[ Started: 2024-03-20 23:03:10 CET ] [ cosmosR v1.5.2 for BioC-3.19 from https://github.com/saezlab/cosmosR@master ] [1] "Libraries: " "/home/omnipath/local/R/4.4-3.19" [3] "/home/omnipath/local/R/4.4" "/opt/R-devel/lib/R/library" Bioconductor version 3.19 (BiocManager 1.30.22), R Under development (unstable) (2024-03-19 r86153) Old packages: 'BiocStyle' trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/BiocStyle_2.31.0.tar.gz' Content type 'application/x-gzip' length 788268 bytes (769 KB) ================================================== downloaded 769 KB * installing *source* package ‘BiocStyle’ ... ** 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 (BiocStyle) The downloaded source packages are in ‘/tmp/Rtmp46swm2/downloaded_packages’ Bioconductor version 3.19 (BiocManager 1.30.22), R Under development (unstable) (2024-03-19 r86153) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' colorspace (NA -> 2.1-0 ) [CRAN] viridisLite (NA -> 0.4.2 ) [CRAN] RColorBrewer (NA -> 1.1-3 ) [CRAN] munsell (NA -> 0.5.0 ) [CRAN] labeling (NA -> 0.4.3 ) [CRAN] farver (NA -> 2.1.1 ) [CRAN] htmlwidgets (NA -> 1.6.4 ) [CRAN] commonmark (NA -> 1.9.1 ) [CRAN] sourcetools (NA -> 0.1.7-1) [CRAN] xtable (NA -> 1.8-4 ) [CRAN] httpuv (NA -> 1.6.14 ) [CRAN] later (NA -> 1.3.2 ) [CRAN] promises (NA -> 1.2.1 ) [CRAN] shiny (NA -> 1.8.0 ) [CRAN] crosstalk (NA -> 1.2.1 ) [CRAN] formatR (NA -> 1.14 ) [CRAN] futile.op... (NA -> 1.0.1 ) [CRAN] lambda.r (NA -> 1.2.4 ) [CRAN] isoband (NA -> 0.2.7 ) [CRAN] gtable (NA -> 0.3.4 ) [CRAN] snow (NA -> 0.4-4 ) [CRAN] futile.lo... (NA -> 1.4.3 ) [CRAN] scales (NA -> 1.3.0 ) [CRAN] fastmatch (NA -> 1.1-4 ) [CRAN] cowplot (NA -> 1.1.3 ) [CRAN] ggplot2 (NA -> 3.5.0 ) [CRAN] BiocParallel (NA -> 1.36.0 ) [CRAN] data.table (NA -> 1.15.2 ) [CRAN] statmod (NA -> 1.5.0 ) [CRAN] limma (NA -> 3.58.1 ) [CRAN] sets (NA -> 1.0-25 ) [CRAN] slam (NA -> 0.1-50 ) [CRAN] caTools (NA -> 1.18.2 ) [CRAN] gtools (NA -> 3.9.5 ) [CRAN] zlibbioc (NA -> 1.48.2 ) [CRAN] GenomeInf... (NA -> 1.2.11 ) [CRAN] GenomeInfoDb (NA -> 1.38.8 ) [CRAN] XVector (NA -> 0.42.0 ) [CRAN] Biostrings (NA -> 2.70.3 ) [CRAN] png (NA -> 0.1-8 ) [CRAN] KEGGREST (NA -> 1.42.0 ) [CRAN] S4Vectors (NA -> 0.40.2 ) [CRAN] IRanges (NA -> 2.36.0 ) [CRAN] Annotatio... (NA -> 1.64.1 ) [CRAN] broom (NA -> 1.0.5 ) [CRAN] visNetwork (NA -> 2.1.2 ) [CRAN] shinydash... (NA -> 0.7.2 ) [CRAN] shinyjs (NA -> 2.1.0 ) [CRAN] DT (NA -> 0.32 ) [CRAN] fgsea (NA -> 1.28.0 ) [CRAN] marray (NA -> 1.80.0 ) [CRAN] relations (NA -> 0.6-13 ) [CRAN] gplots (NA -> 3.1.3.1) [CRAN] annotate (NA -> 1.80.0 ) [CRAN] decoupleR (NA -> 2.8.0 ) [CRAN] bcellViper (NA -> 1.38.0 ) [CRAN] piano (NA -> 2.18.0 ) [CRAN] GSEABase (NA -> 1.64.0 ) [CRAN] dorothea (NA -> 1.14.1 ) [CRAN] CARNIVAL (NA -> 2.12.0 ) [CRAN] Skipping 3 packages ahead of CRAN: BiocGenerics, Biobase, graph Installing 60 packages: colorspace, viridisLite, RColorBrewer, munsell, labeling, farver, htmlwidgets, commonmark, sourcetools, xtable, httpuv, later, promises, shiny, crosstalk, formatR, futile.options, lambda.r, isoband, gtable, snow, futile.logger, scales, fastmatch, cowplot, ggplot2, BiocParallel, data.table, statmod, limma, sets, slam, caTools, gtools, zlibbioc, GenomeInfoDbData, GenomeInfoDb, XVector, Biostrings, png, KEGGREST, S4Vectors, IRanges, AnnotationDbi, broom, visNetwork, shinydashboard, shinyjs, DT, fgsea, marray, relations, gplots, annotate, decoupleR, bcellViper, piano, GSEABase, dorothea, CARNIVAL trying URL 'https://cran.uni-muenster.de/src/contrib/colorspace_2.1-0.tar.gz' Content type 'application/x-gzip' length 2116339 bytes (2.0 MB) ================================================== downloaded 2.0 MB trying URL 'https://cran.uni-muenster.de/src/contrib/viridisLite_0.4.2.tar.gz' Content type 'application/x-gzip' length 1267121 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://cran.uni-muenster.de/src/contrib/RColorBrewer_1.1-3.tar.gz' Content type 'application/x-gzip' length 11638 bytes (11 KB) ================================================== downloaded 11 KB trying URL 'https://cran.uni-muenster.de/src/contrib/munsell_0.5.0.tar.gz' Content type 'application/x-gzip' length 182653 bytes (178 KB) ================================================== downloaded 178 KB trying URL 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'https://bioconductor.org/packages/3.18/bioc/src/contrib/marray_1.80.0.tar.gz' Content type 'application/x-gzip' length 5056102 bytes (4.8 MB) ================================================== downloaded 4.8 MB trying URL 'https://cran.uni-muenster.de/src/contrib/relations_0.6-13.tar.gz' Content type 'application/x-gzip' length 294624 bytes (287 KB) ================================================== downloaded 287 KB trying URL 'https://cran.uni-muenster.de/src/contrib/gplots_3.1.3.1.tar.gz' Content type 'application/x-gzip' length 520586 bytes (508 KB) ================================================== downloaded 508 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/annotate_1.80.0.tar.gz' Content type 'application/x-gzip' length 1497628 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/decoupleR_2.8.0.tar.gz' Content type 'application/x-gzip' length 4413221 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downloaded 33.0 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/CARNIVAL_2.12.0.tar.gz' Content type 'application/x-gzip' length 2146283 bytes (2.0 MB) ================================================== downloaded 2.0 MB * installing *source* package ‘colorspace’ ... ** package ‘colorspace’ 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-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c colorspace.c -o colorspace.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -shared -L/usr/local/lib -o colorspace.so colorspace.o init.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-colorspace/00new/colorspace/libs ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** 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 (colorspace) * installing *source* package ‘viridisLite’ ... ** package ‘viridisLite’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (viridisLite) * installing *source* package ‘RColorBrewer’ ... ** package ‘RColorBrewer’ 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 (RColorBrewer) * installing *source* package ‘labeling’ ... ** package ‘labeling’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (labeling) * installing *source* package ‘farver’ ... ** package ‘farver’ successfully unpacked and MD5 sums checked ** 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-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ColorSpace.cpp -o ColorSpace.o g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Comparison.cpp -o Comparison.o g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Conversion.cpp -o Conversion.o g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c encode.cpp -o encode.o g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c farver.cpp -o farver.o g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.cpp -o init.o g++ -std=gnu++11 -shared -L/usr/local/lib -o farver.so ColorSpace.o Comparison.o Conversion.o encode.o farver.o init.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-farver/00new/farver/libs ** R ** 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 ** 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 (farver) * installing *source* package ‘htmlwidgets’ ... ** package ‘htmlwidgets’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (htmlwidgets) * installing *source* package ‘commonmark’ ... ** package ‘commonmark’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ rm -f cmark/cmark.o cmark/node.o cmark/iterator.o cmark/blocks.o cmark/inlines.o cmark/scanners.o cmark/utf8.o cmark/buffer.o cmark/references.o cmark/render.o cmark/man.o cmark/xml.o cmark/html.o cmark/commonmark.o cmark/latex.o cmark/houdini_href_e.o cmark/houdini_html_e.o cmark/houdini_html_u.o cmark/cmark_ctype.o cmark/arena.o cmark/linked_list.o cmark/plugin.o cmark/registry.o cmark/syntax_extension.o cmark/plaintext.o cmark/footnotes.o cmark/map.o extensions/autolink.o extensions/core-extensions.o extensions/ext_scanners.o extensions/strikethrough.o extensions/table.o extensions/tagfilter.o extensions/tasklist.o extensions.o init.o wrapper.o commonmark.so cmark/libstatcmark.a gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c extensions.c -o extensions.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c wrapper.c -o wrapper.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/cmark.c -o cmark/cmark.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/node.c -o cmark/node.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/iterator.c -o cmark/iterator.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/blocks.c -o cmark/blocks.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/inlines.c -o cmark/inlines.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/scanners.c -o cmark/scanners.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/utf8.c -o cmark/utf8.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/buffer.c -o cmark/buffer.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/references.c -o cmark/references.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/render.c -o cmark/render.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/man.c -o cmark/man.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/xml.c -o cmark/xml.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/html.c -o cmark/html.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/commonmark.c -o cmark/commonmark.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/latex.c -o cmark/latex.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/houdini_href_e.c -o cmark/houdini_href_e.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/houdini_html_e.c -o cmark/houdini_html_e.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/houdini_html_u.c -o cmark/houdini_html_u.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/cmark_ctype.c -o cmark/cmark_ctype.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/arena.c -o cmark/arena.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/linked_list.c -o cmark/linked_list.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/plugin.c -o cmark/plugin.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/registry.c -o cmark/registry.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/syntax_extension.c -o cmark/syntax_extension.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/plaintext.c -o cmark/plaintext.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/footnotes.c -o cmark/footnotes.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cmark/map.c -o cmark/map.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c extensions/autolink.c -o extensions/autolink.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c extensions/core-extensions.c -o extensions/core-extensions.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c extensions/ext_scanners.c -o extensions/ext_scanners.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c extensions/strikethrough.c -o extensions/strikethrough.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c extensions/table.c -o extensions/table.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c extensions/tagfilter.c -o extensions/tagfilter.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c extensions/tasklist.c -o extensions/tasklist.o ar rcs cmark/libstatcmark.a cmark/cmark.o cmark/node.o cmark/iterator.o cmark/blocks.o cmark/inlines.o cmark/scanners.o cmark/utf8.o cmark/buffer.o cmark/references.o cmark/render.o cmark/man.o cmark/xml.o cmark/html.o cmark/commonmark.o cmark/latex.o cmark/houdini_href_e.o cmark/houdini_html_e.o cmark/houdini_html_u.o cmark/cmark_ctype.o cmark/arena.o cmark/linked_list.o cmark/plugin.o cmark/registry.o cmark/syntax_extension.o cmark/plaintext.o cmark/footnotes.o cmark/map.o extensions/autolink.o extensions/core-extensions.o extensions/ext_scanners.o extensions/strikethrough.o extensions/table.o extensions/tagfilter.o extensions/tasklist.o gcc -shared -L/usr/local/lib -o commonmark.so extensions.o init.o wrapper.o -Lcmark -lstatcmark installing to /home/omnipath/local/R/4.4-3.19/00LOCK-commonmark/00new/commonmark/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 (commonmark) * installing *source* package ‘sourcetools’ ... ** package ‘sourcetools’ 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’ g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I/usr/local/include -fpic -g -O2 -c Reader.cpp -o Reader.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I/usr/local/include -fpic -g -O2 -c Tokenizer.cpp -o Tokenizer.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I/usr/local/include -fpic -g -O2 -c sourcetools-init.c -o sourcetools-init.o g++ -std=gnu++17 -shared -L/usr/local/lib -o sourcetools.so Reader.o Tokenizer.o sourcetools-init.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-sourcetools/00new/sourcetools/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 (sourcetools) * installing *source* package ‘xtable’ ... ** package ‘xtable’ 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 ** 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 (xtable) * installing *source* package ‘later’ ... ** package ‘later’ successfully unpacked and MD5 sums checked ** using staged installation Running configure script -latomic linker flag not needed. ** 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-devel/lib/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -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-devel/lib/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c callback_registry.cpp -o callback_registry.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c debug.cpp -o debug.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c init.c -o init.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c later.cpp -o later.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c later_posix.cpp -o later_posix.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c later_win32.cpp -o later_win32.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c timer_posix.cpp -o timer_posix.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c timestamp_unix.cpp -o timestamp_unix.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c timestamp_win32.cpp -o timestamp_win32.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c tinycthread.c -o tinycthread.o g++ -std=gnu++17 -shared -L/usr/local/lib -o later.so RcppExports.o callback_registry.o debug.o init.o later.o later_posix.o later_win32.o timer_posix.o timestamp_unix.o timestamp_win32.o tinycthread.o -pthread installing to /home/omnipath/local/R/4.4-3.19/00LOCK-later/00new/later/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 (later) * installing *source* package ‘crosstalk’ ... ** package ‘crosstalk’ 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 (crosstalk) * installing *source* package ‘formatR’ ... ** package ‘formatR’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (formatR) * installing *source* package ‘futile.options’ ... ** package ‘futile.options’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (futile.options) * installing *source* package ‘isoband’ ... ** package ‘isoband’ successfully unpacked and MD5 sums checked ** 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-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c clip-lines.cpp -o clip-lines.o g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.cpp -o init.o g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c isoband.cpp -o isoband.o g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c polygon.cpp -o polygon.o g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c separate-polygons.cpp -o separate-polygons.o g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c test-clip-lines.cpp -o test-clip-lines.o g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c test-runner.cpp -o test-runner.o g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c test-separate-polygons.cpp -o test-separate-polygons.o g++ -std=gnu++11 -shared -L/usr/local/lib -o isoband.so clip-lines.o init.o isoband.o polygon.o separate-polygons.o test-clip-lines.o test-runner.o test-separate-polygons.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-isoband/00new/isoband/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 (isoband) * 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 ‘snow’ ... ** package ‘snow’ 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 (snow) * installing *source* package ‘fastmatch’ ... ** package ‘fastmatch’ 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-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ctapply.c -o ctapply.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dummy.c -o dummy.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c fasthash.c -o fasthash.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c fastmatch.c -o fastmatch.o gcc -shared -L/usr/local/lib -o fastmatch.so ctapply.o dummy.o fasthash.o fastmatch.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-fastmatch/00new/fastmatch/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 (fastmatch) * installing *source* package ‘data.table’ ... ** package ‘data.table’ successfully unpacked and MD5 sums checked ** using staged installation gcc 11.4.0 zlib 1.2.11 is available ok R CMD SHLIB supports OpenMP without any extra hint ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c assign.c -o assign.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c between.c -o between.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c bmerge.c -o bmerge.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c chmatch.c -o chmatch.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c cj.c -o cj.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c coalesce.c -o coalesce.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c dogroups.c -o dogroups.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fastmean.c -o fastmean.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fcast.c -o fcast.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fifelse.c -o fifelse.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fmelt.c -o fmelt.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c forder.c -o forder.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c frank.c -o frank.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fread.c -o fread.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c freadR.c -o freadR.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c froll.c -o froll.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c frollR.c -o frollR.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c frolladaptive.c -o frolladaptive.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fsort.c -o fsort.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fwrite.c -o fwrite.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fwriteR.c -o fwriteR.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c gsumm.c -o gsumm.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c idatetime.c -o idatetime.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c ijoin.c -o ijoin.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c inrange.c -o inrange.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c nafill.c -o nafill.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c negate.c -o negate.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c nqrecreateindices.c -o nqrecreateindices.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c openmp-utils.c -o openmp-utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c programming.c -o programming.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c quickselect.c -o quickselect.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c rbindlist.c -o rbindlist.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c reorder.c -o reorder.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c shift.c -o shift.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c snprintf.c -o snprintf.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c subset.c -o subset.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c transpose.c -o transpose.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c types.c -o types.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c uniqlist.c -o uniqlist.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c utils.c -o utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c vecseq.c -o vecseq.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c wrappers.c -o wrappers.o gcc -shared -L/usr/local/lib -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -lz PKG_CFLAGS = -fopenmp PKG_LIBS = -fopenmp -lz if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi installing to /home/omnipath/local/R/4.4-3.19/00LOCK-data.table/00new/data.table/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 (data.table) * installing *source* package ‘statmod’ ... ** package ‘statmod’ 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 Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c expectedDeviance.c -o expectedDeviance.o gfortran -fpic -g -O2 -c gaussq2.f -o gaussq2.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -shared -L/usr/local/lib -o statmod.so expectedDeviance.o gaussq2.o init.o -lgfortran -lm -lquadmath installing to /home/omnipath/local/R/4.4-3.19/00LOCK-statmod/00new/statmod/libs ** 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 ** 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 (statmod) * installing *source* package ‘sets’ ... ** package ‘sets’ 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-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c closure.c -o closure.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -shared -L/usr/local/lib -o sets.so closure.o init.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-sets/00new/sets/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 (sets) * installing *source* package ‘slam’ ... ** package ‘slam’ 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-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c apply.c -o apply.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dll.c -o dll.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c grouped.c -o grouped.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sparse.c -o sparse.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c util.c -o util.o gcc -shared -L/usr/local/lib -o slam.so apply.o dll.o grouped.o sparse.o util.o -L/opt/R-devel/lib/R/lib -lRblas -lgfortran -lm -lquadmath installing to /home/omnipath/local/R/4.4-3.19/00LOCK-slam/00new/slam/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 (slam) * installing *source* package ‘caTools’ ... ** package ‘caTools’ 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’ g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Gif2R.cpp -o Gif2R.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c GifTools.cpp -o GifTools.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c caTools_init.c -o caTools_init.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c runfunc.c -o runfunc.o g++ -std=gnu++17 -shared -L/usr/local/lib -o caTools.so Gif2R.o GifTools.o caTools_init.o runfunc.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-caTools/00new/caTools/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 (caTools) * installing *source* package ‘gtools’ ... ** package ‘gtools’ 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-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c roman2int.c -o roman2int.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c setTCPNoDelay.c -o setTCPNoDelay.o gcc -shared -L/usr/local/lib -o gtools.so init.o roman2int.o setTCPNoDelay.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-gtools/00new/gtools/libs ** 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 ** 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 (gtools) * installing *source* package ‘zlibbioc’ ... ** using staged installation configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ mkdir -p "/home/omnipath/local/R/4.4-3.19/00LOCK-zlibbioc/00new/zlibbioc/include" gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c R_init_zlibbioc.c -o R_init_zlibbioc.o gcc -shared -L/usr/local/lib -o zlibbioc.so R_init_zlibbioc.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-zlibbioc/00new/zlibbioc/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 (zlibbioc) * installing *source* package ‘GenomeInfoDbData’ ... ** using staged installation ** data ** inst ** 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 (GenomeInfoDbData) * installing *source* package ‘png’ ... ** package ‘png’ 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-devel/lib/R/include" -DNDEBUG -I/usr/local/include `libpng-config --cflags` -fpic -g -O2 -c dummy.c -o dummy.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include `libpng-config --cflags` -fpic -g -O2 -c read.c -o read.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include `libpng-config --cflags` -fpic -g -O2 -c write.c -o write.o gcc -shared -L/usr/local/lib -o png.so dummy.o read.o write.o -lpng16 -lm -lz -lm installing to /home/omnipath/local/R/4.4-3.19/00LOCK-png/00new/png/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 (png) * 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-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c AEbufs.c -o AEbufs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c DataFrame_class.c -o DataFrame_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Hits_class.c -o Hits_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c LLint_class.c -o LLint_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c List_class.c -o List_class.o gcc -I"/opt/R-devel/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-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rle_class.c -o Rle_class.o Rle_class.c: In function ‘_subset_Rle_by_ranges’: Rle_class.c:1136:17: warning: format not a string literal and no format arguments [-Wformat-security] 1136 | error(errmsg); | ^~~~~ Rle_class.c: In function ‘_subset_Rle_by_positions’: Rle_class.c:1161:17: warning: format not a string literal and no format arguments [-Wformat-security] 1161 | error(errmsg); | ^~~~~ Rle_class.c: In function ‘Rle_extract_range’: Rle_class.c:1190:17: warning: format not a string literal and no format arguments [-Wformat-security] 1190 | error(errmsg); | ^~~~~ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rle_utils.c -o Rle_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c SEXP_utils.c -o SEXP_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c SimpleList_class.c -o SimpleList_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c anyMissing.c -o anyMissing.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c character_utils.c -o character_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c eval_utils.c -o eval_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c hash_utils.c -o hash_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c integer_utils.c -o integer_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c logical_utils.c -o logical_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c map_ranges_to_runs.c -o map_ranges_to_runs.o map_ranges_to_runs.c: In function ‘map_ranges’: map_ranges_to_runs.c:682:17: warning: format not a string literal and no format arguments [-Wformat-security] 682 | error(errmsg); | ^~~~~ map_ranges_to_runs.c: In function ‘map_positions’: map_ranges_to_runs.c:709:17: warning: format not a string literal and no format arguments [-Wformat-security] 709 | error(errmsg); | ^~~~~ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c raw_utils.c -o raw_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c safe_arithm.c -o safe_arithm.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sort_utils.c -o sort_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c subsetting_utils.c -o subsetting_utils.o gcc -I"/opt/R-devel/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 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (S4Vectors) * installing *source* package ‘broom’ ... ** package ‘broom’ 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 (broom) * installing *source* package ‘bcellViper’ ... ** using staged installation ** data ** inst ** 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 (bcellViper) * installing *source* package ‘CARNIVAL’ ... ** 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 (CARNIVAL) * installing *source* package ‘munsell’ ... ** package ‘munsell’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (munsell) * installing *source* package ‘promises’ ... ** package ‘promises’ 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-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/later/include' -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-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c promise_task.cpp -o promise_task.o g++ -std=gnu++17 -shared -L/usr/local/lib -o promises.so RcppExports.o promise_task.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-promises/00new/promises/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 (promises) * installing *source* package ‘lambda.r’ ... ** package ‘lambda.r’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (lambda.r) * 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-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c normexp.c -o normexp.o gcc -I"/opt/R-devel/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 ‘IRanges’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c CompressedList_class.c -o CompressedList_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c Grouping_class.c -o Grouping_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c IPosRanges_comparison.c -o IPosRanges_comparison.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c IRanges_class.c -o IRanges_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c IRanges_constructor.c -o IRanges_constructor.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c NCList.c -o NCList.o gcc -I"/opt/R-devel/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_IRanges.c -o R_init_IRanges.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c Ranges_class.c -o Ranges_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c RleViews_utils.c -o RleViews_utils.o gcc -I"/opt/R-devel/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-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c coverage_methods.c -o coverage_methods.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c extractListFragments.c -o extractListFragments.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c inter_range_methods.c -o inter_range_methods.o gcc -shared -L/usr/local/lib -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-IRanges/00new/IRanges/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘startsWith’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘endsWith’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (IRanges) * installing *source* package ‘visNetwork’ ... ** package ‘visNetwork’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (visNetwork) * installing *source* package ‘relations’ ... ** package ‘relations’ 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 ** 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 (relations) * installing *source* package ‘gplots’ ... ** package ‘gplots’ 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 ** 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 (gplots) * installing *source* package ‘decoupleR’ ... ** 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 (decoupleR) * installing *source* package ‘httpuv’ ... ** package ‘httpuv’ successfully unpacked and MD5 sums checked ** using staged installation ** Using bundled copy of libuv ** PKG_CFLAGS=-Ilibuv/include ** PKG_LIBS=./libuv/.libs/libuv.a ** 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-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c callback.cpp -o callback.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c callbackqueue.cpp -o callbackqueue.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c filedatasource-unix.cpp -o filedatasource-unix.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c filedatasource-win.cpp -o filedatasource-win.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c fs.cpp -o fs.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c gzipdatasource.cpp -o gzipdatasource.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c http.cpp -o http.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c httprequest.cpp -o httprequest.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c httpresponse.cpp -o httpresponse.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c httpuv.cpp -o httpuv.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c md5.c -o md5.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c mime.cpp -o mime.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c socket.cpp -o socket.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c staticpath.cpp -o staticpath.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c thread.cpp -o thread.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c timegm.cpp -o timegm.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c utils.cpp -o utils.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c uvutil.cpp -o uvutil.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c webapplication.cpp -o webapplication.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c websockets-base.cpp -o websockets-base.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c websockets-hixie76.cpp -o websockets-hixie76.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c websockets-hybi03.cpp -o websockets-hybi03.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c websockets-ietf.cpp -o websockets-ietf.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c websockets.cpp -o websockets.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c winutils.cpp -o winutils.o cp -p -f libuv/m4/lt_obsolete.m4 libuv/m4/lt~obsolete.m4 cd libuv; \ if ! command -v automake >/dev/null 2>&1 ; then \ echo "automake not found. Touching files so configure will not try to run automake."; \ touch aclocal.m4; \ touch -r aclocal.m4 configure Makefile.in; \ else \ echo "automake found. Running autoupdate and autogen.sh."; \ autoupdate; \ sh autogen.sh; \ fi; \ chmod +x configure; \ CC="gcc" CFLAGS="-g -O2 -fpic -fvisibility=hidden -DNDEBUG" CPPFLAGS="-I/usr/local/include" AR="ar" RANLIB="ranlib" LDFLAGS="-L/usr/local/lib" ./configure "--quiet" automake found. Running autoupdate and autogen.sh. + libtoolize --copy + aclocal -I m4 + autoconf configure.ac:46: warning: $as_echo is obsolete; use AS_ECHO(["message"]) instead lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... m4/ax_pthread.m4:88: AX_PTHREAD is expanded from... configure.ac:46: the top level + automake --add-missing --copy make --directory=libuv \ HAVE_DTRACE=0 make[1]: Entering directory '/tmp/RtmpiqBdeV/R.INSTALL8bb5f66dfb27c/httpuv/src/libuv' 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/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 src/unix/thread.c: In function ‘uv__thread_stack_size’: src/unix/thread.c:195:24: warning: comparison of integer expressions of different signedness: ‘rlim_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 195 | if (lim.rlim_cur >= PTHREAD_STACK_MIN) | ^~ src/unix/thread.c: In function ‘uv_thread_create_ex’: src/unix/thread.c:243:20: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 243 | if (stack_size < PTHREAD_STACK_MIN) | ^ 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 ar: `u' modifier ignored since `D' is the default (see `U') make[1]: Leaving directory '/tmp/RtmpiqBdeV/R.INSTALL8bb5f66dfb27c/httpuv/src/libuv' gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c http-parser/http_parser.c -o http-parser/http_parser.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c sha1/sha1.c -o sha1/sha1.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c base64/base64.cpp -o base64/base64.o g++ -std=gnu++17 -shared -L/usr/local/lib -o httpuv.so RcppExports.o callback.o callbackqueue.o filedatasource-unix.o filedatasource-win.o fs.o gzipdatasource.o http.o httprequest.o httpresponse.o httpuv.o md5.o mime.o socket.o staticpath.o thread.o timegm.o utils.o uvutil.o webapplication.o websockets-base.o websockets-hixie76.o websockets-hybi03.o websockets-ietf.o websockets.o winutils.o ./libuv/.libs/libuv.a ./http-parser/http_parser.o ./sha1/sha1.o ./base64/base64.o -pthread installing to /home/omnipath/local/R/4.4-3.19/00LOCK-httpuv/00new/httpuv/libs ** R ** demo ** 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 (httpuv) * installing *source* package ‘futile.logger’ ... ** package ‘futile.logger’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (futile.logger) * installing *source* package ‘scales’ ... ** package ‘scales’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** 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 (scales) * installing *source* package ‘GenomeInfoDb’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GenomeInfoDb) * installing *source* package ‘XVector’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-devel/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/usr/local/include -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/opt/R-devel/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/usr/local/include -fpic -g -O2 -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o gcc -I"/opt/R-devel/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/usr/local/include -fpic -g -O2 -c RDS_random_access.c -o RDS_random_access.o RDS_random_access.c: In function ‘RDS_read_chars’: RDS_random_access.c:136:17: warning: format not a string literal and no format arguments [-Wformat-security] 136 | error(errmsg); | ^~~~~ RDS_random_access.c: In function ‘RDS_read_vector_length’: RDS_random_access.c:218:17: warning: format not a string literal and no format arguments [-Wformat-security] 218 | error(errmsg); | ^~~~~ RDS_random_access.c:226:17: warning: format not a string literal and no format arguments [-Wformat-security] 226 | error(errmsg); | ^~~~~ RDS_random_access.c: In function ‘RDS_read_string’: RDS_random_access.c:277:17: warning: format not a string literal and no format arguments [-Wformat-security] 277 | error(errmsg); | ^~~~~ RDS_random_access.c:283:25: warning: format not a string literal and no format arguments [-Wformat-security] 283 | error(errmsg); | ^~~~~ RDS_random_access.c: In function ‘RDS_read_atomic_vector’: RDS_random_access.c:360:17: warning: format not a string literal and no format arguments [-Wformat-security] 360 | error(errmsg); | ^~~~~ RDS_random_access.c: In function ‘RDS_read_attrib_separator’: RDS_random_access.c:406:17: warning: format not a string literal and no format arguments [-Wformat-security] 406 | error(errmsg); | ^~~~~ RDS_random_access.c: In function ‘RDS_read_symbol’: RDS_random_access.c:428:17: warning: format not a string literal and no format arguments [-Wformat-security] 428 | error(errmsg); | ^~~~~ RDS_random_access.c: In function ‘RDS_read_object’: RDS_random_access.c:497:17: warning: format not a string literal and no format arguments [-Wformat-security] 497 | error(errmsg); | ^~~~~ RDS_random_access.c: In function ‘RDS_read_file_header’: RDS_random_access.c:559:17: warning: format not a string literal and no format arguments [-Wformat-security] 559 | error(errmsg); | ^~~~~ RDS_random_access.c: In function ‘extract_top_level_object_type’: RDS_random_access.c:618:17: warning: format not a string literal and no format arguments [-Wformat-security] 618 | error(errmsg); | ^~~~~ RDS_random_access.c: In function ‘RDS_read_atom_at_offset’: RDS_random_access.c:675:17: warning: format not a string literal and no format arguments [-Wformat-security] 675 | error(errmsg); | ^~~~~ RDS_random_access.c:698:17: warning: format not a string literal and no format arguments [-Wformat-security] 698 | error(errmsg); | ^~~~~ RDS_random_access.c: In function ‘RDS_extract_subvector’: RDS_random_access.c:772:17: warning: format not a string literal and no format arguments [-Wformat-security] 772 | error(errmsg); | ^~~~~ gcc -I"/opt/R-devel/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/usr/local/include -fpic -g -O2 -c R_init_XVector.c -o R_init_XVector.o gcc -I"/opt/R-devel/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/usr/local/include -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/opt/R-devel/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/usr/local/include -fpic -g -O2 -c SharedDouble_class.c -o SharedDouble_class.o gcc -I"/opt/R-devel/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/usr/local/include -fpic -g -O2 -c SharedInteger_class.c -o SharedInteger_class.o gcc -I"/opt/R-devel/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/usr/local/include -fpic -g -O2 -c SharedRaw_class.c -o SharedRaw_class.o gcc -I"/opt/R-devel/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/usr/local/include -fpic -g -O2 -c SharedVector_class.c -o SharedVector_class.o gcc -I"/opt/R-devel/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/usr/local/include -fpic -g -O2 -c XDouble_class.c -o XDouble_class.o gcc -I"/opt/R-devel/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/usr/local/include -fpic -g -O2 -c XInteger_class.c -o XInteger_class.o gcc -I"/opt/R-devel/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/usr/local/include -fpic -g -O2 -c XRawList_comparison.c -o XRawList_comparison.o XRawList_comparison.c: In function ‘XRawList_rank’: XRawList_comparison.c:245:39: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘SEXP’ {aka ‘struct SEXPREC *’} [-Wformat=] 245 | error("ties_method \"%s\" is not supported", ties_method); | ~^ ~~~~~~~~~~~ | | | | char * SEXP {aka struct SEXPREC *} gcc -I"/opt/R-devel/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/usr/local/include -fpic -g -O2 -c XRaw_class.c -o XRaw_class.o gcc -I"/opt/R-devel/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/usr/local/include -fpic -g -O2 -c XVectorList_class.c -o XVectorList_class.o gcc -I"/opt/R-devel/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/usr/local/include -fpic -g -O2 -c XVector_class.c -o XVector_class.o gcc -I"/opt/R-devel/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/usr/local/include -fpic -g -O2 -c io_utils.c -o io_utils.o gcc -I"/opt/R-devel/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/usr/local/include -fpic -g -O2 -c slice_methods.c -o slice_methods.o gcc -I"/opt/R-devel/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/usr/local/include -fpic -g -O2 -c vector_copy.c -o vector_copy.o gcc -I"/opt/R-devel/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/usr/local/include -fpic -g -O2 -c view_summarization_methods.c -o view_summarization_methods.o gcc -shared -L/usr/local/lib -o XVector.so IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XDouble_class.o XInteger_class.o XRawList_comparison.o XRaw_class.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -lz installing to /home/omnipath/local/R/4.4-3.19/00LOCK-XVector/00new/XVector/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (XVector) * installing *source* package ‘marray’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (marray) * installing *source* package ‘dorothea’ ... ** 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 (dorothea) * installing *source* package ‘shiny’ ... ** package ‘shiny’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (shiny) * 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 ‘BiocParallel’ ... ** 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 for library containing shm_open... none required 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 sys/mman.h... yes configure: creating ./config.status config.status: creating src/Makevars ** 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-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/BH/include' -I'/home/omnipath/local/R/4.4-3.19/cpp11/include' -I/usr/local/include -fpic -g -O2 -c cpp11.cpp -o cpp11.o g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/BH/include' -I'/home/omnipath/local/R/4.4-3.19/cpp11/include' -I/usr/local/include -fpic -g -O2 -c ipcmutex.cpp -o ipcmutex.o g++ -std=gnu++11 -shared -L/usr/local/lib -o BiocParallel.so cpp11.o ipcmutex.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-BiocParallel/00new/BiocParallel/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 (BiocParallel) * 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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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 align_needwunsQS.c -o align_needwunsQS.o gcc -I"/opt/R-devel/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 align_pairwiseAlignment.c -o align_pairwiseAlignment.o gcc -I"/opt/R-devel/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 align_utils.c -o align_utils.o gcc -I"/opt/R-devel/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-devel/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-devel/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-devel/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 letter_frequency.c: In function ‘XString_letterFrequencyInSlidingView’: letter_frequency.c:536:31: warning: too many arguments for format [-Wformat-extra-args] 536 | error("Biostrings internal error in " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ letter_frequency.c: In function ‘XStringSet_letterFrequency’: letter_frequency.c:589:31: warning: too many arguments for format [-Wformat-extra-args] 589 | error("Biostrings internal error in " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/opt/R-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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 match_pdict_ACtree2.c: In function ‘ACtree2_summary’: match_pdict_ACtree2.c:732:45: warning: unknown conversion type character ‘)’ in format [-Wformat=] 732 | Rprintf("| - %u nodes (%.2f%) with %d links\n", | ^ gcc -I"/opt/R-devel/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-devel/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-devel/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 match_reporting.c: In function ‘_new_MatchBuf’: match_reporting.c:49:23: warning: too many arguments for format [-Wformat-extra-args] 49 | error("Biostrings internal error in _new_MatchBuf(): ", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/opt/R-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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 strutils.c: In function ‘MP_longestConsecutive’: strutils.c:50:72: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 50 | error("'letter' must contain exactly one character but contains %d.", | ~^ | | | int | %ld 51 | strlen(pc)); | ~~~~~~~~~~ | | | size_t {aka long unsigned int} gcc -I"/opt/R-devel/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-devel/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-devel/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-devel/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 align_needwunsQS.o align_pairwiseAlignment.o align_utils.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 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 ** 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 (Biostrings) * installing *source* package ‘DT’ ... ** package ‘DT’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DT) * installing *source* package ‘cowplot’ ... ** package ‘cowplot’ 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 (cowplot) * 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) * installing *source* package ‘shinydashboard’ ... ** package ‘shinydashboard’ 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 (shinydashboard) * installing *source* package ‘shinyjs’ ... ** package ‘shinyjs’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (shinyjs) * installing *source* package ‘AnnotationDbi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’ Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’ Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’ Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’ Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’ ** 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 (AnnotationDbi) * 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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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 ‘annotate’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (annotate) * installing *source* package ‘piano’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (piano) * installing *source* package ‘GSEABase’ ... ** 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 (GSEABase) The downloaded source packages are in ‘/tmp/Rtmp46swm2/downloaded_packages’ [ Finished: 2024-03-20 23:12:27 CET ]