[ Started: 2024-03-26 12:25:11 CET ] [ CARNIVAL v2.7.2 for BioC-3.19 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ] [1] "Libraries: " "/home/omnipath/local/R/4.4-3.19" [3] "/home/omnipath/local/R/4.4" "/opt/R-devel/lib/R/library" trying URL 'https://cran.uni-muenster.de/src/contrib/callr_3.7.6.tar.gz' Content type 'application/x-gzip' length 104358 bytes (101 KB) ================================================== downloaded 101 KB trying URL 'https://cran.uni-muenster.de/src/contrib/htmltools_0.5.8.tar.gz' Content type 'application/x-gzip' length 134961 bytes (131 KB) ================================================== downloaded 131 KB trying URL 'https://cran.uni-muenster.de/src/contrib/xfun_0.43.tar.gz' Content type 'application/x-gzip' length 144495 bytes (141 KB) ================================================== downloaded 141 KB * installing *source* package ‘callr’ ... ** package ‘callr’ 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 (callr) * installing *source* package ‘htmltools’ ... ** package ‘htmltools’ 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 template.c -o template.o gcc -shared -L/usr/local/lib -o htmltools.so init.o template.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-htmltools/00new/htmltools/libs ** 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 ** 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 (htmltools) * installing *source* package ‘xfun’ ... ** package ‘xfun’ 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 base64.c -o base64.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 xfun.so base64.o init.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-xfun/00new/xfun/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 (xfun) The downloaded source packages are in ‘/tmp/RtmpyAgOf6/downloaded_packages’ Bioconductor version 3.19 (BiocManager 1.30.22), R Under development (unstable) (2024-03-23 r86179) Old packages: 'edgeR', 'httpuv', 'shiny', 'wppi' trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/edgeR_4.1.19.tar.gz' Content type 'application/x-gzip' length 3571884 bytes (3.4 MB) ================================================== downloaded 3.4 MB trying URL 'https://cloud.r-project.org/src/contrib/httpuv_1.6.15.tar.gz' Content type 'application/x-gzip' length 1879369 bytes (1.8 MB) ================================================== downloaded 1.8 MB trying URL 'https://cloud.r-project.org/src/contrib/shiny_1.8.1.tar.gz' Content type 'application/x-gzip' length 3049469 bytes (2.9 MB) ================================================== downloaded 2.9 MB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/wppi_1.11.0.tar.gz' Content type 'application/x-gzip' length 662120 bytes (646 KB) ================================================== downloaded 646 KB * installing *source* package ‘edgeR’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_add_prior_count.cpp -o R_add_prior_count.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_ave_log_cpm.cpp -o R_ave_log_cpm.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_calculate_cpm.cpp -o R_calculate_cpm.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_check_poisson_bound.cpp -o R_check_poisson_bound.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_compute_apl.cpp -o R_compute_apl.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_compute_nbdev.cpp -o R_compute_nbdev.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_fit_levenberg.cpp -o R_fit_levenberg.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_fit_one_group.cpp -o R_fit_one_group.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_get_one_way_fitted.cpp -o R_get_one_way_fitted.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_initialize_levenberg.cpp -o R_initialize_levenberg.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_loess_by_col.cpp -o R_loess_by_col.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_ql_glm.c -o R_ql_glm.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c R_simple_good_turing.cpp -o R_simple_good_turing.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c add_prior.cpp -o add_prior.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c adj_coxreid.cpp -o adj_coxreid.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c fmm_spline.c -o fmm_spline.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c glm_levenberg.cpp -o glm_levenberg.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c glm_one_group.cpp -o glm_one_group.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c init.cpp -o init.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c interpolator.cpp -o interpolator.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c nbdev.c -o nbdev.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c objects.cpp -o objects.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ql_glm.c -o ql_glm.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ql_weights.c -o ql_weights.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c qr_hat.c -o qr_hat.o g++ -std=gnu++17 -shared -L/usr/local/lib -o edgeR.so R_add_prior_count.o R_ave_log_cpm.o R_calculate_cpm.o R_check_poisson_bound.o R_compute_apl.o R_compute_nbdev.o R_exact_test_by_deviance.o R_fit_levenberg.o R_fit_one_group.o R_get_one_way_fitted.o R_initialize_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_process_hairpin_reads.o R_ql_glm.o R_simple_good_turing.o add_prior.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o nbdev.o objects.o ql_glm.o ql_weights.o qr_hat.o -llapack -L/opt/R-devel/lib/R/lib -lRblas -lgfortran -lm -lquadmath installing to /home/omnipath/local/R/4.4-3.19/00LOCK-edgeR/00new/edgeR/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (edgeR) * installing *source* package ‘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/Rtmp35WgmG/R.INSTALL2dcf752ef8dbbe/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/Rtmp35WgmG/R.INSTALL2dcf752ef8dbbe/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 ‘wppi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading [2024-03-26 12:28:37] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-03-26 12:28:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-26 12:28:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-26 12:28:37] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-26 12:28:37] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-26 12:28:37] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-26 12:28:37] [TRACE] [OmnipathR] Contains 1 files. [2024-03-26 12:28:37] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-26 12:28:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-26 12:28:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-26 12:28:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-26 12:28:37] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-26 12:28:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-26 12:28:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-26 12:28:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-26 12:28:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-26 12:28:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-26 12:28:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-26 12:28:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-26 12:28:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-26 12:28:38] [TRACE] [OmnipathR] Cache locked: FALSE Note: wrong number of arguments to '/' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2024-03-26 12:28:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-26 12:28:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-26 12:28:40] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-26 12:28:40] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-26 12:28:40] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-26 12:28:40] [TRACE] [OmnipathR] Contains 1 files. [2024-03-26 12:28:40] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-26 12:28:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-26 12:28:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-26 12:28:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-26 12:28:40] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-26 12:28:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-26 12:28:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-26 12:28:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-26 12:28:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-26 12:28:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-26 12:28:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-26 12:28:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-26 12:28:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-26 12:28:40] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-03-26 12:28:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-26 12:28:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-26 12:28:41] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-26 12:28:41] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-26 12:28:41] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-26 12:28:41] [TRACE] [OmnipathR] Contains 1 files. [2024-03-26 12:28:41] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-26 12:28:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-26 12:28:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-26 12:28:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-26 12:28:41] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-26 12:28:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-26 12:28:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-26 12:28:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-26 12:28:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-26 12:28:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-26 12:28:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-26 12:28:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-26 12:28:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-26 12:28:41] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (wppi) * 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) The downloaded source packages are in ‘/tmp/RtmpyAgOf6/downloaded_packages’ Bioconductor version 3.19 (BiocManager 1.30.22), R Under development (unstable) (2024-03-23 r86179) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' Skipping 1 packages ahead of CRAN: BiocStyle [ Finished: 2024-03-26 12:28:59 CET ]