* installing *source* package ‘ClusterGVis’ ... ** this is package ‘ClusterGVis’ version ‘0.1.4’ ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Installing package into ‘/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1’ (as ‘lib’ is unspecified) * installing *source* package ‘BiocManager’ ... ** this is package ‘BiocManager’ version ‘1.30.26’ ** 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) 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: file:///srv/R/Repositories/CRAN Bioconductor version 3.22 (BiocManager 1.30.26), R Under development (unstable) (2025-06-22 r88341) Installing package(s) 'BiocVersion', 'SingleCellExperiment' also installing the dependencies ‘sys’, ‘askpass’, ‘curl’, ‘openssl’, ‘httr’, ‘matrixStats’, ‘UCSC.utils’, ‘crayon’, ‘MatrixGenerics’, ‘Biobase’, ‘IRanges’, ‘GenomeInfoDb’, ‘S4Arrays’, ‘XVector’, ‘SparseArray’, ‘SummarizedExperiment’, ‘S4Vectors’, ‘BiocGenerics’, ‘GenomicRanges’, ‘DelayedArray’ trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/UCSC.utils_1.5.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/MatrixGenerics_1.21.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/Biobase_2.69.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/IRanges_2.43.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/GenomeInfoDb_1.45.4.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/S4Arrays_1.9.1.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/XVector_0.49.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/SparseArray_1.9.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/SummarizedExperiment_1.39.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/S4Vectors_0.47.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/BiocGenerics_0.55.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/GenomicRanges_1.61.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/DelayedArray_0.35.2.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/BiocVersion_3.22.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/SingleCellExperiment_1.31.0.tar.gz' * installing *source* package ‘sys’ ... ** this is package ‘sys’ version ‘3.4.3’ ** package ‘sys’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘Debian clang version 19.1.7 (3+b1)’ clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c exec.c -o exec.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c init.c -o init.o clang-19 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o sys.so exec.o init.o -L/home/hornik/tmp/R/lib -lR installing to /tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/00LOCK-sys/00new/sys/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (sys) * installing *source* package ‘curl’ ... ** this is package ‘curl’ version ‘6.4.0’ ** package ‘curl’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 Using PKG_LIBS=-lcurl ** libs using C compiler: ‘Debian clang version 19.1.7 (3+b1)’ clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c callbacks.c -o callbacks.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c curl.c -o curl.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c download.c -o download.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c dryrun.c -o dryrun.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c escape.c -o escape.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c fetch.c -o fetch.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c findport.c -o findport.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c form.c -o form.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c getdate.c -o getdate.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c handle.c -o handle.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c ieproxy.c -o ieproxy.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c init.c -o init.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c interrupt.c -o interrupt.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c multi.c -o multi.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c nslookup.c -o nslookup.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c options.c -o options.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c reflist.c -o reflist.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c split.c -o split.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c ssl.c -o ssl.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c typechecking.c -o typechecking.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c urlparser.c -o urlparser.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c utils.c -o utils.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c version.c -o version.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c winidn.c -o winidn.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -isystem /usr/include/mit-krb5 -I/usr/include/p11-kit-1 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O3 -Wall -pedantic -c writer.c -o writer.o clang-19 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o curl.so callbacks.o curl.o download.o dryrun.o escape.o fetch.o findport.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o urlparser.o utils.o version.o winidn.o writer.o -lcurl -L/home/hornik/tmp/R/lib -lR installing to /tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/00LOCK-curl/00new/curl/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 (curl) * installing *source* package ‘matrixStats’ ... ** this is package ‘matrixStats’ version ‘1.5.0’ ** package ‘matrixStats’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘Debian clang version 19.1.7 (3+b1)’ clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c 000.init.c -o 000.init.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c allocMatrix2.c -o allocMatrix2.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c anyMissing.c -o anyMissing.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c binCounts.c -o binCounts.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c binMeans.c -o binMeans.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c colCounts.c -o colCounts.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c colOrderStats.c -o colOrderStats.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c colRanges.c -o colRanges.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c diff2.c -o diff2.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c indexByRow.c -o indexByRow.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c logSumExp.c -o logSumExp.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c mean2.c -o mean2.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c naming.c -o naming.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c productExpSumLog.c -o productExpSumLog.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c psortKM.c -o psortKM.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rowCounts.c -o rowCounts.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rowCummaxs.c -o rowCummaxs.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rowCummins.c -o rowCummins.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rowCumprods.c -o rowCumprods.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rowCumsums.c -o rowCumsums.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rowDiffs.c -o rowDiffs.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rowLogSumExp.c -o rowLogSumExp.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rowMads.c -o rowMads.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rowMeans2.c -o rowMeans2.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rowMedians.c -o rowMedians.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rowOrderStats.c -o rowOrderStats.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rowRanges.c -o rowRanges.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rowRanksWithTies.c -o rowRanksWithTies.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rowSums2.c -o rowSums2.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rowVars.c -o rowVars.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c signTabulate.c -o signTabulate.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c sum2.c -o sum2.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c validateIndices.c -o validateIndices.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c weightedMean.c -o weightedMean.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c weightedMedian.c -o weightedMedian.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c x_OP_y.c -o x_OP_y.o clang-19 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o matrixStats.so 000.init.o allocMatrix2.o anyMissing.o binCounts.o binMeans.o colCounts.o colOrderStats.o colRanges.o diff2.o indexByRow.o logSumExp.o mean2.o naming.o productExpSumLog.o psortKM.o rowCounts.o rowCummaxs.o rowCummins.o rowCumprods.o rowCumsums.o rowDiffs.o rowLogSumExp.o rowMads.o rowMeans2.o rowMedians.o rowOrderStats.o rowRanges.o rowRanksWithTies.o rowSums2.o rowVars.o signTabulate.o sum2.o validateIndices.o weightedMean.o weightedMedian.o x_OP_y.o -L/home/hornik/tmp/R/lib -lR installing to /tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/00LOCK-matrixStats/00new/matrixStats/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 (matrixStats) * installing *source* package ‘crayon’ ... ** this is package ‘crayon’ version ‘1.5.3’ ** package ‘crayon’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (crayon) * installing *source* package ‘BiocGenerics’ ... ** this is package ‘BiocGenerics’ version ‘0.55.0’ ** package ‘BiocGenerics’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘aperm’ in package ‘BiocGenerics’ Creating a new generic function for ‘append’ in package ‘BiocGenerics’ Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’ Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’ Creating a new generic function for ‘rbind’ in package ‘BiocGenerics’ Creating a new generic function for ‘do.call’ in package ‘BiocGenerics’ Creating a new generic function for ‘duplicated’ in package ‘BiocGenerics’ Creating a new generic function for ‘anyDuplicated’ in package ‘BiocGenerics’ Creating a new generic function for ‘eval’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmax’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmin’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmax.int’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmin.int’ in package ‘BiocGenerics’ Creating a new generic function for ‘Reduce’ in package ‘BiocGenerics’ Creating a new generic function for ‘Filter’ in package ‘BiocGenerics’ Creating a new generic function for ‘Find’ in package ‘BiocGenerics’ Creating a new generic function for ‘Map’ in package ‘BiocGenerics’ Creating a new generic function for ‘Position’ in package ‘BiocGenerics’ Creating a new generic function for ‘get’ in package ‘BiocGenerics’ Creating a new generic function for ‘mget’ in package ‘BiocGenerics’ Creating a new generic function for ‘grep’ in package ‘BiocGenerics’ Creating a new generic function for ‘grepl’ in package ‘BiocGenerics’ Creating a new generic function for ‘is.unsorted’ in package ‘BiocGenerics’ Creating a new generic function for ‘lapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘sapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘mapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘match’ in package ‘BiocGenerics’ Creating a new generic function for ‘order’ in package ‘BiocGenerics’ Creating a new generic function for ‘paste’ in package ‘BiocGenerics’ Creating a new generic function for ‘rank’ in package ‘BiocGenerics’ Creating a new generic function for ‘rownames’ in package ‘BiocGenerics’ Creating a new generic function for ‘colnames’ in package ‘BiocGenerics’ Creating a new generic function for ‘saveRDS’ in package ‘BiocGenerics’ Creating a new generic function for ‘table’ in package ‘BiocGenerics’ Creating a new generic function for ‘tapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘unique’ in package ‘BiocGenerics’ Creating a new generic function for ‘unsplit’ in package ‘BiocGenerics’ Creating a new generic function for ‘which.min’ in package ‘BiocGenerics’ Creating a new generic function for ‘which.max’ in package ‘BiocGenerics’ Creating a new generic function for ‘IQR’ in package ‘BiocGenerics’ Creating a new generic function for ‘mad’ in package ‘BiocGenerics’ Creating a new generic function for ‘var’ in package ‘BiocGenerics’ Creating a new generic function for ‘sd’ in package ‘BiocGenerics’ Creating a new generic function for ‘xtabs’ in package ‘BiocGenerics’ Creating a new generic function for ‘basename’ in package ‘BiocGenerics’ Creating a new generic function for ‘dirname’ in package ‘BiocGenerics’ ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocGenerics) * installing *source* package ‘BiocVersion’ ... ** this is package ‘BiocVersion’ version ‘3.22.0’ ** package ‘BiocVersion’ successfully unpacked and MD5 sums checked ** using staged installation ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocVersion) * installing *source* package ‘askpass’ ... ** this is package ‘askpass’ version ‘1.2.1’ ** package ‘askpass’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘Debian clang version 19.1.7 (3+b1)’ clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c askpass.c -o askpass.o clang-19 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o askpass.so askpass.o -L/home/hornik/tmp/R/lib -lR installing to /tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/00LOCK-askpass/00new/askpass/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (askpass) * installing *source* package ‘MatrixGenerics’ ... ** this is package ‘MatrixGenerics’ version ‘1.21.0’ ** package ‘MatrixGenerics’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘rowAlls’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colAlls’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowAnyNAs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colAnyNAs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowAnys’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colAnys’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowAvgsPerColSet’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colAvgsPerRowSet’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCollapse’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCollapse’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCounts’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCounts’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCummaxs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCummaxs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCummins’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCummins’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCumprods’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCumprods’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCumsums’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCumsums’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowIQRDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colIQRDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowIQRs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colIQRs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowLogSumExps’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colLogSumExps’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMadDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMadDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMads’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMads’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMaxs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMaxs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMeans2’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMeans2’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMedians’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMedians’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMins’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMins’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowOrderStats’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colOrderStats’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowProds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colProds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowQuantiles’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colQuantiles’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowRanges’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colRanges’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowRanks’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colRanks’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowSdDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colSdDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowSds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colSds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowSums2’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colSums2’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowTabulates’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colTabulates’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowVarDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colVarDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowVars’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colVars’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowWeightedMads’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colWeightedMads’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowWeightedMeans’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colWeightedMeans’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowWeightedMedians’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colWeightedMedians’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowWeightedSds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colWeightedSds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowWeightedVars’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colWeightedVars’ in package ‘MatrixGenerics’ ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MatrixGenerics) * installing *source* package ‘Biobase’ ... ** this is package ‘Biobase’ version ‘2.69.0’ ** package ‘Biobase’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘Debian clang version 19.1.7 (3+b1)’ clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c Rinit.c -o Rinit.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c anyMissing.c -o anyMissing.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c envir.c -o envir.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c matchpt.c -o matchpt.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rowMedians.c -o rowMedians.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c sublist_extract.c -o sublist_extract.o clang-19 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/home/hornik/tmp/R/lib -lR installing to /tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/00LOCK-Biobase/00new/Biobase/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Biobase) * installing *source* package ‘S4Vectors’ ... ** this is package ‘S4Vectors’ version ‘0.47.0’ ** package ‘S4Vectors’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘Debian clang version 19.1.7 (3+b1)’ clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c AEbufs.c -o AEbufs.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c DataFrame_class.c -o DataFrame_class.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c Hits_class.c -o Hits_class.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c LLint_class.c -o LLint_class.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c List_class.c -o List_class.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c R_init_S4Vectors.c -o R_init_S4Vectors.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c Rle_class.c -o Rle_class.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c Rle_utils.c -o Rle_utils.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SEXP_utils.c -o SEXP_utils.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SimpleList_class.c -o SimpleList_class.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c anyMissing.c -o anyMissing.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c character_utils.c -o character_utils.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c eval_utils.c -o eval_utils.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c hash_utils.c -o hash_utils.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c integer_utils.c -o integer_utils.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c logical_utils.c -o logical_utils.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c map_ranges_to_runs.c -o map_ranges_to_runs.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c raw_utils.c -o raw_utils.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c safe_arithm.c -o safe_arithm.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c sort_utils.c -o sort_utils.o sort_utils.c:267:13: warning: unused function 'sort_uchar_array' [-Wunused-function] 267 | static void sort_uchar_array(unsigned char *x, int nelt, int desc) | ^~~~~~~~~~~~~~~~ 1 warning generated. clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c subsetting_utils.c -o subsetting_utils.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c vector_utils.c -o vector_utils.o clang-19 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o raw_utils.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o -L/home/hornik/tmp/R/lib -lR installing to /tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/00LOCK-S4Vectors/00new/S4Vectors/libs ** R ** inst ** byte-compile and prepare package for lazy loading in method for ‘normalizeSingleBracketReplacementValue’ with signature ‘"List"’: no definition for class “List” Creating a new generic function for ‘unname’ in package ‘S4Vectors’ Creating a new generic function for ‘expand.grid’ in package ‘S4Vectors’ Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’ in method for ‘coerce’ with signature ‘"Hits","DFrame"’: no definition for class “DFrame” Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘tabulate’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘cov’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘cor’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘substr’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘substring’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘chartr’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘tolower’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘toupper’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘sub’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘gsub’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘nlevels’ from package ‘base’ in package ‘S4Vectors’ in method for ‘coerce’ with signature ‘"data.table","DFrame"’: no definition for class “data.table” Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’ ** 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 (S4Vectors) * installing *source* package ‘openssl’ ... ** this is package ‘openssl’ version ‘2.3.3’ ** package ‘openssl’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS= Using PKG_LIBS=-l:libssl.so.3 -l:libcrypto.so.3 ** libs using C compiler: ‘Debian clang version 19.1.7 (3+b1)’ rm -f aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o openssl.so bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c aes.c -o aes.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c base64.c -o base64.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c bignum.c -o bignum.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c cert.c -o cert.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c compatibility.c -o compatibility.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c diffie.c -o diffie.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c envelope.c -o envelope.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c error.c -o error.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c hash.c -o hash.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c info.c -o info.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c keygen.c -o keygen.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c keys.c -o keys.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c onload.c -o onload.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c openssh.c -o openssh.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c password.c -o password.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c pbkdf.c -o pbkdf.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c pem.c -o pem.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c pkcs12.c -o pkcs12.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c pkcs7.c -o pkcs7.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rand.c -o rand.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rsa.c -o rsa.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c signing.c -o signing.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c ssl.c -o ssl.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c stream.c -o stream.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c write.c -o write.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c x25519.c -o x25519.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c bcrypt/bcrypt_pbkdf.c -o bcrypt/bcrypt_pbkdf.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c bcrypt/blowfish.c -o bcrypt/blowfish.o ar rcs bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o clang-19 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o openssl.so aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o -Lbcrypt -lstatbcrypt -l:libssl.so.3 -l:libcrypto.so.3 -L/home/hornik/tmp/R/lib -lR installing to /tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/00LOCK-openssl/00new/openssl/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 (openssl) * installing *source* package ‘IRanges’ ... ** this is package ‘IRanges’ version ‘2.43.0’ ** package ‘IRanges’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘Debian clang version 19.1.7 (3+b1)’ clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c CompressedList_class.c -o CompressedList_class.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c Grouping_class.c -o Grouping_class.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c IPosRanges_comparison.c -o IPosRanges_comparison.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c IRanges_class.c -o IRanges_class.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c IRanges_constructor.c -o IRanges_constructor.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c NCList.c -o NCList.o NCList.c:202:22: warning: unused function 'next_top_down' [-Wunused-function] 202 | static const NCList *next_top_down(const NCList *nclist) | ^~~~~~~~~~~~~ NCList.c:1173:13: warning: function 'NCList_get_y_overlaps_rec' is not needed and will not be emitted [-Wunneeded-internal-declaration] 1173 | static void NCList_get_y_overlaps_rec(const NCList *x_nclist, | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c R_init_IRanges.c -o R_init_IRanges.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c Ranges_class.c -o Ranges_class.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c RleViews_utils.c -o RleViews_utils.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c coverage_methods.c -o coverage_methods.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c extractListFragments.c -o extractListFragments.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c inter_range_methods.c -o inter_range_methods.o clang-19 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o -L/home/hornik/tmp/R/lib -lR installing to /tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/00LOCK-IRanges/00new/IRanges/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘startsWith’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘endsWith’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’ ** 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 (IRanges) * installing *source* package ‘httr’ ... ** this is package ‘httr’ version ‘1.4.7’ ** package ‘httr’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (httr) * installing *source* package ‘S4Arrays’ ... ** this is package ‘S4Arrays’ version ‘1.9.1’ ** package ‘S4Arrays’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘Debian clang version 19.1.7 (3+b1)’ clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c R_init_S4Arrays.c -o R_init_S4Arrays.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c abind.c -o abind.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c array_selection.c -o array_selection.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c dim_tuning_utils.c -o dim_tuning_utils.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rowsum.c -o rowsum.o clang-19 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o S4Arrays.so R_init_S4Arrays.o S4Vectors_stubs.o abind.o array_selection.o dim_tuning_utils.o rowsum.o -L/home/hornik/tmp/R/lib -lR installing to /tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/00LOCK-S4Arrays/00new/S4Arrays/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘rowsum’ in package ‘S4Arrays’ Creating a new generic function for ‘abind’ in package ‘S4Arrays’ ** 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 (S4Arrays) * installing *source* package ‘XVector’ ... ** this is package ‘XVector’ version ‘0.49.0’ ** package ‘XVector’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘Debian clang version 19.1.7 (3+b1)’ clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c RDS_random_access.c -o RDS_random_access.o RDS_random_access.c:793:11: warning: variable 'x_type' set but not used [-Wunused-but-set-variable] 793 | SEXPTYPE x_type; | ^ RDS_random_access.c:796:18: warning: unused variable 'ans' [-Wunused-variable] 796 | SEXP subscript, ans; | ^~~ 2 warnings generated. clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c R_init_XVector.c -o R_init_XVector.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SharedDouble_class.c -o SharedDouble_class.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SharedInteger_class.c -o SharedInteger_class.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SharedRaw_class.c -o SharedRaw_class.o SharedRaw_class.c:396:13: warning: variable 'src_tag' set but not used [-Wunused-but-set-variable] 396 | SEXP dest, src_tag; | ^ 1 warning generated. clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SharedVector_class.c -o SharedVector_class.o SharedVector_class.c:110:31: warning: format specifies type 'void *' but the argument has type 'SEXP' (aka 'struct SEXPREC *') [-Wformat-pedantic] 110 | Rprintf(" x address: %p\n", x); | ~~ ^ SharedVector_class.c:114:41: warning: format specifies type 'void *' but the argument has type 'SEXP' (aka 'struct SEXPREC *') [-Wformat-pedantic] 114 | Rprintf(" R_ExternalPtrTag(x): %p\n", s); | ~~ ^ SharedVector_class.c:118:47: warning: format specifies type 'void *' but the argument has type 'SEXP' (aka 'struct SEXPREC *') [-Wformat-pedantic] 118 | Rprintf(" R_ExternalPtrProtected(x): %p\n", s); | ~~ ^ 3 warnings generated. clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c XDouble_class.c -o XDouble_class.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c XInteger_class.c -o XInteger_class.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c XRawList_comparison.c -o XRawList_comparison.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c XRaw_class.c -o XRaw_class.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c XVectorList_class.c -o XVectorList_class.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c XVector_class.c -o XVector_class.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c io_utils.c -o io_utils.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c slice_methods.c -o slice_methods.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c vector_copy.c -o vector_copy.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c view_summarization_methods.c -o view_summarization_methods.o clang-19 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o XVector.so IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XDouble_class.o XInteger_class.o XRawList_comparison.o XRaw_class.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -lz -L/home/hornik/tmp/R/lib -lR installing to /tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/00LOCK-XVector/00new/XVector/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (XVector) * installing *source* package ‘UCSC.utils’ ... ** this is package ‘UCSC.utils’ version ‘1.5.0’ ** package ‘UCSC.utils’ 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 (UCSC.utils) * installing *source* package ‘SparseArray’ ... ** this is package ‘SparseArray’ version ‘1.9.0’ ** package ‘SparseArray’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘Debian clang version 19.1.7 (3+b1)’ clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c OPBufTree.c -o OPBufTree.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c R_init_SparseArray.c -o R_init_SparseArray.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c Rvector_summarization.c -o Rvector_summarization.o Rvector_summarization.c:1360:12: warning: unused function 'any_NA_list_elt' [-Wunused-function] 1360 | static int any_NA_list_elt(SEXP x) | ^~~~~~~~~~~~~~~ Rvector_summarization.c:1370:12: warning: unused function 'count_NA_list_elts' [-Wunused-function] 1370 | static int count_NA_list_elts(SEXP x) | ^~~~~~~~~~~~~~~~~~ 2 warnings generated. clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c Rvector_utils.c -o Rvector_utils.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SBT_utils.c -o SBT_utils.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SparseArray_Arith_methods.c -o SparseArray_Arith_methods.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SparseArray_Compare_methods.c -o SparseArray_Compare_methods.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SparseArray_Logic_methods.c -o SparseArray_Logic_methods.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SparseArray_abind.c -o SparseArray_abind.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SparseArray_aperm.c -o SparseArray_aperm.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SparseArray_matrixStats.c -o SparseArray_matrixStats.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SparseArray_misc_methods.c -o SparseArray_misc_methods.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SparseArray_subassignment.c -o SparseArray_subassignment.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SparseArray_subassignment_OLD.c -o SparseArray_subassignment_OLD.o SparseArray_subassignment_OLD.c:245:19: warning: unused function 'descend_to_bottom_by_coords0' [-Wunused-function] 245 | static inline int descend_to_bottom_by_coords0(SEXP SVT, SEXP SVT0, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1 warning generated. clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SparseArray_subsetting.c -o SparseArray_subsetting.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SparseArray_summarization.c -o SparseArray_summarization.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SparseMatrix_mult.c -o SparseMatrix_mult.o SparseMatrix_mult.c:306:13: warning: unused function 'crossprod2_doubleSV_doublemat' [-Wunused-function] 306 | static void crossprod2_doubleSV_doublemat( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SparseMatrix_mult.c:346:13: warning: unused function 'crossprod2_doublemat_doubleSV' [-Wunused-function] 346 | static void crossprod2_doublemat_doubleSV( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SparseVec.c -o SparseVec.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SparseVec_Arith.c -o SparseVec_Arith.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SparseVec_Compare.c -o SparseVec_Compare.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SparseVec_Logic.c -o SparseVec_Logic.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SparseVec_Math.c -o SparseVec_Math.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SparseVec_dotprod.c -o SparseVec_dotprod.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c XVector_stubs.c -o XVector_stubs.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c argcheck_utils.c -o argcheck_utils.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c coerceVector2.c -o coerceVector2.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c leaf_utils.c -o leaf_utils.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c randomSparseArray.c -o randomSparseArray.o randomSparseArray.c:42:19: warning: unused function 'binary_find_interval' [-Wunused-function] 42 | static inline int binary_find_interval(double u, | ^~~~~~~~~~~~~~~~~~~~ 1 warning generated. clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c readSparseCSV.c -o readSparseCSV.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rowsum_methods.c -o rowsum_methods.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c sparseMatrix_utils.c -o sparseMatrix_utils.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c test.c -o test.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/XVector/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c thread_control.c -o thread_control.o clang-19 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o SparseArray.so ExtendableJaggedArray.o IRanges_stubs.o OPBufTree.o R_init_SparseArray.o Rvector_summarization.o Rvector_utils.o S4Vectors_stubs.o SBT_utils.o SVT_SparseArray_class.o SparseArray_Arith_methods.o SparseArray_Compare_methods.o SparseArray_Complex_methods.o SparseArray_Logic_methods.o SparseArray_Math_methods.o SparseArray_abind.o SparseArray_aperm.o SparseArray_dim_tuning.o SparseArray_matrixStats.o SparseArray_misc_methods.o SparseArray_subassignment.o SparseArray_subassignment_OLD.o SparseArray_subsetting.o SparseArray_summarization.o SparseMatrix_mult.o SparseVec.o SparseVec_Arith.o SparseVec_Compare.o SparseVec_Logic.o SparseVec_Math.o SparseVec_dotprod.o XVector_stubs.o argcheck_utils.o coerceVector2.o leaf_utils.o randomSparseArray.o readSparseCSV.o rowsum_methods.o sparseMatrix_utils.o test.o thread_control.o -L/home/hornik/tmp/R/lib -lR installing to /tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/00LOCK-SparseArray/00new/SparseArray/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 (SparseArray) * installing *source* package ‘GenomeInfoDb’ ... ** this is package ‘GenomeInfoDb’ version ‘1.45.4’ ** package ‘GenomeInfoDb’ 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 (GenomeInfoDb) * installing *source* package ‘DelayedArray’ ... ** this is package ‘DelayedArray’ version ‘0.35.2’ ** package ‘DelayedArray’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘Debian clang version 19.1.7 (3+b1)’ clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c R_init_DelayedArray.c -o R_init_DelayedArray.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c compress_atomic_vector.c -o compress_atomic_vector.o clang-19 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o DelayedArray.so R_init_DelayedArray.o S4Vectors_stubs.o compress_atomic_vector.o -L/home/hornik/tmp/R/lib -lR installing to /tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/00LOCK-DelayedArray/00new/DelayedArray/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘apply’ in package ‘DelayedArray’ Creating a new generic function for ‘sweep’ in package ‘DelayedArray’ Creating a new generic function for ‘scale’ in package ‘DelayedArray’ Creating a generic function for ‘dnorm’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘pnorm’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qnorm’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘dbinom’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘pbinom’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qbinom’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘dpois’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘ppois’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qpois’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘dlogis’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘plogis’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qlogis’ from package ‘stats’ in package ‘DelayedArray’ ** 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 (DelayedArray) * installing *source* package ‘GenomicRanges’ ... ** this is package ‘GenomicRanges’ version ‘1.61.0’ ** package ‘GenomicRanges’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘Debian clang version 19.1.7 (3+b1)’ clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang-19 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/S4Vectors/include' -I'/tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/IRanges/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c transcript_utils.c -o transcript_utils.o clang-19 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -L/home/hornik/tmp/R/lib -lR installing to /tmp/RtmpgK6VLT/working_dir/RtmpvQnkhG/RLIBS_2578f65b70dbf1/00LOCK-GenomicRanges/00new/GenomicRanges/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 (GenomicRanges) * installing *source* package ‘SummarizedExperiment’ ... ** this is package ‘SummarizedExperiment’ version ‘1.39.0’ ** package ‘SummarizedExperiment’ 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 (SummarizedExperiment) * installing *source* package ‘SingleCellExperiment’ ... ** this is package ‘SingleCellExperiment’ version ‘1.31.0’ ** package ‘SingleCellExperiment’ 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 (SingleCellExperiment) The downloaded source packages are in ‘/tmp/RtmpgK6VLT/working_dir/RtmpSPrLg7/downloaded_packages’ in method for ‘pseudotime’ with signature ‘"cell_data_set"’: no definition for class “cell_data_set” in method for ‘exprs’ with signature ‘"cell_data_set"’: no definition for class “cell_data_set” ** 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 (ClusterGVis)