[ Started: 2022-04-23 15:29:04 ] SingleCel... (1.17.2 -> 66063b74c...) [Bioc] scran (1.23.1 -> 5849abcdc...) [Bioc] scater (1.23.6 -> 813ccd043...) [Bioc] OmnipathR (178582759... -> 4b6b9ba11...) [GitHub] parallelly (1.31.0 -> 1.31.1 ) [CRAN] GenomeInfoDb (1.31.7 -> 1.31.10 ) [CRAN] BiocManager (1.30.16 -> 1.30.17 ) [CRAN] checkmate (2.0.0 -> 2.1.0 ) [CRAN] edgeR (3.37.1 -> 3.37.3 ) [CRAN] Installing 5 packages: parallelly, GenomeInfoDb, BiocManager, checkmate, edgeR trying URL 'https://cloud.r-project.org/src/contrib/parallelly_1.31.1.tar.gz' Content type 'application/x-gzip' length 121211 bytes (118 KB) ================================================== downloaded 118 KB trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/GenomeInfoDb_1.31.10.tar.gz' Content type 'application/x-gzip' length 3452600 bytes (3.3 MB) ================================================== downloaded 3.3 MB trying URL 'https://cloud.r-project.org/src/contrib/BiocManager_1.30.17.tar.gz' Content type 'application/x-gzip' length 287948 bytes (281 KB) ================================================== downloaded 281 KB trying URL 'https://cloud.r-project.org/src/contrib/checkmate_2.1.0.tar.gz' Content type 'application/x-gzip' length 170034 bytes (166 KB) ================================================== downloaded 166 KB trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/edgeR_3.37.3.tar.gz' Content type 'application/x-gzip' length 1409091 bytes (1.3 MB) ================================================== downloaded 1.3 MB * installing *source* package ‘parallelly’ ... ** package ‘parallelly’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (parallelly) * installing *source* package ‘GenomeInfoDb’ ... ** 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 (GenomeInfoDb) * installing *source* package ‘BiocManager’ ... ** package ‘BiocManager’ 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 (BiocManager) * installing *source* package ‘checkmate’ ... ** package ‘checkmate’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c all_missing.c -o all_missing.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c any_infinite.c -o any_infinite.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c any_missing.c -o any_missing.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c any_nan.c -o any_nan.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c checks.c -o checks.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c find_nchar.c -o find_nchar.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c guess_type.c -o guess_type.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c helper.c -o helper.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c init.c -o init.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c integerish.c -o integerish.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c is_sorted.c -o is_sorted.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c qassert.c -o qassert.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c which_first.c -o which_first.o gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o checkmate.so all_missing.o any_infinite.o any_missing.o any_nan.o checks.o find_nchar.o guess_type.o helper.o init.o integerish.o is_sorted.o qassert.o which_first.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-checkmate/00new/checkmate/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 (checkmate) * installing *source* package ‘edgeR’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_add_prior_count.cpp -o R_add_prior_count.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_ave_log_cpm.cpp -o R_ave_log_cpm.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_calculate_cpm.cpp -o R_calculate_cpm.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_check_poisson_bound.cpp -o R_check_poisson_bound.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_compute_apl.cpp -o R_compute_apl.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_compute_nbdev.cpp -o R_compute_nbdev.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_fit_levenberg.cpp -o R_fit_levenberg.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_fit_one_group.cpp -o R_fit_one_group.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_get_one_way_fitted.cpp -o R_get_one_way_fitted.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_initialize_levenberg.cpp -o R_initialize_levenberg.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_loess_by_col.cpp -o R_loess_by_col.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_simple_good_turing.cpp -o R_simple_good_turing.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c add_prior.cpp -o add_prior.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c adj_coxreid.cpp -o adj_coxreid.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c fmm_spline.c -o fmm_spline.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c glm_levenberg.cpp -o glm_levenberg.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c glm_one_group.cpp -o glm_one_group.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c init.cpp -o init.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c interpolator.cpp -o interpolator.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c nbdev.cpp -o nbdev.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c objects.cpp -o objects.o g++ -std=gnu++11 -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o edgeR.so R_add_prior_count.o R_ave_log_cpm.o R_calculate_cpm.o R_check_poisson_bound.o R_compute_apl.o R_compute_nbdev.o R_exact_test_by_deviance.o R_fit_levenberg.o R_fit_one_group.o R_get_one_way_fitted.o R_initialize_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_process_hairpin_reads.o R_simple_good_turing.o add_prior.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o nbdev.o objects.o -L/opt/R-rc/lib/R/lib -lRlapack -L/opt/R-rc/lib/R/lib -lRblas -lgfortran -lm -lquadmath -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-edgeR/00new/edgeR/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 (edgeR) The downloaded source packages are in ‘/tmp/RtmpQMgGvY/downloaded_packages’ Downloading Bioconductor repo https://git.bioconductor.org/packages/SingleCellExperiment GenomeInfoDb (1.31.7 -> 1.31.10) [CRAN] Installing 1 packages: GenomeInfoDb trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/GenomeInfoDb_1.31.10.tar.gz' Content type 'application/x-gzip' length 3452600 bytes (3.3 MB) ================================================== downloaded 3.3 MB * installing *source* package ‘GenomeInfoDb’ ... ** 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 (GenomeInfoDb) The downloaded source packages are in ‘/tmp/RtmpQMgGvY/downloaded_packages’ * checking for file ‘/tmp/RtmpQMgGvY/file31799c710e01d1/DESCRIPTION’ ... OK * preparing ‘SingleCellExperiment’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘SingleCellExperiment_1.12.0.tar.gz’ * installing *source* package ‘SingleCellExperiment’ ... ** 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 (SingleCellExperiment) Downloading Bioconductor repo https://git.bioconductor.org/packages/scran GenomeInfoDb (1.31.7 -> 1.31.10) [CRAN] edgeR (3.37.1 -> 3.37.3 ) [CRAN] Installing 2 packages: GenomeInfoDb, edgeR trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/GenomeInfoDb_1.31.10.tar.gz' Content type 'application/x-gzip' length 3452600 bytes (3.3 MB) ================================================== downloaded 3.3 MB trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/edgeR_3.37.3.tar.gz' Content type 'application/x-gzip' length 1409091 bytes (1.3 MB) ================================================== downloaded 1.3 MB * installing *source* package ‘GenomeInfoDb’ ... ** 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 (GenomeInfoDb) * installing *source* package ‘edgeR’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_add_prior_count.cpp -o R_add_prior_count.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_ave_log_cpm.cpp -o R_ave_log_cpm.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_calculate_cpm.cpp -o R_calculate_cpm.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_check_poisson_bound.cpp -o R_check_poisson_bound.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_compute_apl.cpp -o R_compute_apl.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_compute_nbdev.cpp -o R_compute_nbdev.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_fit_levenberg.cpp -o R_fit_levenberg.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_fit_one_group.cpp -o R_fit_one_group.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_get_one_way_fitted.cpp -o R_get_one_way_fitted.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_initialize_levenberg.cpp -o R_initialize_levenberg.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_loess_by_col.cpp -o R_loess_by_col.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c R_simple_good_turing.cpp -o R_simple_good_turing.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c add_prior.cpp -o add_prior.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c adj_coxreid.cpp -o adj_coxreid.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c fmm_spline.c -o fmm_spline.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c glm_levenberg.cpp -o glm_levenberg.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c glm_one_group.cpp -o glm_one_group.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c init.cpp -o init.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c interpolator.cpp -o interpolator.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c nbdev.cpp -o nbdev.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -Wall -pedantic -c objects.cpp -o objects.o g++ -std=gnu++11 -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o edgeR.so R_add_prior_count.o R_ave_log_cpm.o R_calculate_cpm.o R_check_poisson_bound.o R_compute_apl.o R_compute_nbdev.o R_exact_test_by_deviance.o R_fit_levenberg.o R_fit_one_group.o R_get_one_way_fitted.o R_initialize_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_process_hairpin_reads.o R_simple_good_turing.o add_prior.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o nbdev.o objects.o -L/opt/R-rc/lib/R/lib -lRlapack -L/opt/R-rc/lib/R/lib -lRblas -lgfortran -lm -lquadmath -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-edgeR/00new/edgeR/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 (edgeR) The downloaded source packages are in ‘/tmp/RtmpQMgGvY/downloaded_packages’ * checking for file ‘/tmp/RtmpQMgGvY/file31799c47cda95e/DESCRIPTION’ ... OK * preparing ‘scran’: * checking DESCRIPTION meta-information ... OK * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘scran_1.18.7.tar.gz’ * installing *source* package ‘scran’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I'/opt/R-rc/lib/R/library/beachmat/include' -I'/opt/R-rc/lib/R/library/BH/include' -I'/opt/R-rc/lib/R/library/dqrng/include' -I'/opt/R-rc/lib/R/library/scuttle/include' -I/usr/local/include -fpic -Wall -pedantic -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I'/opt/R-rc/lib/R/library/beachmat/include' -I'/opt/R-rc/lib/R/library/BH/include' -I'/opt/R-rc/lib/R/library/dqrng/include' -I'/opt/R-rc/lib/R/library/scuttle/include' -I/usr/local/include -fpic -Wall -pedantic -c combine_rho.cpp -o combine_rho.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I'/opt/R-rc/lib/R/library/beachmat/include' -I'/opt/R-rc/lib/R/library/BH/include' -I'/opt/R-rc/lib/R/library/dqrng/include' -I'/opt/R-rc/lib/R/library/scuttle/include' -I/usr/local/include -fpic -Wall -pedantic -c combine_simes.cpp -o combine_simes.o combine_simes.cpp: In instantiation of ‘size_t instantiate_list(Rcpp::List, std::vector&, std::string) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long unsigned int; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string]’: combine_simes.cpp:28:70: required from here combine_simes.cpp:13:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 13 | for (size_t c=0; c&, std::string) [with V = Rcpp::Vector<13>; size_t = long unsigned int; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string]’: combine_simes.cpp:145:67: required from here combine_simes.cpp:13:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I'/opt/R-rc/lib/R/library/beachmat/include' -I'/opt/R-rc/lib/R/library/BH/include' -I'/opt/R-rc/lib/R/library/dqrng/include' -I'/opt/R-rc/lib/R/library/scuttle/include' -I/usr/local/include -fpic -Wall -pedantic -c compute_blocked_stats.cpp -o compute_blocked_stats.o In file included from /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:12, from /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:11, from /opt/R-rc/lib/R/library/beachmat/include/beachmat3/beachmat.h:24, from compute_blocked_stats.cpp:2: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from ‘beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: 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] 535 | if (nnz != x.size()) { /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from ‘beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: 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] 535 | if (nnz != x.size()) { /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from ‘beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: 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] 535 | if (nnz != x.size()) { /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from ‘beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from ‘beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] 250 | if (idex != *pIt && static_cast(i[idex]) == r) { | ~~~~~^~~~~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from ‘beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from ‘beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from ‘beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from ‘beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from ‘beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from ‘beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I'/opt/R-rc/lib/R/library/beachmat/include' -I'/opt/R-rc/lib/R/library/BH/include' -I'/opt/R-rc/lib/R/library/dqrng/include' -I'/opt/R-rc/lib/R/library/scuttle/include' -I/usr/local/include -fpic -Wall -pedantic -c compute_residual_stats.cpp -o compute_residual_stats.o In file included from /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:12, from /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:11, from /opt/R-rc/lib/R/library/beachmat/include/beachmat3/beachmat.h:24, from compute_residual_stats.cpp:2: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from ‘beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: 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] 535 | if (nnz != x.size()) { /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from ‘beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: 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] 535 | if (nnz != x.size()) { /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from ‘beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: 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] 535 | if (nnz != x.size()) { /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from ‘beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from ‘beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] 250 | if (idex != *pIt && static_cast(i[idex]) == r) { | ~~~~~^~~~~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from ‘beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from ‘beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from ‘beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from ‘beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from ‘beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from ‘beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I'/opt/R-rc/lib/R/library/beachmat/include' -I'/opt/R-rc/lib/R/library/BH/include' -I'/opt/R-rc/lib/R/library/dqrng/include' -I'/opt/R-rc/lib/R/library/scuttle/include' -I/usr/local/include -fpic -Wall -pedantic -c compute_rho_null.cpp -o compute_rho_null.o In file included from /opt/R-rc/lib/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /opt/R-rc/lib/R/library/BH/include/boost/mpl/arg.hpp:25, from /opt/R-rc/lib/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /opt/R-rc/lib/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /opt/R-rc/lib/R/library/BH/include/boost/iterator/iterator_concepts.hpp:10, from /opt/R-rc/lib/R/library/BH/include/boost/range/concepts.hpp:20, from /opt/R-rc/lib/R/library/BH/include/boost/range/size_type.hpp:20, from /opt/R-rc/lib/R/library/BH/include/boost/range/size.hpp:21, from /opt/R-rc/lib/R/library/BH/include/boost/random/hyperexponential_distribution.hpp:29, from /opt/R-rc/lib/R/library/BH/include/boost/random.hpp:70, from rand_custom.h:6, from compute_rho_null.cpp:3: /opt/R-rc/lib/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /opt/R-rc/lib/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I'/opt/R-rc/lib/R/library/beachmat/include' -I'/opt/R-rc/lib/R/library/BH/include' -I'/opt/R-rc/lib/R/library/dqrng/include' -I'/opt/R-rc/lib/R/library/scuttle/include' -I/usr/local/include -fpic -Wall -pedantic -c compute_rho_pairs.cpp -o compute_rho_pairs.o g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I'/opt/R-rc/lib/R/library/beachmat/include' -I'/opt/R-rc/lib/R/library/BH/include' -I'/opt/R-rc/lib/R/library/dqrng/include' -I'/opt/R-rc/lib/R/library/scuttle/include' -I/usr/local/include -fpic -Wall -pedantic -c cyclone_scores.cpp -o cyclone_scores.o In file included from /opt/R-rc/lib/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /opt/R-rc/lib/R/library/BH/include/boost/mpl/arg.hpp:25, from /opt/R-rc/lib/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /opt/R-rc/lib/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /opt/R-rc/lib/R/library/BH/include/boost/iterator/iterator_concepts.hpp:10, from /opt/R-rc/lib/R/library/BH/include/boost/range/concepts.hpp:20, from /opt/R-rc/lib/R/library/BH/include/boost/range/algorithm.hpp:29, from cyclone_scores.cpp:4: /opt/R-rc/lib/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /opt/R-rc/lib/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ In file included from /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:12, from /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:11, from /opt/R-rc/lib/R/library/beachmat/include/beachmat3/beachmat.h:24, from cyclone_scores.cpp:3: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from ‘beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: 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] 535 | if (nnz != x.size()) { /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from ‘beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: 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] 535 | if (nnz != x.size()) { /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from ‘beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: 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] 535 | if (nnz != x.size()) { /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from ‘beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from ‘beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] 250 | if (idex != *pIt && static_cast(i[idex]) == r) { | ~~~~~^~~~~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from ‘beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from ‘beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from ‘beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from ‘beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from ‘beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from ‘beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I'/opt/R-rc/lib/R/library/beachmat/include' -I'/opt/R-rc/lib/R/library/BH/include' -I'/opt/R-rc/lib/R/library/dqrng/include' -I'/opt/R-rc/lib/R/library/scuttle/include' -I/usr/local/include -fpic -Wall -pedantic -c overlap_exprs.cpp -o overlap_exprs.o In file included from /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:12, from /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:11, from /opt/R-rc/lib/R/library/beachmat/include/beachmat3/beachmat.h:24, from overlap_exprs.cpp:3: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from ‘beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: 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] 535 | if (nnz != x.size()) { /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from ‘beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: 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] 535 | if (nnz != x.size()) { /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from ‘beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: 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] 535 | if (nnz != x.size()) { /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from ‘beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from ‘beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] 250 | if (idex != *pIt && static_cast(i[idex]) == r) { | ~~~~~^~~~~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from ‘beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from ‘beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from ‘beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from ‘beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from ‘beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from ‘beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I'/opt/R-rc/lib/R/library/beachmat/include' -I'/opt/R-rc/lib/R/library/BH/include' -I'/opt/R-rc/lib/R/library/dqrng/include' -I'/opt/R-rc/lib/R/library/scuttle/include' -I/usr/local/include -fpic -Wall -pedantic -c pool_size_factors.cpp -o pool_size_factors.o pool_size_factors.cpp: In function ‘Rcpp::List pool_size_factors(Rcpp::RObject, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::IntegerVector)’: pool_size_factors.cpp:48:15: 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] 48 | if (ngenes!=pseudo_cell.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~ pool_size_factors.cpp:53:22: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 53 | if (order.size() < ncells*2-1) { | ~~~~~~~~~~~~~^~~~~~~~~~~~ pool_size_factors.cpp:153:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 153 | for (auto i=0; i::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from ‘beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: 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] 535 | if (nnz != x.size()) { /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from ‘beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: 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] 535 | if (nnz != x.size()) { /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from ‘beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: 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] 535 | if (nnz != x.size()) { /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from ‘beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from ‘beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] 250 | if (idex != *pIt && static_cast(i[idex]) == r) { | ~~~~~^~~~~~~ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from ‘beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from ‘beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from ‘beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from ‘beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’: /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from ‘beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from ‘beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ /opt/R-rc/lib/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here /opt/R-rc/lib/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] g++ -std=gnu++11 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I'/opt/R-rc/lib/R/library/Rcpp/include' -I'/opt/R-rc/lib/R/library/beachmat/include' -I'/opt/R-rc/lib/R/library/BH/include' -I'/opt/R-rc/lib/R/library/dqrng/include' -I'/opt/R-rc/lib/R/library/scuttle/include' -I/usr/local/include -fpic -Wall -pedantic -c rand_custom.cpp -o rand_custom.o In file included from /opt/R-rc/lib/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /opt/R-rc/lib/R/library/BH/include/boost/mpl/arg.hpp:25, from /opt/R-rc/lib/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /opt/R-rc/lib/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /opt/R-rc/lib/R/library/BH/include/boost/iterator/iterator_concepts.hpp:10, from /opt/R-rc/lib/R/library/BH/include/boost/range/concepts.hpp:20, from /opt/R-rc/lib/R/library/BH/include/boost/range/size_type.hpp:20, from /opt/R-rc/lib/R/library/BH/include/boost/range/size.hpp:21, from /opt/R-rc/lib/R/library/BH/include/boost/random/hyperexponential_distribution.hpp:29, from /opt/R-rc/lib/R/library/BH/include/boost/random.hpp:70, from rand_custom.h:6, from rand_custom.cpp:1: /opt/R-rc/lib/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /opt/R-rc/lib/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++11 -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o scran.so RcppExports.o combine_rho.o combine_simes.o compute_blocked_stats.o compute_residual_stats.o compute_rho_null.o compute_rho_pairs.o cyclone_scores.o overlap_exprs.o pool_size_factors.o rand_custom.o -L/opt/R-rc/lib/R/lib -lRlapack -L/opt/R-rc/lib/R/lib -lRblas -lgfortran -lm -lquadmath -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-scran/00new/scran/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 (scran) Downloading Bioconductor repo https://git.bioconductor.org/packages/scater GenomeInfoDb (1.31.7 -> 1.31.10) [CRAN] Installing 1 packages: GenomeInfoDb trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/GenomeInfoDb_1.31.10.tar.gz' Content type 'application/x-gzip' length 3452600 bytes (3.3 MB) ================================================== downloaded 3.3 MB * installing *source* package ‘GenomeInfoDb’ ... ** 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 (GenomeInfoDb) The downloaded source packages are in ‘/tmp/RtmpQMgGvY/downloaded_packages’ * checking for file ‘/tmp/RtmpQMgGvY/file31799c5e80cb3e/DESCRIPTION’ ... OK * preparing ‘scater’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘scater_1.18.6.tar.gz’ * installing *source* package ‘scater’ ... ** 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 (scater) Downloading GitHub repo saezlab/OmnipathR@HEAD checkmate (2.0.0 -> 2.1.0) [CRAN] Installing 1 packages: checkmate trying URL 'https://cloud.r-project.org/src/contrib/checkmate_2.1.0.tar.gz' Content type 'application/x-gzip' length 170034 bytes (166 KB) ================================================== downloaded 166 KB * installing *source* package ‘checkmate’ ... ** package ‘checkmate’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c all_missing.c -o all_missing.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c any_infinite.c -o any_infinite.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c any_missing.c -o any_missing.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c any_nan.c -o any_nan.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c checks.c -o checks.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c find_nchar.c -o find_nchar.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c guess_type.c -o guess_type.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c helper.c -o helper.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c init.c -o init.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c integerish.c -o integerish.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c is_sorted.c -o is_sorted.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c qassert.c -o qassert.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c which_first.c -o which_first.o gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o checkmate.so all_missing.o any_infinite.o any_missing.o any_nan.o checks.o find_nchar.o guess_type.o helper.o init.o integerish.o is_sorted.o qassert.o which_first.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-checkmate/00new/checkmate/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 (checkmate) The downloaded source packages are in ‘/tmp/RtmpQMgGvY/downloaded_packages’ * checking for file ‘/tmp/RtmpQMgGvY/remotes31799c2f24f65/saezlab-OmnipathR-4b6b9ba/DESCRIPTION’ ... OK * preparing ‘OmnipathR’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added * building ‘OmnipathR_3.3.25.tar.gz’ * installing *source* package ‘OmnipathR’ ... ** 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 [2022-04-23 15:36:05] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2022-04-23 15:36:05] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2022-04-23 15:36:05] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2022-04-23 15:36:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2022-04-23 15:36:05] [INFO] [OmnipathR] Welcome to OmnipathR! [2022-04-23 15:36:05] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2022-04-23 15:36:06] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2022-04-23 15:36:06] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2022-04-23 15:36:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2022-04-23 15:36:06] [INFO] [OmnipathR] Welcome to OmnipathR! [2022-04-23 15:36:06] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR) [ Finished: 2022-04-23 15:36:07 ]