[ Started: 2025-03-18 00:53:55 CET ] [ cosmosR v1.9.1 for BioC-3.21 from https://github.com/saezlab/cosmosR@master (ef9d5aa 2025-03-09 13:20:11) ] [1] "Libraries: " "/home/omnipath/local/R/4.5-3.21" [3] "/home/omnipath/local/R/4.5" "/opt/R-devel/lib/R/library" Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable) (2025-02-12 r87715) Old packages: 'writexl' trying URL 'https://cloud.r-project.org/src/contrib/writexl_1.5.2.tar.gz' Content type 'application/x-gzip' length 278079 bytes (271 KB) ================================================== downloaded 271 KB * installing *source* package ‘writexl’ ... ** this is package ‘writexl’ version ‘1.5.2’ ** package ‘writexl’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c write_xlsx.c -o write_xlsx.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/app.c -o libxlsxwriter/app.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/format.c -o libxlsxwriter/format.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/theme.c -o libxlsxwriter/theme.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/chart.c -o libxlsxwriter/chart.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/hash_table.c -o libxlsxwriter/hash_table.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/utility.c -o libxlsxwriter/utility.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/content_types.c -o libxlsxwriter/content_types.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/packager.c -o libxlsxwriter/packager.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/workbook.c -o libxlsxwriter/workbook.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/core.c -o libxlsxwriter/core.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/relationships.c -o libxlsxwriter/relationships.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/worksheet.c -o libxlsxwriter/worksheet.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/custom.c -o libxlsxwriter/custom.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/shared_strings.c -o libxlsxwriter/shared_strings.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/xmlwriter.c -o libxlsxwriter/xmlwriter.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/drawing.c -o libxlsxwriter/drawing.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/styles.c -o libxlsxwriter/styles.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c tmpfileplus/tmpfileplus.c -o tmpfileplus/tmpfileplus.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/chartsheet.c -o libxlsxwriter/chartsheet.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c minizip/ioapi.c -o minizip/ioapi.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c minizip/zip.c -o minizip/zip.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/metadata.c -o libxlsxwriter/metadata.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/comment.c -o libxlsxwriter/comment.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/vml.c -o libxlsxwriter/vml.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c md5/md5.c -o md5/md5.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/table.c -o libxlsxwriter/table.o ar rcs libxlsxwriter/libstatxlsxwriter.a libxlsxwriter/app.o libxlsxwriter/format.o libxlsxwriter/theme.o libxlsxwriter/chart.o libxlsxwriter/hash_table.o libxlsxwriter/utility.o libxlsxwriter/content_types.o libxlsxwriter/packager.o libxlsxwriter/workbook.o libxlsxwriter/core.o libxlsxwriter/relationships.o libxlsxwriter/worksheet.o libxlsxwriter/custom.o libxlsxwriter/shared_strings.o libxlsxwriter/xmlwriter.o libxlsxwriter/drawing.o libxlsxwriter/styles.o tmpfileplus/tmpfileplus.o libxlsxwriter/chartsheet.o minizip/ioapi.o minizip/zip.o libxlsxwriter/metadata.o libxlsxwriter/comment.o libxlsxwriter/vml.o md5/md5.o libxlsxwriter/table.o gcc -shared -L/usr/local/lib -o writexl.so write_xlsx.o -Llibxlsxwriter -lstatxlsxwriter -lz rm -f libxlsxwriter/app.o libxlsxwriter/format.o libxlsxwriter/theme.o libxlsxwriter/chart.o libxlsxwriter/hash_table.o libxlsxwriter/utility.o libxlsxwriter/content_types.o libxlsxwriter/packager.o libxlsxwriter/workbook.o libxlsxwriter/core.o libxlsxwriter/relationships.o libxlsxwriter/worksheet.o libxlsxwriter/custom.o libxlsxwriter/shared_strings.o libxlsxwriter/xmlwriter.o libxlsxwriter/drawing.o libxlsxwriter/styles.o tmpfileplus/tmpfileplus.o libxlsxwriter/chartsheet.o minizip/ioapi.o minizip/zip.o libxlsxwriter/metadata.o libxlsxwriter/comment.o libxlsxwriter/vml.o md5/md5.o libxlsxwriter/table.o libxlsxwriter/libstatxlsxwriter.a installing to /home/omnipath/local/R/4.5-3.21/00LOCK-writexl/00new/writexl/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (writexl) The downloaded source packages are in ‘/tmp/RtmpjyQnGj/downloaded_packages’ Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable) (2025-02-12 r87715) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' Skipping 2 packages ahead of CRAN: mime, commonmark [ Finished: 2025-03-18 00:54:13 CET ]