downloading reverse dependencies ‘hicream’ trying URL 'file:///data/Repositories/CRAN/src/contrib/hicream_0.0.2.tar.gz' Content type 'unknown' length 742423 bytes (725 KB) ================================================== installing dependencies ‘adjclust’, ‘auk’, ‘csaw’, ‘diffHic’, ‘InteractionSet’ also installing the dependency ‘metapod’ begin installing package ‘metapod’ begin installing package ‘adjclust’ begin installing package ‘auk’ begin installing package ‘InteractionSet’ * installing *source* package ‘auk’ ... ** this is package ‘auk’ version ‘0.9.0’ ** 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 ‘adjclust’ ... ** this is package ‘adjclust’ version ‘0.6.11’ ** package ‘adjclust’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpt4Uykd/R.INSTALL394f4d661c1394/adjclust/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -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-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -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-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mainFunctions.c -o mainFunctions.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o adjclust.so RcppExports.o adjClustFast.o mainFunctions.o -fopenmp -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpt4Uykd/R.INSTALL394f4d661c1394/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 ‘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 15.2.0-11) 15.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpcJ35Tg/R.INSTALL394f4935d67bdc/metapod/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c 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++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c 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++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c 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++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c 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++17 -shared -L/home/hornik/tmp/R-d-gcc-15/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-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpcJ35Tg/R.INSTALL394f4935d67bdc/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 ‘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 15.2.0-11) 15.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp8okcvh/R.INSTALL394f4b689f78ac/InteractionSet/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c 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++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c detect_overlaps.cpp -o detect_overlaps.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c init.cpp -o init.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c link_overlaps.cpp -o link_overlaps.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c overlap_utils.cpp -o overlap_utils.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/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-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp8okcvh/R.INSTALL394f4b689f78ac/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) * 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 15.2.0-11) 15.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpB32rgj/R.INSTALL39505c7c519c6a/csaw/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/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++17 -I"/home/hornik/tmp/R-d-gcc-15/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++17 -I"/home/hornik/tmp/R-d-gcc-15/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++17 -I"/home/hornik/tmp/R-d-gcc-15/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++17 -I"/home/hornik/tmp/R-d-gcc-15/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++17 -I"/home/hornik/tmp/R-d-gcc-15/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++17 -I"/home/hornik/tmp/R-d-gcc-15/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++17 -I"/home/hornik/tmp/R-d-gcc-15/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++17 -I"/home/hornik/tmp/R-d-gcc-15/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++17 -I"/home/hornik/tmp/R-d-gcc-15/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++17 -I"/home/hornik/tmp/R-d-gcc-15/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++17 -I"/home/hornik/tmp/R-d-gcc-15/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++17 -I"/home/hornik/tmp/R-d-gcc-15/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++17 -I"/home/hornik/tmp/R-d-gcc-15/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++17 -shared -L/home/hornik/tmp/R-d-gcc-15/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-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpB32rgj/R.INSTALL39505c7c519c6a/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 ‘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 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp1vY5Ui/R.INSTALL3952dc3780d08a/diffHic/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/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-d-gcc-15/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-d-gcc-15/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-d-gcc-15/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-d-gcc-15/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-d-gcc-15/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= 4.1.0) Imports: assertthat, countrycode (>= 1.0.0), dplyr (>= 0.7.8), httr, magrittr, readr (>= 2.0.0), rlang (>= 0.3.0), stringi, stringr, tidyr (>= 0.8.0) Timings: user system elapsed auk 48.611 6.027 62.369 Results: Check status summary: OK Source packages 1 Reverse depends 1 Check results summary: auk ... OK rdepends_hicream ... OK