[ Started: 2024-04-29 15:18:14 CEST ] [ CARNIVAL v2.7.2 for BioC-3.19 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ] [1] "Libraries: " "/home/omnipath/local/R/4.4-3.19" [3] "/home/omnipath/local/R/4.4" "/opt/R-alpha/lib/R/library" trying URL 'https://cran.uni-muenster.de/src/contrib/ape_5.8.tar.gz' Content type 'application/x-gzip' length 1579438 bytes (1.5 MB) ================================================== downloaded 1.5 MB trying URL 'https://cran.uni-muenster.de/src/contrib/bookdown_0.39.tar.gz' Content type 'application/x-gzip' length 858950 bytes (838 KB) ================================================== downloaded 838 KB trying URL 'https://cran.uni-muenster.de/src/contrib/brio_1.1.5.tar.gz' Content type 'application/x-gzip' length 13172 bytes (12 KB) ================================================== downloaded 12 KB trying URL 'https://cran.uni-muenster.de/src/contrib/fs_1.6.4.tar.gz' Content type 'application/x-gzip' length 1201506 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://cran.uni-muenster.de/src/contrib/ggplot2_3.5.1.tar.gz' Content type 'application/x-gzip' length 3604371 bytes (3.4 MB) ================================================== downloaded 3.4 MB trying URL 'https://cran.uni-muenster.de/src/contrib/gtable_0.3.5.tar.gz' Content type 'application/x-gzip' length 130227 bytes (127 KB) ================================================== downloaded 127 KB trying URL 'https://cran.uni-muenster.de/src/contrib/iml_0.11.3.tar.gz' Content type 'application/x-gzip' length 176861 bytes (172 KB) ================================================== downloaded 172 KB trying URL 'https://cran.uni-muenster.de/src/contrib/matrixStats_1.3.0.tar.gz' Content type 'application/x-gzip' length 213441 bytes (208 KB) ================================================== downloaded 208 KB trying URL 'https://cran.uni-muenster.de/src/contrib/openssl_2.1.2.tar.gz' Content type 'application/x-gzip' length 1211054 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://cran.uni-muenster.de/src/contrib/pkgdown_2.0.9.tar.gz' Content type 'application/x-gzip' length 855137 bytes (835 KB) ================================================== downloaded 835 KB trying URL 'https://cran.uni-muenster.de/src/contrib/prediction_0.3.17.tar.gz' Content type 'application/x-gzip' length 74982 bytes (73 KB) ================================================== downloaded 73 KB trying URL 'https://cran.uni-muenster.de/src/contrib/RcppArmadillo_0.12.8.2.1.tar.gz' Content type 'application/x-gzip' length 1405114 bytes (1.3 MB) ================================================== downloaded 1.3 MB trying URL 'https://cran.uni-muenster.de/src/contrib/reticulate_1.36.1.tar.gz' Content type 'application/x-gzip' length 1637384 bytes (1.6 MB) ================================================== downloaded 1.6 MB trying URL 'https://cran.uni-muenster.de/src/contrib/segmented_2.0-4.tar.gz' Content type 'application/x-gzip' length 287660 bytes (280 KB) ================================================== downloaded 280 KB trying URL 'https://cran.uni-muenster.de/src/contrib/testthat_3.2.1.1.tar.gz' Content type 'application/x-gzip' length 739761 bytes (722 KB) ================================================== downloaded 722 KB trying URL 'https://cran.uni-muenster.de/src/contrib/uwot_0.2.2.tar.gz' Content type 'application/x-gzip' length 602996 bytes (588 KB) ================================================== downloaded 588 KB trying URL 'https://cran.uni-muenster.de/src/contrib/xopen_1.0.1.tar.gz' Content type 'application/x-gzip' length 11855 bytes (11 KB) ================================================== downloaded 11 KB * installing *source* package ‘ape’ ... ** package ‘ape’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c BIONJ.c -o BIONJ.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c NNI.c -o NNI.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c SPR.c -o SPR.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c additive.c -o additive.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ape.c -o ape.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c bNNI.c -o bNNI.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c bionjs.c -o bionjs.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c bipartition.c -o bipartition.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c bitsplits.c -o bitsplits.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c delta_plot.c -o delta_plot.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c dist_dna.c -o dist_dna.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c dist_nodes.c -o dist_nodes.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ewLasso.c -o ewLasso.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c heap.c -o heap.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c mat_expo.c -o mat_expo.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c me.c -o me.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c me_balanced.c -o me_balanced.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c me_ols.c -o me_ols.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c mvr.c -o mvr.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c mvrs.c -o mvrs.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c nj.c -o nj.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c njs.c -o njs.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c pic.c -o pic.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c plot_phylo.c -o plot_phylo.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c prop_part.cpp -o prop_part.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c rTrait.c -o rTrait.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c read_dna.c -o read_dna.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c reorder_Rcpp.cpp -o reorder_Rcpp.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c reorder_phylo.c -o reorder_phylo.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c treePop.c -o treePop.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c tree_build.c -o tree_build.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c tree_phylo.c -o tree_phylo.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c triangMtd.c -o triangMtd.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c triangMtds.c -o triangMtds.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ultrametric.c -o ultrametric.o g++ -std=gnu++17 -shared -L/usr/local/lib -o ape.so BIONJ.o NNI.o RcppExports.o SPR.o additive.o ape.o bNNI.o bionjs.o bipartition.o bitsplits.o delta_plot.o dist_dna.o dist_nodes.o ewLasso.o heap.o mat_expo.o me.o me_balanced.o me_ols.o mvr.o mvrs.o nj.o njs.o pic.o plot_phylo.o prop_part.o rTrait.o read_dna.o reorder_Rcpp.o reorder_phylo.o treePop.o tree_build.o tree_phylo.o triangMtd.o triangMtds.o ultrametric.o -llapack -L/opt/R-alpha/lib/R/lib -lRblas -lgfortran -lm -lquadmath installing to /home/omnipath/local/R/4.4-3.19/00LOCK-ape/00new/ape/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 (ape) * installing *source* package ‘bookdown’ ... ** package ‘bookdown’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** 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 (bookdown) * installing *source* package ‘brio’ ... ** package ‘brio’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c brio.c -o brio.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c file_line_endings.c -o file_line_endings.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c read_file.c -o read_file.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c read_file_raw.c -o read_file_raw.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c read_lines.c -o read_lines.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c write_file.c -o write_file.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c write_file_raw.c -o write_file_raw.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c write_lines.c -o write_lines.o gcc -shared -L/usr/local/lib -o brio.so brio.o file_line_endings.o init.o read_file.o read_file_raw.o read_lines.o write_file.o write_file_raw.o write_lines.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-brio/00new/brio/libs ** 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 ** 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 (brio) * installing *source* package ‘fs’ ... ** package ‘fs’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c dir.cc -o dir.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c error.cc -o error.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c file.cc -o file.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c fs.cc -o fs.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c getmode.cc -o getmode.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c id.cc -o id.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c init.cc -o init.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c link.cc -o link.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c path.cc -o path.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c utils.cc -o utils.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c unix/getmode.cc -o unix/getmode.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c bsd/setmode.c -o bsd/setmode.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c bsd/strmode.c -o bsd/strmode.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c bsd/reallocarray.c -o bsd/reallocarray.o (cd libuv-1.44.2 \ && CC="gcc" CPPFLAGS="-I/usr/local/include" CFLAGS="-g -O2 -fpic -fvisibility=hidden -std=c99" AR="ar" RANLIB="ranlib" LDFLAGS="-L/usr/local/lib" ./configure --quiet) make --directory=libuv-1.44.2 \ HAVE_DTRACE=0 make[1]: Entering directory '/tmp/RtmppkzrS1/R.INSTALLe1482b505601/fs/src/libuv-1.44.2' CC src/libuv_la-fs-poll.lo CC src/libuv_la-idna.lo CC src/libuv_la-inet.lo CC src/libuv_la-random.lo CC src/libuv_la-strscpy.lo CC src/libuv_la-threadpool.lo CC src/libuv_la-timer.lo CC src/libuv_la-uv-data-getter-setters.lo CC src/libuv_la-uv-common.lo CC src/libuv_la-version.lo CC src/libuv_la-strtok.lo CC src/unix/libuv_la-async.lo CC src/unix/libuv_la-core.lo CC src/unix/libuv_la-dl.lo CC src/unix/libuv_la-fs.lo CC src/unix/libuv_la-getaddrinfo.lo CC src/unix/libuv_la-getnameinfo.lo CC src/unix/libuv_la-loop-watcher.lo CC src/unix/libuv_la-loop.lo CC src/unix/libuv_la-pipe.lo CC src/unix/libuv_la-poll.lo CC src/unix/libuv_la-process.lo CC src/unix/libuv_la-random-devurandom.lo CC src/unix/libuv_la-signal.lo CC src/unix/libuv_la-stream.lo CC src/unix/libuv_la-tcp.lo CC src/unix/libuv_la-thread.lo CC src/unix/libuv_la-tty.lo CC src/unix/libuv_la-udp.lo CC src/unix/libuv_la-linux-core.lo CC src/unix/libuv_la-linux-inotify.lo CC src/unix/libuv_la-linux-syscalls.lo CC src/unix/libuv_la-procfs-exepath.lo CC src/unix/libuv_la-proctitle.lo CC src/unix/libuv_la-random-getrandom.lo CC src/unix/libuv_la-random-sysctl-linux.lo CC src/unix/libuv_la-epoll.lo CCLD libuv.la make[1]: Leaving directory '/tmp/RtmppkzrS1/R.INSTALLe1482b505601/fs/src/libuv-1.44.2' g++ -std=gnu++17 -shared -L/usr/local/lib -o fs.so dir.o error.o file.o fs.o getmode.o id.o init.o link.o path.o utils.o unix/getmode.o bsd/setmode.o bsd/strmode.o bsd/reallocarray.o ./libuv-1.44.2/.libs/libuv.a -pthread installing to /home/omnipath/local/R/4.4-3.19/00LOCK-fs/00new/fs/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fs) * installing *source* package ‘gtable’ ... ** package ‘gtable’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** 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 (gtable) * installing *source* package ‘matrixStats’ ... ** package ‘matrixStats’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c 000.init.c -o 000.init.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c allocMatrix2.c -o allocMatrix2.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c anyMissing.c -o anyMissing.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c binCounts.c -o binCounts.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c binMeans.c -o binMeans.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c colCounts.c -o colCounts.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c colOrderStats.c -o colOrderStats.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c colRanges.c -o colRanges.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c diff2.c -o diff2.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c indexByRow.c -o indexByRow.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c logSumExp.c -o logSumExp.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c mean2.c -o mean2.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c naming.c -o naming.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c productExpSumLog.c -o productExpSumLog.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c psortKM.c -o psortKM.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rowCounts.c -o rowCounts.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rowCummaxs.c -o rowCummaxs.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rowCummins.c -o rowCummins.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rowCumprods.c -o rowCumprods.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rowCumsums.c -o rowCumsums.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rowDiffs.c -o rowDiffs.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rowLogSumExp.c -o rowLogSumExp.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rowMads.c -o rowMads.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rowMeans2.c -o rowMeans2.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rowMedians.c -o rowMedians.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rowOrderStats.c -o rowOrderStats.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rowRanges.c -o rowRanges.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rowRanksWithTies.c -o rowRanksWithTies.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rowSums2.c -o rowSums2.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rowVars.c -o rowVars.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c signTabulate.c -o signTabulate.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sum2.c -o sum2.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c validateIndices.c -o validateIndices.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c weightedMean.c -o weightedMean.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c weightedMedian.c -o weightedMedian.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c x_OP_y.c -o x_OP_y.o gcc -shared -L/usr/local/lib -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 installing to /home/omnipath/local/R/4.4-3.19/00LOCK-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 ‘openssl’ ... ** 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: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ 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 gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c aes.c -o aes.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c base64.c -o base64.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c bignum.c -o bignum.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c cert.c -o cert.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c compatibility.c -o compatibility.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c diffie.c -o diffie.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c envelope.c -o envelope.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c error.c -o error.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c hash.c -o hash.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c info.c -o info.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c keygen.c -o keygen.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c keys.c -o keys.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c onload.c -o onload.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c openssh.c -o openssh.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c password.c -o password.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c pbkdf.c -o pbkdf.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c pem.c -o pem.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c pkcs12.c -o pkcs12.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c pkcs7.c -o pkcs7.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c rand.c -o rand.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c rsa.c -o rsa.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c signing.c -o signing.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c ssl.c -o ssl.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c stream.c -o stream.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c write.c -o write.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c x25519.c -o x25519.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c bcrypt/bcrypt_pbkdf.c -o bcrypt/bcrypt_pbkdf.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -I/usr/local/include -fpic -g -O2 -c bcrypt/blowfish.c -o bcrypt/blowfish.o ar rcs bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o gcc -shared -L/usr/local/lib -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 installing to /home/omnipath/local/R/4.4-3.19/00LOCK-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 ‘prediction’ ... ** package ‘prediction’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (prediction) * installing *source* package ‘RcppArmadillo’ ... ** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ -std=gnu++17 accepts -g... yes checking for g++ -std=gnu++17 option to enable C++11 features... none needed checking how to run the C++ preprocessor... g++ -std=gnu++17 -E checking whether the compiler supports GNU C++... (cached) yes checking whether g++ -std=gnu++17 accepts -g... (cached) yes checking for g++ -std=gnu++17 option to enable C++11 features... (cached) none needed checking whether we have a suitable tempdir... /tmp checking whether R CMD SHLIB can already compile programs using OpenMP... yes checking LAPACK_LIBS... system LAPACK found configure: creating ./config.status config.status: creating inst/include/RcppArmadillo/config/RcppArmadilloConfigGenerated.h config.status: creating src/Makevars ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppArmadillo.cpp -o RcppArmadillo.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c fastLm.cpp -o fastLm.o g++ -std=gnu++17 -shared -L/usr/local/lib -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -fopenmp -llapack -L/opt/R-alpha/lib/R/lib -lRblas -lgfortran -lm -lquadmath installing to /home/omnipath/local/R/4.4-3.19/00LOCK-RcppArmadillo/00new/RcppArmadillo/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 (RcppArmadillo) * installing *source* package ‘reticulate’ ... ** package ‘reticulate’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c event_loop.cpp -o event_loop.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c libpython.cpp -o libpython.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c output.cpp -o output.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c python.cpp -o python.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c readline.cpp -o readline.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c signals.cpp -o signals.o g++ -std=gnu++17 -shared -L/usr/local/lib -o reticulate.so RcppExports.o event_loop.o libpython.o output.o python.o readline.o signals.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-reticulate/00new/reticulate/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (reticulate) * installing *source* package ‘segmented’ ... ** package ‘segmented’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (segmented) * installing *source* package ‘uwot’ ... ** package ‘uwot’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.4-3.19/dqrng/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.19/RcppAnnoy/include' -I'/home/omnipath/local/R/4.4-3.19/RcppProgress/include' -I/usr/local/include -DRCPP_NO_RTTI -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.4-3.19/dqrng/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.19/RcppAnnoy/include' -I'/home/omnipath/local/R/4.4-3.19/RcppProgress/include' -I/usr/local/include -DRCPP_NO_RTTI -fpic -g -O2 -c connected_components.cpp -o connected_components.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.4-3.19/dqrng/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.19/RcppAnnoy/include' -I'/home/omnipath/local/R/4.4-3.19/RcppProgress/include' -I/usr/local/include -DRCPP_NO_RTTI -fpic -g -O2 -c nn_parallel.cpp -o nn_parallel.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.4-3.19/dqrng/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.19/RcppAnnoy/include' -I'/home/omnipath/local/R/4.4-3.19/RcppProgress/include' -I/usr/local/include -DRCPP_NO_RTTI -fpic -g -O2 -c perplexity.cpp -o perplexity.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.4-3.19/dqrng/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.19/RcppAnnoy/include' -I'/home/omnipath/local/R/4.4-3.19/RcppProgress/include' -I/usr/local/include -DRCPP_NO_RTTI -fpic -g -O2 -c r_uwot.cpp -o r_uwot.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.4-3.19/dqrng/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.19/RcppAnnoy/include' -I'/home/omnipath/local/R/4.4-3.19/RcppProgress/include' -I/usr/local/include -DRCPP_NO_RTTI -fpic -g -O2 -c smooth_knn.cpp -o smooth_knn.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.4-3.19/dqrng/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.19/RcppAnnoy/include' -I'/home/omnipath/local/R/4.4-3.19/RcppProgress/include' -I/usr/local/include -DRCPP_NO_RTTI -fpic -g -O2 -c supervised.cpp -o supervised.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.4-3.19/dqrng/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.19/RcppAnnoy/include' -I'/home/omnipath/local/R/4.4-3.19/RcppProgress/include' -I/usr/local/include -DRCPP_NO_RTTI -fpic -g -O2 -c thread.cpp -o thread.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.4-3.19/dqrng/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.19/RcppAnnoy/include' -I'/home/omnipath/local/R/4.4-3.19/RcppProgress/include' -I/usr/local/include -DRCPP_NO_RTTI -fpic -g -O2 -c transform.cpp -o transform.o g++ -std=gnu++17 -shared -L/usr/local/lib -o uwot.so RcppExports.o connected_components.o nn_parallel.o perplexity.o r_uwot.o smooth_knn.o supervised.o thread.o transform.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-uwot/00new/uwot/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (uwot) * installing *source* package ‘xopen’ ... ** package ‘xopen’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (xopen) * installing *source* package ‘ggplot2’ ... ** package ‘ggplot2’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggplot2) * installing *source* package ‘pkgdown’ ... ** package ‘pkgdown’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** 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 (pkgdown) * installing *source* package ‘testthat’ ... ** package ‘testthat’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -g -O2 -c reassign.c -o reassign.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -g -O2 -c test-catch.cpp -o test-catch.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -g -O2 -c test-example.cpp -o test-example.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -g -O2 -c test-runner.cpp -o test-runner.o g++ -std=gnu++17 -shared -L/usr/local/lib -o testthat.so init.o reassign.o test-catch.o test-example.o test-runner.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-testthat/00new/testthat/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (testthat) * installing *source* package ‘iml’ ... ** package ‘iml’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** 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 (iml) The downloaded source packages are in ‘/tmp/RtmpXJ8hmk/downloaded_packages’ Warning message: package ‘remotes’ was built under R version 4.5.0 Warning message: package ‘BiocManager’ was built under R version 4.5.0 Bioconductor version 3.19 (BiocManager 1.30.22), R 4.4.0 alpha (2024-04-04 r86334) Old packages: 'AnnotationHub', 'basilisk.utils', 'BiocCheck', 'Biostrings', 'DelayedMatrixStats', 'DESeq2', 'edgeR', 'ExperimentHub', 'fgsea', 'GenomeInfoDb', 'graph', 'GSVA', 'KEGGREST', 'limma', 'MatrixGenerics', 'rhdf5', 'rhdf5filters', 'S4Arrays', 'S4Vectors', 'SparseArray', 'sparseMatrixStats', 'UCSC.utils', 'wppi' trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/AnnotationHub_3.11.5.tar.gz' Content type 'application/x-gzip' length 997511 bytes (974 KB) ================================================== downloaded 974 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/basilisk.utils_1.15.2.tar.gz' Content type 'application/x-gzip' length 240383 bytes (234 KB) ================================================== downloaded 234 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/BiocCheck_1.39.35.tar.gz' Content type 'application/x-gzip' length 4378663 bytes (4.2 MB) ================================================== downloaded 4.2 MB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/Biostrings_2.71.6.tar.gz' Content type 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'https://bioconductor.org/packages/3.19/bioc/src/contrib/KEGGREST_1.43.1.tar.gz' Content type 'application/x-gzip' length 22975 bytes (22 KB) ================================================== downloaded 22 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/limma_3.59.10.tar.gz' Content type 'application/x-gzip' length 2809327 bytes (2.7 MB) ================================================== downloaded 2.7 MB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/MatrixGenerics_1.15.1.tar.gz' Content type 'application/x-gzip' length 31725 bytes (30 KB) ================================================== downloaded 30 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/rhdf5_2.47.7.tar.gz' Content type 'application/x-gzip' length 1273593 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/rhdf5filters_1.15.5.tar.gz' Content type 'application/x-gzip' length 1180013 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/S4Arrays_1.3.7.tar.gz' Content type 'application/x-gzip' length 282279 bytes (275 KB) ================================================== downloaded 275 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/S4Vectors_0.41.7.tar.gz' Content type 'application/x-gzip' length 881931 bytes (861 KB) ================================================== downloaded 861 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/SparseArray_1.3.5.tar.gz' Content type 'application/x-gzip' length 367906 bytes (359 KB) ================================================== downloaded 359 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/sparseMatrixStats_1.15.1.tar.gz' Content type 'application/x-gzip' length 703377 bytes (686 KB) ================================================== downloaded 686 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/UCSC.utils_0.99.7.tar.gz' Content type 'application/x-gzip' length 235831 bytes (230 KB) ================================================== downloaded 230 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/wppi_1.11.0.tar.gz' Content type 'application/x-gzip' length 662182 bytes (646 KB) ================================================== downloaded 646 KB * installing *source* package ‘basilisk.utils’ ... ** 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 (basilisk.utils) * installing *source* package ‘fgsea’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++11 g++ -std=gnu++11 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.19/BH/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.19/BH/include' -I/usr/local/include -fpic -g -O2 -c ScoreCalculation.cpp -o ScoreCalculation.o g++ -std=gnu++11 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.19/BH/include' -I/usr/local/include -fpic -g -O2 -c ScoreRuler.cpp -o ScoreRuler.o In file included from /home/omnipath/local/R/4.4-3.19/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /home/omnipath/local/R/4.4-3.19/BH/include/boost/math/special_functions/math_fwd.hpp:29, from /home/omnipath/local/R/4.4-3.19/BH/include/boost/math/special_functions/digamma.hpp:15, from util.h:5, from ScoreRuler.cpp:2: /home/omnipath/local/R/4.4-3.19/BH/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ g++ -std=gnu++11 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.19/BH/include' -I/usr/local/include -fpic -g -O2 -c esCalculation.cpp -o esCalculation.o g++ -std=gnu++11 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.19/BH/include' -I/usr/local/include -fpic -g -O2 -c fastGSEA.cpp -o fastGSEA.o In file included from /home/omnipath/local/R/4.4-3.19/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /home/omnipath/local/R/4.4-3.19/BH/include/boost/math/special_functions/math_fwd.hpp:29, from /home/omnipath/local/R/4.4-3.19/BH/include/boost/math/special_functions/digamma.hpp:15, from util.h:5, from fastGSEA.cpp:13: /home/omnipath/local/R/4.4-3.19/BH/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ g++ -std=gnu++11 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.19/BH/include' -I/usr/local/include -fpic -g -O2 -c fgseaMultilevel.cpp -o fgseaMultilevel.o g++ -std=gnu++11 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.19/BH/include' -I/usr/local/include -fpic -g -O2 -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o In file included from /home/omnipath/local/R/4.4-3.19/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /home/omnipath/local/R/4.4-3.19/BH/include/boost/math/special_functions/math_fwd.hpp:29, from /home/omnipath/local/R/4.4-3.19/BH/include/boost/math/special_functions/digamma.hpp:15, from util.h:5, from fgseaMultilevelSupplement.cpp:3: /home/omnipath/local/R/4.4-3.19/BH/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ g++ -std=gnu++11 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.19/BH/include' -I/usr/local/include -fpic -g -O2 -c geseca.cpp -o geseca.o g++ -std=gnu++11 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.19/BH/include' -I/usr/local/include -fpic -g -O2 -c util.cpp -o util.o In file included from /home/omnipath/local/R/4.4-3.19/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /home/omnipath/local/R/4.4-3.19/BH/include/boost/math/special_functions/math_fwd.hpp:29, from /home/omnipath/local/R/4.4-3.19/BH/include/boost/math/special_functions/digamma.hpp:15, from util.h:5, from util.cpp:1: /home/omnipath/local/R/4.4-3.19/BH/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ g++ -std=gnu++11 -shared -L/usr/local/lib -o fgsea.so RcppExports.o ScoreCalculation.o ScoreRuler.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o geseca.o util.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-fgsea/00new/fgsea/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fgsea) * installing *source* package ‘graph’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c graph.c -o graph.o gcc -shared -L/usr/local/lib -o graph.so graph.o mv graph.so BioC_graph.so installing to /home/omnipath/local/R/4.4-3.19/00LOCK-graph/00new/graph/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning message: package ‘BiocGenerics’ was built under R version 4.5.0 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: package ‘BiocGenerics’ was built under R version 4.5.0 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: package ‘BiocGenerics’ was built under R version 4.5.0 ** testing if installed package keeps a record of temporary installation path * DONE (graph) * installing *source* package ‘limma’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c normexp.c -o normexp.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c weighted_lowess.c -o weighted_lowess.o gcc -shared -L/usr/local/lib -o limma.so init.o normexp.o weighted_lowess.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-limma/00new/limma/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 (limma) * installing *source* package ‘MatrixGenerics’ ... ** 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 ‘rhdf5filters’ ... ** using staged installation checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed configure: is NOT Bioc build machine configure: configuring BZIP2 filter... checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for bzlib.h... yes checking for BZ2_bzDecompressInit in -lbz2... yes configure: Using system bzip2 library configure: configuring the Zstd filter... checking for zstd.h... yes checking for ZSTD_decompress in -lzstd... yes configure: Using system Zstd library configure: configuring the BLOSC filter... checking for blosc.h... yes checking for blosc_compress in -lblosc... yes configure: Using system BLOSC library configure: configuring the VBZ filter checking whether C compiler accepts -mavx... yes checking for x86 avx instruction support... yes configure: creating ./config.status config.status: creating src/bzip2/Makefile config.status: creating src/zstd/Makefile config.status: creating src/blosc/lib/blosc-1.20.1/Makefile config.status: creating src/blosc/Makefile config.status: creating src/vbz/Makefile config.status: creating src/vbz/vbz/Makefile config.status: creating src/vbz/third_party/streamvbyte/Makefile config.status: creating src/Makevars ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ make -C zstd make[1]: Entering directory '/tmp/RtmpwWXSk8/R.INSTALLff3329d6b5e9/rhdf5filters/src/zstd' gcc -g -O2 -fpic -shared H5Zzstd.c -I/usr/local/include -I"/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include" \ -lzstd -L/usr/local/lib -o libH5Zzstd.so make[1]: Leaving directory '/tmp/RtmpwWXSk8/R.INSTALLff3329d6b5e9/rhdf5filters/src/zstd' make -C blosc make[1]: Entering directory '/tmp/RtmpwWXSk8/R.INSTALLff3329d6b5e9/rhdf5filters/src/blosc' g++ -std=gnu++17 -g -O2 -fpic -shared -I/usr/local/include -I"/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include" H5Zblosc.cpp \ -L/usr/local/lib -lblosc -lzstd -lz -o libH5Zblosc.so make[1]: Leaving directory '/tmp/RtmpwWXSk8/R.INSTALLff3329d6b5e9/rhdf5filters/src/blosc' make -C bzip2 make[1]: Entering directory '/tmp/RtmpwWXSk8/R.INSTALLff3329d6b5e9/rhdf5filters/src/bzip2' gcc -g -O2 -fpic -shared H5Zbzip2.c -I/usr/local/include -I"/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include" \ -lbz2 -L/usr/local/lib -o libH5Zbz2.so make[1]: Leaving directory '/tmp/RtmpwWXSk8/R.INSTALLff3329d6b5e9/rhdf5filters/src/bzip2' make -C lzf make[1]: Entering directory '/tmp/RtmpwWXSk8/R.INSTALLff3329d6b5e9/rhdf5filters/src/lzf' make -C lzf make[2]: Entering directory '/tmp/RtmpwWXSk8/R.INSTALLff3329d6b5e9/rhdf5filters/src/lzf/lzf' gcc -g -O2 -fpic -c lzf_c.c gcc -g -O2 -fpic -c lzf_d.c rm -f liblzf.a ar cq liblzf.a lzf_c.o lzf_d.o ranlib liblzf.a make[2]: Leaving directory '/tmp/RtmpwWXSk8/R.INSTALLff3329d6b5e9/rhdf5filters/src/lzf/lzf' gcc -g -O2 -fpic -shared H5Zlzf.c -I/usr/local/include -I"/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include" \ -I./lzf/ ./lzf/liblzf.a -L/usr/local/lib -o libH5Zlzf.so make[1]: Leaving directory '/tmp/RtmpwWXSk8/R.INSTALLff3329d6b5e9/rhdf5filters/src/lzf' make -C vbz make[1]: Entering directory '/tmp/RtmpwWXSk8/R.INSTALLff3329d6b5e9/rhdf5filters/src/vbz' make -C third_party/streamvbyte make[2]: Entering directory '/tmp/RtmpwWXSk8/R.INSTALLff3329d6b5e9/rhdf5filters/src/vbz/third_party/streamvbyte' gcc -std=gnu99 -fpic -Iinclude -c ./src/streamvbyte_decode.c gcc -std=gnu99 -fpic -Iinclude -c ./src/streamvbyte_encode.c gcc -std=gnu99 -fpic -Iinclude -c ./src/streamvbytedelta_decode.c gcc -std=gnu99 -fpic -Iinclude -c ./src/streamvbytedelta_encode.c gcc -std=gnu99 -fpic -Iinclude -c ./src/streamvbyte_0124_encode.c gcc -std=gnu99 -fpic -Iinclude -c ./src/streamvbyte_0124_decode.c gcc -std=gnu99 -fpic -Iinclude -c ./src/streamvbyte_zigzag.c rm -f libstreamvbyte.a ar cq libstreamvbyte.a streamvbyte_decode.o streamvbyte_encode.o streamvbytedelta_decode.o streamvbytedelta_encode.o streamvbyte_0124_encode.o streamvbyte_0124_decode.o streamvbyte_zigzag.o ranlib libstreamvbyte.a make[2]: Leaving directory '/tmp/RtmpwWXSk8/R.INSTALLff3329d6b5e9/rhdf5filters/src/vbz/third_party/streamvbyte' make -C vbz make[2]: Entering directory '/tmp/RtmpwWXSk8/R.INSTALLff3329d6b5e9/rhdf5filters/src/vbz/vbz' g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include" -I../third_party/streamvbyte/include/ -I../third_party/ -I../../zstd/ -mssse3 -c vbz.cpp -o vbz.o g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include" -I../third_party/streamvbyte/include/ -I../third_party/ -I../../zstd/ -mssse3 -c v0/vbz_streamvbyte.cpp -o v0/vbz_streamvbyte.o g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include" -I../third_party/streamvbyte/include/ -I../third_party/ -I../../zstd/ -mssse3 -c v1/vbz_streamvbyte.cpp -o v1/vbz_streamvbyte.o make[2]: Leaving directory '/tmp/RtmpwWXSk8/R.INSTALLff3329d6b5e9/rhdf5filters/src/vbz/vbz' rm -f libvbz.a ar cq libvbz.a vbz/vbz.o vbz/v0/vbz_streamvbyte.o vbz/v1/vbz_streamvbyte.o ranlib libvbz.a g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include" -shared vbz_plugin.cpp \ libvbz.a -L/usr/local/lib -lzstd third_party/streamvbyte/libstreamvbyte.a -o libH5Zvbz.so make[1]: Leaving directory '/tmp/RtmpwWXSk8/R.INSTALLff3329d6b5e9/rhdf5filters/src/vbz' mkdir -p "/home/omnipath/local/R/4.4-3.19/00LOCK-rhdf5filters/00new/rhdf5filters/lib/" cp bzip2/libH5Zbz2.so blosc/libH5Zblosc.so lzf/libH5Zlzf.so zstd/libH5Zzstd.so vbz/libH5Zvbz.so "/home/omnipath/local/R/4.4-3.19/00LOCK-rhdf5filters/00new/rhdf5filters/lib/" gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -I"/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include" -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -g -O2 -fpic -g -O2 -c rhdf5filters.c -o rhdf5filters.o gcc -shared -L/usr/local/lib -o rhdf5filters.so rhdf5filters.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-rhdf5filters/00new/rhdf5filters/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rhdf5filters) * installing *source* package ‘S4Vectors’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c AEbufs.c -o AEbufs.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c DataFrame_class.c -o DataFrame_class.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Hits_class.c -o Hits_class.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c LLint_class.c -o LLint_class.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c List_class.c -o List_class.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c R_init_S4Vectors.c -o R_init_S4Vectors.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rle_class.c -o Rle_class.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rle_utils.c -o Rle_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c SEXP_utils.c -o SEXP_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c SimpleList_class.c -o SimpleList_class.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c anyMissing.c -o anyMissing.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c character_utils.c -o character_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c eval_utils.c -o eval_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c hash_utils.c -o hash_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c integer_utils.c -o integer_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c logical_utils.c -o logical_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c map_ranges_to_runs.c -o map_ranges_to_runs.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c raw_utils.c -o raw_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c safe_arithm.c -o safe_arithm.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sort_utils.c -o sort_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c subsetting_utils.c -o subsetting_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c vector_utils.c -o vector_utils.o gcc -shared -L/usr/local/lib -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 installing to /home/omnipath/local/R/4.4-3.19/00LOCK-S4Vectors/00new/S4Vectors/libs ** R ** inst ** byte-compile and prepare package for lazy loading Warning message: package ‘BiocGenerics’ was built under R version 4.5.0 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’ Creating a generic function for ‘setequal’ from package ‘base’ 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 Warning: package ‘BiocGenerics’ was built under R version 4.5.0 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: package ‘BiocGenerics’ was built under R version 4.5.0 ** testing if installed package keeps a record of temporary installation path * DONE (S4Vectors) * installing *source* package ‘wppi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading [2024-04-29 15:23:26] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-04-29 15:23:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-29 15:23:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:23:26] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-04-29 15:23:26] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-04-29 15:23:26] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-04-29 15:23:26] [TRACE] [OmnipathR] Contains 1 files. [2024-04-29 15:23:26] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-04-29 15:23:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-29 15:23:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:23:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-04-29 15:23:27] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-04-29 15:23:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-04-29 15:23:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:23:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-04-29 15:23:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:23:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-04-29 15:23:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:23:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-04-29 15:23:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:23:27] [TRACE] [OmnipathR] Cache locked: FALSE Note: wrong number of arguments to '/' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2024-04-29 15:23:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-29 15:23:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:23:29] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-04-29 15:23:29] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-04-29 15:23:29] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-04-29 15:23:29] [TRACE] [OmnipathR] Contains 1 files. [2024-04-29 15:23:29] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-04-29 15:23:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-29 15:23:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:23:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-04-29 15:23:29] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-04-29 15:23:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-04-29 15:23:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:23:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-04-29 15:23:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:23:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-04-29 15:23:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:23:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-04-29 15:23:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:23:29] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-04-29 15:23:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-29 15:23:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:23:30] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-04-29 15:23:30] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-04-29 15:23:30] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-04-29 15:23:30] [TRACE] [OmnipathR] Contains 1 files. [2024-04-29 15:23:30] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-04-29 15:23:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-29 15:23:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:23:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-04-29 15:23:30] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-04-29 15:23:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-04-29 15:23:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:23:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-04-29 15:23:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:23:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-04-29 15:23:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:23:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-04-29 15:23:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:23:31] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (wppi) * installing *source* package ‘AnnotationHub’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning messages: 1: package ‘BiocGenerics’ was built under R version 4.5.0 2: package ‘BiocFileCache’ was built under R version 4.5.0 3: package ‘dbplyr’ was built under R version 4.5.0 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: package ‘BiocGenerics’ was built under R version 4.5.0 Warning: package ‘BiocFileCache’ was built under R version 4.5.0 Warning: package ‘dbplyr’ was built under R version 4.5.0 ** testing if installed package can be loaded from final location Warning: package ‘BiocGenerics’ was built under R version 4.5.0 Warning: package ‘BiocFileCache’ was built under R version 4.5.0 Warning: package ‘dbplyr’ was built under R version 4.5.0 ** testing if installed package keeps a record of temporary installation path * DONE (AnnotationHub) * installing *source* package ‘BiocCheck’ ... ** 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 (BiocCheck) * installing *source* package ‘DESeq2’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.19/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c DESeq2.cpp -o DESeq2.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.19/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -shared -L/usr/local/lib -o DESeq2.so DESeq2.o RcppExports.o -llapack -L/opt/R-alpha/lib/R/lib -lRblas -lgfortran -lm -lquadmath installing to /home/omnipath/local/R/4.4-3.19/00LOCK-DESeq2/00new/DESeq2/libs ** R ** inst ** byte-compile and prepare package for lazy loading Warning messages: 1: package ‘BiocGenerics’ was built under R version 4.5.0 2: package ‘IRanges’ was built under R version 4.5.0 3: package ‘GenomicRanges’ was built under R version 4.5.0 4: package ‘SummarizedExperiment’ was built under R version 4.5.0 5: package ‘Biobase’ was built under R version 4.5.0 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: package ‘BiocGenerics’ was built under R version 4.5.0 Warning: package ‘IRanges’ was built under R version 4.5.0 Warning: package ‘GenomicRanges’ was built under R version 4.5.0 Warning: package ‘SummarizedExperiment’ was built under R version 4.5.0 Warning: package ‘Biobase’ was built under R version 4.5.0 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: package ‘BiocGenerics’ was built under R version 4.5.0 Warning: package ‘IRanges’ was built under R version 4.5.0 Warning: package ‘GenomicRanges’ was built under R version 4.5.0 Warning: package ‘SummarizedExperiment’ was built under R version 4.5.0 Warning: package ‘Biobase’ was built under R version 4.5.0 ** testing if installed package keeps a record of temporary installation path * DONE (DESeq2) * installing *source* package ‘edgeR’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_add_prior_count.cpp -o R_add_prior_count.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_ave_log_cpm.cpp -o R_ave_log_cpm.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_calculate_cpm.cpp -o R_calculate_cpm.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_check_poisson_bound.cpp -o R_check_poisson_bound.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_compute_apl.cpp -o R_compute_apl.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_compute_nbdev.cpp -o R_compute_nbdev.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_fit_levenberg.cpp -o R_fit_levenberg.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_fit_one_group.cpp -o R_fit_one_group.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_get_one_way_fitted.cpp -o R_get_one_way_fitted.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_initialize_levenberg.cpp -o R_initialize_levenberg.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_loess_by_col.cpp -o R_loess_by_col.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_ql_glm.c -o R_ql_glm.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_simple_good_turing.cpp -o R_simple_good_turing.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c add_prior.cpp -o add_prior.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c adj_coxreid.cpp -o adj_coxreid.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c fmm_spline.c -o fmm_spline.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c glm_levenberg.cpp -o glm_levenberg.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c glm_one_group.cpp -o glm_one_group.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c init.cpp -o init.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c interpolator.cpp -o interpolator.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c nbdev.c -o nbdev.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c objects.cpp -o objects.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ql_glm.c -o ql_glm.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ql_weights.c -o ql_weights.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c qr_hat.c -o qr_hat.o g++ -std=gnu++17 -shared -L/usr/local/lib -o edgeR.so R_add_prior_count.o R_ave_log_cpm.o R_calculate_cpm.o R_check_poisson_bound.o R_compute_apl.o R_compute_nbdev.o R_exact_test_by_deviance.o R_fit_levenberg.o R_fit_one_group.o R_get_one_way_fitted.o R_initialize_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_process_hairpin_reads.o R_ql_glm.o R_simple_good_turing.o add_prior.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o nbdev.o objects.o ql_glm.o ql_weights.o qr_hat.o -llapack -L/opt/R-alpha/lib/R/lib -lRblas -lgfortran -lm -lquadmath installing to /home/omnipath/local/R/4.4-3.19/00LOCK-edgeR/00new/edgeR/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (edgeR) * installing *source* package ‘rhdf5’ ... ** using staged installation configure: creating ./config.status config.status: creating src/external_filters.h ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5.c -o H5.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5A.c -o H5A.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5D.c -o H5D.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5E.c -o H5E.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5F.c -o H5F.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5G.c -o H5G.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5I.c -o H5I.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5L.c -o H5L.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5O.c -o H5O.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5P.c -o H5P.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5PL.c -o H5PL.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5R.c -o H5R.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5S.c -o H5S.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5S_extras.c -o H5S_extras.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5T.c -o H5T.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5T_extras.c -o H5T_extras.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5Z.c -o H5Z.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5constants.c -o H5constants.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c HandleList.cpp -o HandleList.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c HandleListWrap.c -o HandleListWrap.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c bit64conversion.c -o bit64conversion.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c external_filters.c -o external_filters.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5dump.c -o h5dump.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5ls.c -o h5ls.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5testLock.c -o h5testLock.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5writeDataFrame.c -o h5writeDataFrame.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c printdatatype.c -o printdatatype.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c utils.c -o utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c wrap.c -o wrap.o g++ -std=gnu++17 -shared -L/usr/local/lib -o rhdf5.so H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5PL.o H5R.o H5S.o H5S_extras.o H5T.o H5T_extras.o H5Z.o H5constants.o HandleList.o HandleListWrap.o bit64conversion.o external_filters.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o /home/omnipath/local/R/4.4-3.19/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm installing to /home/omnipath/local/R/4.4-3.19/00LOCK-rhdf5/00new/rhdf5/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rhdf5) * installing *source* package ‘S4Arrays’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c R_init_S4Arrays.c -o R_init_S4Arrays.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c abind.c -o abind.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c array_selection.c -o array_selection.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c dim_tuning_utils.c -o dim_tuning_utils.o gcc -shared -L/usr/local/lib -o S4Arrays.so R_init_S4Arrays.o S4Vectors_stubs.o abind.o array_selection.o dim_tuning_utils.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-S4Arrays/00new/S4Arrays/libs ** R ** inst ** byte-compile and prepare package for lazy loading Warning messages: 1: package ‘abind’ was built under R version 4.5.0 2: package ‘BiocGenerics’ was built under R version 4.5.0 3: package ‘IRanges’ was built under R version 4.5.0 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 Warning: package ‘abind’ was built under R version 4.5.0 Warning: package ‘BiocGenerics’ was built under R version 4.5.0 Warning: package ‘IRanges’ was built under R version 4.5.0 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: package ‘abind’ was built under R version 4.5.0 Warning: package ‘BiocGenerics’ was built under R version 4.5.0 Warning: package ‘IRanges’ was built under R version 4.5.0 ** testing if installed package keeps a record of temporary installation path * DONE (S4Arrays) * installing *source* package ‘sparseMatrixStats’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++11 g++ -std=gnu++11 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c SparseMatrixView.cpp -o SparseMatrixView.o g++ -std=gnu++11 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c methods.cpp -o methods.o g++ -std=gnu++11 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c row_methods.cpp -o row_methods.o g++ -std=gnu++11 -shared -L/usr/local/lib -o sparseMatrixStats.so RcppExports.o SparseMatrixView.o methods.o row_methods.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-sparseMatrixStats/00new/sparseMatrixStats/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (sparseMatrixStats) * installing *source* package ‘UCSC.utils’ ... ** 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 ‘DelayedMatrixStats’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning messages: 1: package ‘DelayedArray’ was built under R version 4.5.0 2: package ‘BiocGenerics’ was built under R version 4.5.0 3: package ‘IRanges’ was built under R version 4.5.0 4: package ‘abind’ was built under R version 4.5.0 5: package ‘SparseArray’ was built under R version 4.5.0 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: package ‘DelayedArray’ was built under R version 4.5.0 Warning: package ‘BiocGenerics’ was built under R version 4.5.0 Warning: package ‘IRanges’ was built under R version 4.5.0 Warning: package ‘abind’ was built under R version 4.5.0 Warning: package ‘SparseArray’ was built under R version 4.5.0 ** testing if installed package can be loaded from final location Warning: package ‘DelayedArray’ was built under R version 4.5.0 Warning: package ‘BiocGenerics’ was built under R version 4.5.0 Warning: package ‘IRanges’ was built under R version 4.5.0 Warning: package ‘abind’ was built under R version 4.5.0 Warning: package ‘SparseArray’ was built under R version 4.5.0 ** testing if installed package keeps a record of temporary installation path * DONE (DelayedMatrixStats) * installing *source* package ‘ExperimentHub’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning messages: 1: package ‘BiocGenerics’ was built under R version 4.5.0 2: package ‘BiocFileCache’ was built under R version 4.5.0 3: package ‘dbplyr’ was built under R version 4.5.0 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: package ‘BiocGenerics’ was built under R version 4.5.0 Warning: package ‘BiocFileCache’ was built under R version 4.5.0 Warning: package ‘dbplyr’ was built under R version 4.5.0 ** testing if installed package can be loaded from final location Warning: package ‘BiocGenerics’ was built under R version 4.5.0 Warning: package ‘BiocFileCache’ was built under R version 4.5.0 Warning: package ‘dbplyr’ was built under R version 4.5.0 ** testing if installed package keeps a record of temporary installation path * DONE (ExperimentHub) * installing *source* package ‘GenomeInfoDb’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning messages: 1: package ‘BiocGenerics’ was built under R version 4.5.0 2: package ‘IRanges’ was built under R version 4.5.0 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: package ‘BiocGenerics’ was built under R version 4.5.0 Warning: package ‘IRanges’ was built under R version 4.5.0 ** testing if installed package can be loaded from final location Warning: package ‘BiocGenerics’ was built under R version 4.5.0 Warning: package ‘IRanges’ was built under R version 4.5.0 ** testing if installed package keeps a record of temporary installation path * DONE (GenomeInfoDb) * installing *source* package ‘SparseArray’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c R_init_SparseArray.c -o R_init_SparseArray.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c Rvector_summarization.c -o Rvector_summarization.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c Rvector_utils.c -o Rvector_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SBT_utils.c -o SBT_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseArray_Ops_methods.c -o SparseArray_Ops_methods.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseArray_abind.c -o SparseArray_abind.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseArray_aperm.c -o SparseArray_aperm.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseArray_class.c -o SparseArray_class.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseArray_subassignment.c -o SparseArray_subassignment.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseArray_subsetting.c -o SparseArray_subsetting.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseArray_summarization.c -o SparseArray_summarization.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseMatrix_mult.c -o SparseMatrix_mult.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c XVector_stubs.c -o XVector_stubs.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c coerceVector2.c -o coerceVector2.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c leaf_vector_Arith.c -o leaf_vector_Arith.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c leaf_vector_Compare.c -o leaf_vector_Compare.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c leaf_vector_Logic.c -o leaf_vector_Logic.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c leaf_vector_dotprod.c -o leaf_vector_dotprod.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c leaf_vector_summarization.c -o leaf_vector_summarization.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c leaf_vector_utils.c -o leaf_vector_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c matrixStats_methods.c -o matrixStats_methods.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c randomSparseArray.c -o randomSparseArray.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c readSparseCSV.c -o readSparseCSV.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c rowsum_methods.c -o rowsum_methods.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c sparseMatrix_utils.c -o sparseMatrix_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c test.c -o test.o gcc -shared -L/usr/local/lib -o SparseArray.so ExtendableJaggedArray.o IRanges_stubs.o R_init_SparseArray.o Rvector_summarization.o Rvector_utils.o S4Vectors_stubs.o SBT_utils.o SVT_SparseArray_class.o SparseArray_Complex_methods.o SparseArray_Math_methods.o SparseArray_Ops_methods.o SparseArray_abind.o SparseArray_aperm.o SparseArray_class.o SparseArray_dim_tuning.o SparseArray_subassignment.o SparseArray_subsetting.o SparseArray_summarization.o SparseMatrix_mult.o XVector_stubs.o coerceVector2.o leaf_vector_Arith.o leaf_vector_Compare.o leaf_vector_Logic.o leaf_vector_dotprod.o leaf_vector_summarization.o leaf_vector_utils.o matrixStats_methods.o randomSparseArray.o readSparseCSV.o rowsum_methods.o sparseMatrix_utils.o test.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-SparseArray/00new/SparseArray/libs ** R ** inst ** byte-compile and prepare package for lazy loading Warning messages: 1: package ‘BiocGenerics’ was built under R version 4.5.0 2: package ‘abind’ was built under R version 4.5.0 3: package ‘IRanges’ was built under R version 4.5.0 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: package ‘BiocGenerics’ was built under R version 4.5.0 Warning: package ‘abind’ was built under R version 4.5.0 Warning: package ‘IRanges’ was built under R version 4.5.0 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: package ‘BiocGenerics’ was built under R version 4.5.0 Warning: package ‘abind’ was built under R version 4.5.0 Warning: package ‘IRanges’ was built under R version 4.5.0 ** testing if installed package keeps a record of temporary installation path * DONE (SparseArray) * installing *source* package ‘Biostrings’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c BAB_class.c -o BAB_class.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c BitMatrix.c -o BitMatrix.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c MIndex_class.c -o MIndex_class.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c PreprocessedTB_class.c -o PreprocessedTB_class.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c R_init_Biostrings.c -o R_init_Biostrings.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c RoSeqs_utils.c -o RoSeqs_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseList_utils.c -o SparseList_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c XStringSetList_class.c -o XStringSetList_class.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c XStringSet_class.c -o XStringSet_class.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c XString_class.c -o XString_class.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c XVector_stubs.c -o XVector_stubs.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c find_palindromes.c -o find_palindromes.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c gtestsim.c -o gtestsim.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c inject_code.c -o inject_code.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c letter_frequency.c -o letter_frequency.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c lowlevel_matching.c -o lowlevel_matching.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c match_PWM.c -o match_PWM.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c match_pattern.c -o match_pattern.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c match_pattern_indels.c -o match_pattern_indels.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c match_pattern_shiftor.c -o match_pattern_shiftor.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c match_pdict.c -o match_pdict.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c match_pdict_Twobit.c -o match_pdict_Twobit.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c match_pdict_utils.c -o match_pdict_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c match_reporting.c -o match_reporting.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c matchprobes.c -o matchprobes.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c pmatchPattern.c -o pmatchPattern.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c read_fasta_files.c -o read_fasta_files.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c read_fastq_files.c -o read_fastq_files.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c replaceAt.c -o replaceAt.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c replace_letter_at.c -o replace_letter_at.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c strutils.c -o strutils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c translate.c -o translate.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c unstrsplit_methods.c -o unstrsplit_methods.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c utils.c -o utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c xscat.c -o xscat.o gcc -shared -L/usr/local/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XString_class.o XVector_stubs.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-Biostrings/00new/Biostrings/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning messages: 1: package ‘BiocGenerics’ was built under R version 4.5.0 2: package ‘IRanges’ was built under R version 4.5.0 3: package ‘XVector’ was built under R version 4.5.0 in method for ‘twoWayAlphabetFrequencyByQuality’ with signature ‘"QualityScaledXStringSet"’: no definition for class “QualityScaledXStringSet” Creating a new generic function for ‘strsplit’ in package ‘Biostrings’ Creating a generic function for ‘ls’ from package ‘base’ in package ‘Biostrings’ Creating a new generic function for ‘pattern’ in package ‘Biostrings’ Creating a new generic function for ‘offset’ in package ‘Biostrings’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: package ‘BiocGenerics’ was built under R version 4.5.0 Warning: package ‘IRanges’ was built under R version 4.5.0 Warning: package ‘XVector’ was built under R version 4.5.0 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: package ‘BiocGenerics’ was built under R version 4.5.0 Warning: package ‘IRanges’ was built under R version 4.5.0 Warning: package ‘XVector’ was built under R version 4.5.0 ** testing if installed package keeps a record of temporary installation path * DONE (Biostrings) * installing *source* package ‘GSVA’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c kernel_estimation.c -o kernel_estimation.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ks_test.c -o ks_test.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c register_cmethods.c -o register_cmethods.o gcc -shared -L/usr/local/lib -o GSVA.so kernel_estimation.o ks_test.o register_cmethods.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-GSVA/00new/GSVA/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 (GSVA) * installing *source* package ‘KEGGREST’ ... ** 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 (KEGGREST) The downloaded source packages are in ‘/tmp/RtmpXJ8hmk/downloaded_packages’ Bioconductor version 3.19 (BiocManager 1.30.22), R 4.4.0 alpha (2024-04-04 r86334) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' Skipping 1 packages ahead of CRAN: BiocStyle [ Finished: 2024-04-29 15:28:06 CEST ]