downloading reverse dependencies ... downloading hicream_0.0.2.tar.gz ... ok downloading SISIR_0.2.3.tar.gz ... ok downloading treediff_0.2.1.tar.gz ... ok installing dependencies ‘adjclust’, ‘auk’, ‘Boruta’, ‘csaw’, ‘diffHic’, ‘HiCDOC’, ‘HiTC’, ‘InteractionSet’, ‘rioja’ also installing the dependencies ‘HiCcompare’, ‘qqman’, ‘aggregation’, ‘metapod’, ‘multiHiCcompare’ begin installing package ‘qqman’ begin installing package ‘aggregation’ begin installing package ‘metapod’ begin installing package ‘rioja’ begin installing package ‘HiTC’ begin installing package ‘adjclust’ begin installing package ‘auk’ begin installing package ‘InteractionSet’ begin installing package ‘Boruta’ * installing *source* package ‘aggregation’ ... ** this is package ‘aggregation’ version ‘1.0.1’ ** package ‘aggregation’ 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 (aggregation) * installing *source* package ‘qqman’ ... ** this is package ‘qqman’ version ‘0.1.9’ ** package ‘qqman’ 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 (qqman) * installing *source* package ‘Boruta’ ... ** this is package ‘Boruta’ version ‘9.0.0’ ** package ‘Boruta’ 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 (Boruta) * installing *source* package ‘auk’ ... ** this is package ‘auk’ version ‘0.8.2’ ** package ‘auk’ 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 (auk) * installing *source* package ‘rioja’ ... ** this is package ‘rioja’ version ‘1.0-7’ ** package ‘rioja’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-7) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-7) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpubpDos/R.INSTALL20530c4518cb33/rioja/src' gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c analog.c -o analog.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c chclust.cpp -o chclust.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c dmatinv.cpp -o dmatinv.o gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mat.cpp -o mat.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mlrc.cpp -o mlrc.o gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c utils2.c -o utils2.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c wapls.cpp -o wapls.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o rioja.so analog.o chclust.o dmatinv.o init.o mat.o mlrc.o utils2.o wapls.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpubpDos/R.INSTALL20530c4518cb33/rioja/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-rioja/00new/rioja/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 (rioja) * installing *source* package ‘metapod’ ... ** this is package ‘metapod’ version ‘1.18.0’ ** package ‘metapod’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-7) 15.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp37LZRQ/R.INSTALL2053174d4eac21/metapod/src' g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c combine_group.cpp -o combine_group.o combine_group.cpp: In instantiation of ‘Rcpp::List compute_grouped(Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::RObject, bool, const PREP&) [with PREP = p_simes; Rcpp::List = Rcpp::Vector<19>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl]’: combine_group.cpp:81:27: required from here 81 | return compute_grouped(pvals, runs, weights, log, p_simes()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ combine_group.cpp:41:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 41 | for (size_t g = 0; g < runs.size(); ++g) { | ~~^~~~~~~~~~~~~ combine_group.cpp:68:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 68 | if (counter != pvals.size()) { | ~~~~~~~~^~~~~~~~~~~~~~~ combine_group.cpp: In instantiation of ‘Rcpp::List compute_grouped(Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::RObject, bool, const PREP&) [with PREP = p_berger; Rcpp::List = Rcpp::Vector<19>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl]’: combine_group.cpp:86:27: required from here 86 | return compute_grouped(pvals, runs, weights, log, p_berger()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ combine_group.cpp:41:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 41 | for (size_t g = 0; g < runs.size(); ++g) { | ~~^~~~~~~~~~~~~ combine_group.cpp:68:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 68 | if (counter != pvals.size()) { | ~~~~~~~~^~~~~~~~~~~~~~~ combine_group.cpp: In instantiation of ‘Rcpp::List compute_grouped(Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::RObject, bool, const PREP&) [with PREP = p_wilkinson; Rcpp::List = Rcpp::Vector<19>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl]’: combine_group.cpp:91:27: required from here 91 | return compute_grouped(pvals, runs, weights, log, p_wilkinson(min_n, min_prop)); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ combine_group.cpp:41:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 41 | for (size_t g = 0; g < runs.size(); ++g) { | ~~^~~~~~~~~~~~~ combine_group.cpp:68:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 68 | if (counter != pvals.size()) { | ~~~~~~~~^~~~~~~~~~~~~~~ combine_group.cpp: In instantiation of ‘Rcpp::List compute_grouped(Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::RObject, bool, const PREP&) [with PREP = p_holm_min; Rcpp::List = Rcpp::Vector<19>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl]’: combine_group.cpp:96:27: required from here 96 | return compute_grouped(pvals, runs, weights, log, p_holm_min(min_n, min_prop)); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ combine_group.cpp:41:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 41 | for (size_t g = 0; g < runs.size(); ++g) { | ~~^~~~~~~~~~~~~ combine_group.cpp:68:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 68 | if (counter != pvals.size()) { | ~~~~~~~~^~~~~~~~~~~~~~~ combine_group.cpp: In instantiation of ‘Rcpp::List compute_grouped(Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::RObject, bool, const PREP&) [with PREP = p_stouffer; Rcpp::List = Rcpp::Vector<19>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl]’: combine_group.cpp:101:27: required from here 101 | return compute_grouped(pvals, runs, weights, log, p_stouffer()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ combine_group.cpp:41:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 41 | for (size_t g = 0; g < runs.size(); ++g) { | ~~^~~~~~~~~~~~~ combine_group.cpp:68:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 68 | if (counter != pvals.size()) { | ~~~~~~~~^~~~~~~~~~~~~~~ combine_group.cpp: In instantiation of ‘Rcpp::List compute_grouped(Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::RObject, bool, const PREP&) [with PREP = p_fisher; Rcpp::List = Rcpp::Vector<19>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl]’: combine_group.cpp:106:27: required from here 106 | return compute_grouped(pvals, runs, weights, log, p_fisher()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ combine_group.cpp:41:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 41 | for (size_t g = 0; g < runs.size(); ++g) { | ~~^~~~~~~~~~~~~ combine_group.cpp:68:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 68 | if (counter != pvals.size()) { | ~~~~~~~~^~~~~~~~~~~~~~~ combine_group.cpp: In instantiation of ‘Rcpp::List compute_grouped(Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::RObject, bool, const PREP&) [with PREP = p_pearson; Rcpp::List = Rcpp::Vector<19>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl]’: combine_group.cpp:111:27: required from here 111 | return compute_grouped(pvals, runs, weights, log, p_pearson()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ combine_group.cpp:41:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 41 | for (size_t g = 0; g < runs.size(); ++g) { | ~~^~~~~~~~~~~~~ combine_group.cpp:68:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 68 | if (counter != pvals.size()) { | ~~~~~~~~^~~~~~~~~~~~~~~ g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c combine_parallel.cpp -o combine_parallel.o combine_parallel.cpp: In constructor ‘parallel_weight_server::parallel_weight_server(size_t, size_t, Rcpp::RObject)’: combine_parallel.cpp:28:36: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 28 | if (wrepeat.size() != nvectors) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~ In file included from p_berger.h:4, from combine_parallel.cpp:1: utils.h: In instantiation of ‘parallel_vectors::parallel_vectors(Rcpp::List) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>]’: combine_parallel.cpp:20:82: required from here 20 | wvecs = parallel_vectors(Rcpp::List(weights)); | ^ utils.h:72:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 72 | if (nelements != vectors[p].size()) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c count_direction.cpp -o count_direction.o count_direction.cpp: In function ‘Rcpp::List count_grouped_direction(Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::NumericVector, int, double, double, bool)’: count_direction.cpp:95:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 95 | for (size_t g = 0; g < runs.size(); ++g) { | ~~^~~~~~~~~~~~~ count_direction.cpp:98:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 98 | if (counter >= pvalues.size()) { | ~~~~~~~~^~~~~~~~~~~~~~~~~ count_direction.cpp:120:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 120 | if (counter != pvalues.size()) { | ~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from count_direction.cpp:2: utils.h: In instantiation of ‘parallel_vectors::parallel_vectors(Rcpp::List) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>]’: count_direction.cpp:40:58: required from here 40 | parallel_vectors Effects(effects); | ^ utils.h:72:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 72 | if (nelements != vectors[p].size()) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c summarize_direction.cpp -o summarize_direction.o summarize_direction.cpp: In function ‘Rcpp::IntegerVector summarize_grouped_direction(Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::LogicalVector, double)’: summarize_direction.cpp:43:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 43 | for (size_t g = 0; g < runs.size(); ++g) { | ~~^~~~~~~~~~~~~ summarize_direction.cpp:46:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 46 | if (counter >= effects.size()) { | ~~~~~~~~^~~~~~~~~~~~~~~~~ summarize_direction.cpp:61:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 61 | if (counter != effects.size()) { | ~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from summarize_direction.cpp:2: utils.h: In instantiation of ‘parallel_vectors::parallel_vectors(Rcpp::List) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>]’: summarize_direction.cpp:10:58: required from here 10 | parallel_vectors Effects(effects); | ^ utils.h:72:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 72 | if (nelements != vectors[p].size()) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ utils.h: In instantiation of ‘parallel_vectors::parallel_vectors(Rcpp::List) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>]’: summarize_direction.cpp:11:66: required from here 11 | parallel_vectors Influential(influential); | ^ utils.h:72:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 72 | if (nelements != vectors[p].size()) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++11 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o metapod.so RcppExports.o combine_group.o combine_parallel.o count_direction.o summarize_direction.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp37LZRQ/R.INSTALL2053174d4eac21/metapod/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-metapod/00new/metapod/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 (metapod) begin installing package ‘csaw’ * installing *source* package ‘adjclust’ ... ** this is package ‘adjclust’ version ‘0.6.11’ ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-7) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-7) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpHMMVJO/R.INSTALL20530e4a250f94/adjclust/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c adjClustFast.cpp -o adjClustFast.o gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mainFunctions.c -o mainFunctions.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o adjclust.so RcppExports.o adjClustFast.o mainFunctions.o -fopenmp -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpHMMVJO/R.INSTALL20530e4a250f94/adjclust/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-adjclust/00new/adjclust/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (adjclust) * installing *source* package ‘HiTC’ ... ** this is package ‘HiTC’ version ‘1.54.0’ ** package ‘HiTC’ 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 (HiTC) * installing *source* package ‘InteractionSet’ ... ** this is package ‘InteractionSet’ version ‘1.38.0’ ** package ‘InteractionSet’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-7) 15.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpjjJb5b/R.INSTALL20531951af74e9/InteractionSet/src' g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c box_bounds.cpp -o box_bounds.o box_bounds.cpp: In function ‘SEXPREC* get_box_bounds(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: box_bounds.cpp:10:13: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 10 | if (npts!=Adex.size()) { | ~~~~^~~~~~~~~~~~~ g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c detect_overlaps.cpp -o detect_overlaps.o g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c init.cpp -o init.o g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c link_overlaps.cpp -o link_overlaps.o g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c overlap_utils.cpp -o overlap_utils.o g++-15 -std=gnu++11 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o InteractionSet.so box_bounds.o detect_overlaps.o init.o link_overlaps.o overlap_utils.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpjjJb5b/R.INSTALL20531951af74e9/InteractionSet/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-InteractionSet/00new/InteractionSet/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 (InteractionSet) begin installing package ‘HiCcompare’ * installing *source* package ‘HiCcompare’ ... ** this is package ‘HiCcompare’ version ‘1.32.0’ ** package ‘HiCcompare’ 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 Note: wrong number of arguments to 'ceiling' ** 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 (HiCcompare) begin installing package ‘multiHiCcompare’ * installing *source* package ‘csaw’ ... ** this is package ‘csaw’ version ‘1.44.0’ ** package ‘csaw’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-7) 15.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp0mxWg4/R.INSTALL2055285ec681b4/csaw/src' g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c annotator.cpp -o annotator.o annotator.cpp: In function ‘SEXPREC* annotate_overlaps(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: annotator.cpp:47:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 47 | while (counter < nolaps && query[counter]==curreg) { | ~~~~~~~~^~~~~~~~ g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c bam_utils.cpp -o bam_utils.o g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c best_in_cluster.cpp -o best_in_cluster.o best_in_cluster.cpp: In function ‘SEXPREC* best_in_cluster(SEXP, SEXP, SEXP)’: best_in_cluster.cpp:11:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 11 | if (nwin!=clustids.size() || nwin!=winweight.size()) { | ~~~~^~~~~~~~~~~~~~~~~ best_in_cluster.cpp:11:42: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 11 | if (nwin!=clustids.size() || nwin!=winweight.size()) { | ~~~~^~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c check_bimodality.cpp -o check_bimodality.o g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c correlate_reads.cpp -o correlate_reads.o g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c find_maxima.cpp -o find_maxima.o g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c get_profile.cpp -o get_profile.o g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c get_rle_counts.cpp -o get_rle_counts.o g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c init.cpp -o init.o g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c intersector.cpp -o intersector.o intersector.cpp: In constructor ‘intersector::intersector(SEXP, SEXP)’: intersector.cpp:8:10: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 8 | if (N!=elements.size()) { | ~^~~~~~~~~~~~~~~~~ intersector.cpp:32:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 32 | if (current < 0 || current >= nelements) { | ~~~~~~~~^~~~~~~~~~~~ g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c merge_windows.cpp -o merge_windows.o g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pair_reads.cpp -o pair_reads.o g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c single_reads.cpp -o single_reads.o g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c utils.cpp -o utils.o g++-15 -std=gnu++11 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o csaw.so annotator.o bam_utils.o best_in_cluster.o check_bimodality.o correlate_reads.o find_maxima.o get_profile.o get_rle_counts.o init.o intersector.o merge_windows.o pair_reads.o single_reads.o utils.o /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp0mxWg4/R.INSTALL2055285ec681b4/csaw/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-csaw/00new/csaw/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 (csaw) begin installing package ‘diffHic’ * installing *source* package ‘multiHiCcompare’ ... ** this is package ‘multiHiCcompare’ version ‘1.28.0’ ** package ‘multiHiCcompare’ 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 (multiHiCcompare) begin installing package ‘HiCDOC’ * installing *source* package ‘HiCDOC’ ... ** this is package ‘HiCDOC’ version ‘1.12.0’ ** package ‘HiCDOC’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-7) 15.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpg3JFk7/R.INSTALL2058fe7aa49fa2/HiCDOC/src' g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c constrainedClustering.cpp -o constrainedClustering.o g++-15 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c parseHiCFile.cpp -o parseHiCFile.o g++-15 -std=gnu++11 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o HiCDOC.so RcppExports.o constrainedClustering.o parseHiCFile.o -lz -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpg3JFk7/R.INSTALL2058fe7aa49fa2/HiCDOC/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-HiCDOC/00new/HiCDOC/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 (HiCDOC) * installing *source* package ‘diffHic’ ... ** this is package ‘diffHic’ version ‘1.42.0’ ** package ‘diffHic’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-7) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmplKxiTv/R.INSTALL2058855f641795/diffHic/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c binner.cpp -o binner.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c check_input.cpp -o check_input.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c cluster_2d.cpp -o cluster_2d.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c count_background.cpp -o count_background.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c count_connect.cpp -o count_connect.o count_connect.cpp: In function ‘SEXPREC* count_connect(SEXP, SEXP)’: count_connect.cpp:57:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 57 | for (size_t odex=0; odex < ncombos; ++odex) { | ~~~~~^~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c count_patch.cpp -o count_patch.o count_patch.cpp: In function ‘SEXPREC* count_patch(SEXP, SEXP, SEXP, SEXP, SEXP)’: count_patch.cpp:45:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 45 | for (size_t vecdex=0; vecdex= 4.0.0) Imports: stats, graphics, grDevices, Rcpp (>= 1.0.6), Matrix, sparseMatrixStats, methods, utils, capushe, ggplot2, dendextend, rlang LinkingTo: Rcpp, RcppArmadillo Timings: user system elapsed adjclust 117.916 9.654 129.747 Results: Check status summary: OK Source packages 1 Reverse depends 3 Check results summary: adjclust ... OK rdepends_hicream ... OK rdepends_SISIR ... OK rdepends_treediff ... OK