[ Started: 2023-01-13 01:01:18 CET ] [ CARNIVAL v2.7.2 for BioC-3.16 from https://github.com/saezlab/CARNIVAL@master ] [1] "Libraries: " "/home/omnipath/local/R/4.2-3.16" [3] "/home/omnipath/local/R/4.2" "/usr/lib/R/library" 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 Patched (2022-11-10 r83330) Old packages: 'curl', 'httpuv', 'ragg' trying URL 'https://cloud.r-project.org/src/contrib/curl_5.0.0.tar.gz' Content type 'application/x-gzip' length 682047 bytes (666 KB) ================================================== downloaded 666 KB trying URL 'https://cloud.r-project.org/src/contrib/httpuv_1.6.8.tar.gz' Content type 'application/x-gzip' length 1875086 bytes (1.8 MB) ================================================== downloaded 1.8 MB trying URL 'https://cloud.r-project.org/src/contrib/ragg_1.2.5.tar.gz' Content type 'application/x-gzip' length 427859 bytes (417 KB) ================================================== downloaded 417 KB * installing *source* package ‘curl’ ... ** package ‘curl’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/usr/include/x86_64-linux-gnu Using PKG_LIBS=-lcurl ** libs rm -f curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c callbacks.c -o callbacks.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c curl.c -o curl.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c download.c -o download.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c escape.c -o escape.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fetch.c -o fetch.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c form.c -o form.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c getdate.c -o getdate.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c handle.c -o handle.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ieproxy.c -o ieproxy.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c interrupt.c -o interrupt.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c multi.c -o multi.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nslookup.c -o nslookup.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c options.c -o options.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c reflist.c -o reflist.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c split.c -o split.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ssl.c -o ssl.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c typechecking.c -o typechecking.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c version.c -o version.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c winidn.c -o winidn.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c writer.c -o writer.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o -lcurl -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-curl/00new/curl/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (curl) * installing *source* package ‘httpuv’ ... ** package ‘httpuv’ successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports-legacy.cpp -o RcppExports-legacy.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c callback.cpp -o callback.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c callbackqueue.cpp -o callbackqueue.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c filedatasource-unix.cpp -o filedatasource-unix.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c filedatasource-win.cpp -o filedatasource-win.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fs.cpp -o fs.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c gzipdatasource.cpp -o gzipdatasource.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c http.cpp -o http.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c httprequest.cpp -o httprequest.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c httpresponse.cpp -o httpresponse.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c httpuv.cpp -o httpuv.o gcc -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c md5.c -o md5.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mime.cpp -o mime.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c socket.cpp -o socket.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c staticpath.cpp -o staticpath.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c thread.cpp -o thread.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c timegm.cpp -o timegm.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.cpp -o utils.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c uvutil.cpp -o uvutil.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c webapplication.cpp -o webapplication.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c websockets-base.cpp -o websockets-base.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c websockets-hixie76.cpp -o websockets-hixie76.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c websockets-hybi03.cpp -o websockets-hybi03.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c websockets-ietf.cpp -o websockets-ietf.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c websockets.cpp -o websockets.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -fvisibility=hidden" AR="ar" RANLIB="ranlib" LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro" ./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/Rtmptn5cKP/R.INSTALL3df306266066ab/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/Rtmptn5cKP/R.INSTALL3df306266066ab/httpuv/src/libuv' gcc -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c http-parser/http_parser.c -o http-parser/http_parser.o gcc -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sha1/sha1.c -o sha1/sha1.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/later/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c base64/base64.cpp -o base64/base64.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o httpuv.so RcppExports-legacy.o 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 -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-httpuv/00new/httpuv/libs ** R ** demo ** 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 ‘ragg’ ... ** package ‘ragg’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu Using PKG_LIBS=-L/usr/local/lib -lfreetype -lpng16 -lz -ltiff -ljpeg -ljpeg ** libs g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/systemfonts/include' -I'/home/omnipath/local/R/4.2-3.16/textshaping/include' -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c capture_dev.cpp -o capture_dev.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/systemfonts/include' -I'/home/omnipath/local/R/4.2-3.16/textshaping/include' -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.cpp -o init.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/systemfonts/include' -I'/home/omnipath/local/R/4.2-3.16/textshaping/include' -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c jpeg_dev.cpp -o jpeg_dev.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/systemfonts/include' -I'/home/omnipath/local/R/4.2-3.16/textshaping/include' -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c png_dev.cpp -o png_dev.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/systemfonts/include' -I'/home/omnipath/local/R/4.2-3.16/textshaping/include' -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ppm_dev.cpp -o ppm_dev.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/systemfonts/include' -I'/home/omnipath/local/R/4.2-3.16/textshaping/include' -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tiff_dev.cpp -o tiff_dev.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/systemfonts/include' -I'/home/omnipath/local/R/4.2-3.16/textshaping/include' -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c agg/src/agg_curves.cpp -o agg/src/agg_curves.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/systemfonts/include' -I'/home/omnipath/local/R/4.2-3.16/textshaping/include' -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c agg/src/agg_font_freetype.cpp -o agg/src/agg_font_freetype.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/systemfonts/include' -I'/home/omnipath/local/R/4.2-3.16/textshaping/include' -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c agg/src/agg_image_filters.cpp -o agg/src/agg_image_filters.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/systemfonts/include' -I'/home/omnipath/local/R/4.2-3.16/textshaping/include' -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c agg/src/agg_trans_affine.cpp -o agg/src/agg_trans_affine.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/systemfonts/include' -I'/home/omnipath/local/R/4.2-3.16/textshaping/include' -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c agg/src/agg_vcgen_dash.cpp -o agg/src/agg_vcgen_dash.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/systemfonts/include' -I'/home/omnipath/local/R/4.2-3.16/textshaping/include' -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c agg/src/agg_vcgen_stroke.cpp -o agg/src/agg_vcgen_stroke.o ar rcs agg/libstatagg.a agg/src/agg_curves.o agg/src/agg_font_freetype.o agg/src/agg_image_filters.o agg/src/agg_trans_affine.o agg/src/agg_vcgen_dash.o agg/src/agg_vcgen_stroke.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o ragg.so capture_dev.o init.o jpeg_dev.o png_dev.o ppm_dev.o tiff_dev.o -Lagg -lstatagg -L/usr/local/lib -lfreetype -lpng16 -lz -ltiff -ljpeg -ljpeg -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-ragg/00new/ragg/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 (ragg) The downloaded source packages are in ‘/tmp/Rtmp9747xk/downloaded_packages’ Skipping 1 packages ahead of CRAN: curl [ Finished: 2023-01-13 01:04:24 CET ]