[ Started: 2023-05-09 01:52:12 CEST ] [ CARNIVAL v2.7.2 for BioC-3.17 from https://github.com/saezlab/CARNIVAL@master ] [1] "Libraries: " "/home/omnipath/local/R/4.3-3.17" [3] "/home/omnipath/local/R/4.3" "/opt/R-devel/lib/R/library" trying URL 'https://cran.uni-muenster.de/src/contrib/httpuv_1.6.10.tar.gz' Content type 'application/x-gzip' length 1875497 bytes (1.8 MB) ================================================== downloaded 1.8 MB * installing *source* package ‘httpuv’ ... ** package ‘httpuv’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c RcppExports-legacy.cpp -o RcppExports-legacy.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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" 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/RtmpO6B6yC/R.INSTALL2931b1142efd29/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/RtmpO6B6yC/R.INSTALL2931b1142efd29/httpuv/src/libuv' gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/later/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-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 installing to /home/omnipath/local/R/4.3-3.17/00LOCK-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) The downloaded source packages are in ‘/tmp/RtmpJlo6zO/downloaded_packages’ Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21) Old packages: 'httr', 'httr2', 'limma' trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.6.tar.gz' Content type 'application/x-gzip' length 157621 bytes (153 KB) ================================================== downloaded 153 KB trying URL 'https://cloud.r-project.org/src/contrib/httr2_0.2.3.tar.gz' Content type 'application/x-gzip' length 123376 bytes (120 KB) ================================================== downloaded 120 KB trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/limma_3.56.1.tar.gz' Content type 'application/x-gzip' length 1514950 bytes (1.4 MB) ================================================== downloaded 1.4 MB * installing *source* package ‘httr’ ... ** package ‘httr’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (httr) * installing *source* package ‘httr2’ ... ** package ‘httr2’ 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 (httr2) * installing *source* package ‘limma’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ 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/4.3-3.17/00LOCK-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) The downloaded source packages are in ‘/tmp/RtmpJlo6zO/downloaded_packages’ Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21) 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: httr [ Finished: 2023-05-09 01:54:26 CEST ]