiled code ... NOTE rdepends_segen ... OK rdepends_SemNeT ... NOTE * checking Rd files ... [0s/0s] NOTE * checking Rd cross-references ... NOTE rdepends_spooky ... OK rdepends_supercells ... OK rdepends_tetragon ... OK