[ Started: 2025-04-16 22:52:38 CEST ] [ CARNIVAL v2.16.0 for BioC-3.20 from https://git.bioconductor.org/packages/CARNIVAL@RELEASE_3_20 (a7305b3 2024-10-29 10:46:30) ] [1] "Libraries: " "/home/omnipath/local/R/4.4-3.20" [3] "/home/omnipath/local/R/4.4" "/usr/lib/R/library" Bioconductor version '3.20' is out-of-date; the current release version '3.21' is available with R version '4.5'; see https://bioconductor.org/install 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14) Old packages: 'globals', 'httpuv' trying URL 'https://cloud.r-project.org/src/contrib/globals_0.17.0.tar.gz' Content type 'application/x-gzip' length 45144 bytes (44 KB) ================================================== downloaded 44 KB trying URL 'https://cloud.r-project.org/src/contrib/httpuv_1.6.16.tar.gz' Content type 'application/x-gzip' length 1890033 bytes (1.8 MB) ================================================== downloaded 1.8 MB * installing *source* package ‘globals’ ... ** package ‘globals’ 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 (globals) * 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.b ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c callback.cpp -o callback.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c callbackqueue.cpp -o callbackqueue.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c filedatasource-unix.cpp -o filedatasource-unix.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c filedatasource-win.cpp -o filedatasource-win.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c fs.cpp -o fs.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c gzipdatasource.cpp -o gzipdatasource.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c http.cpp -o http.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c httprequest.cpp -o httprequest.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c httpresponse.cpp -o httpresponse.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c httpuv.cpp -o httpuv.o gcc -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c md5.c -o md5.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c mime.cpp -o mime.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c socket.cpp -o socket.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c staticpath.cpp -o staticpath.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c thread.cpp -o thread.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c timegm.cpp -o timegm.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c utils.cpp -o utils.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c uvutil.cpp -o uvutil.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c webapplication.cpp -o webapplication.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c websockets-base.cpp -o websockets-base.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c websockets-hixie76.cpp -o websockets-hixie76.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c websockets-hybi03.cpp -o websockets-hybi03.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c websockets-ietf.cpp -o websockets-ietf.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c websockets.cpp -o websockets.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -DNDEBUG" CPPFLAGS="" AR="ar" RANLIB="ranlib" LDFLAGS="-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro" ./configure "--quiet" automake found. Running autoupdate and autogen.sh. + libtoolize --copy libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltversion.m4' + 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/RtmpXcVHwl/R.INSTALL23e0b85ba75d40/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 In file included from src/uv-common.h:42, from src/uv-common.c:23: src/uv-common.c: In function 'uv_walk': src/queue.h:68:19: warning: storing the address of local variable 'queue' in '((void * (**)[2])MEM[(void *[2] * *)loop_13(D) + 16B])[1]' [-Wdangling-pointer=] 68 | QUEUE_PREV(q) = (n); \ | ^ src/queue.h:78:7: note: in expansion of macro 'QUEUE_SPLIT' 78 | QUEUE_SPLIT(h, q, n); \ | ^~~~~~~~~~~ src/uv-common.c:505:3: note: in expansion of macro 'QUEUE_MOVE' 505 | QUEUE_MOVE(&loop->handle_queue, &queue); | ^~~~~~~~~~ src/uv-common.c:501:9: note: 'queue' declared here 501 | QUEUE queue; | ^~~~~ src/uv-common.c:500:25: note: 'loop' declared here 500 | void uv_walk(uv_loop_t* loop, uv_walk_cb walk_cb, void* arg) { | ~~~~~~~~~~~^~~~ CC src/libuv_la-version.lo CC src/unix/libuv_la-async.lo In file included from ./src/uv-common.h:42, from src/unix/internal.h:25, from src/unix/async.c:26: src/unix/async.c: In function 'uv__async_io': ./src/queue.h:68:19: warning: storing the address of local variable 'queue' in '((void * (**)[2])MEM[(void *[2] * *)loop_22(D) + 432B])[1]' [-Wdangling-pointer=] 68 | QUEUE_PREV(q) = (n); \ | ^ ./src/queue.h:78:7: note: in expansion of macro 'QUEUE_SPLIT' 78 | QUEUE_SPLIT(h, q, n); \ | ^~~~~~~~~~~ src/unix/async.c:149:3: note: in expansion of macro 'QUEUE_MOVE' 149 | QUEUE_MOVE(&loop->async_handles, &queue); | ^~~~~~~~~~ src/unix/async.c:125:9: note: 'queue' declared here 125 | QUEUE queue; | ^~~~~ src/unix/async.c:122:37: note: 'loop' declared here 122 | static void uv__async_io(uv_loop_t* loop, uv__io_t* w, unsigned int events) { | ~~~~~~~~~~~^~~~ 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 In file included from ./src/uv-common.h:42, from src/unix/internal.h:25, from src/unix/loop-watcher.c:23: src/unix/loop-watcher.c: In function 'uv__run_prepare': ./src/queue.h:68:19: warning: storing the address of local variable 'queue' in '((void * (**)[2])MEM[(void *[2] * *)loop_12(D) + 384B])[1]' [-Wdangling-pointer=] 68 | QUEUE_PREV(q) = (n); \ | ^ ./src/queue.h:78:7: note: in expansion of macro 'QUEUE_SPLIT' 78 | QUEUE_SPLIT(h, q, n); \ | ^~~~~~~~~~~ src/unix/loop-watcher.c:52:5: note: in expansion of macro 'QUEUE_MOVE' 52 | QUEUE_MOVE(&loop->name##_handles, &queue); \ | ^~~~~~~~~~ src/unix/loop-watcher.c:66:1: note: in expansion of macro 'UV_LOOP_WATCHER_DEFINE' 66 | UV_LOOP_WATCHER_DEFINE(prepare, PREPARE) | ^~~~~~~~~~~~~~~~~~~~~~ src/unix/loop-watcher.c:50:11: note: 'queue' declared here 50 | QUEUE queue; \ | ^~~~~ src/unix/loop-watcher.c:66:1: note: in expansion of macro 'UV_LOOP_WATCHER_DEFINE' 66 | UV_LOOP_WATCHER_DEFINE(prepare, PREPARE) | ^~~~~~~~~~~~~~~~~~~~~~ src/unix/loop-watcher.c:48:34: note: 'loop' declared here 48 | void uv__run_##name(uv_loop_t* loop) { \ | ~~~~~~~~~~~^~~~ src/unix/loop-watcher.c:66:1: note: in expansion of macro 'UV_LOOP_WATCHER_DEFINE' 66 | UV_LOOP_WATCHER_DEFINE(prepare, PREPARE) | ^~~~~~~~~~~~~~~~~~~~~~ src/unix/loop-watcher.c: In function 'uv__run_check': ./src/queue.h:68:19: warning: storing the address of local variable 'queue' in '((void * (**)[2])MEM[(void *[2] * *)loop_12(D) + 400B])[1]' [-Wdangling-pointer=] 68 | QUEUE_PREV(q) = (n); \ | ^ ./src/queue.h:78:7: note: in expansion of macro 'QUEUE_SPLIT' 78 | QUEUE_SPLIT(h, q, n); \ | ^~~~~~~~~~~ src/unix/loop-watcher.c:52:5: note: in expansion of macro 'QUEUE_MOVE' 52 | QUEUE_MOVE(&loop->name##_handles, &queue); \ | ^~~~~~~~~~ src/unix/loop-watcher.c:67:1: note: in expansion of macro 'UV_LOOP_WATCHER_DEFINE' 67 | UV_LOOP_WATCHER_DEFINE(check, CHECK) | ^~~~~~~~~~~~~~~~~~~~~~ src/unix/loop-watcher.c:50:11: note: 'queue' declared here 50 | QUEUE queue; \ | ^~~~~ src/unix/loop-watcher.c:67:1: note: in expansion of macro 'UV_LOOP_WATCHER_DEFINE' 67 | UV_LOOP_WATCHER_DEFINE(check, CHECK) | ^~~~~~~~~~~~~~~~~~~~~~ src/unix/loop-watcher.c:48:34: note: 'loop' declared here 48 | void uv__run_##name(uv_loop_t* loop) { \ | ~~~~~~~~~~~^~~~ src/unix/loop-watcher.c:67:1: note: in expansion of macro 'UV_LOOP_WATCHER_DEFINE' 67 | UV_LOOP_WATCHER_DEFINE(check, CHECK) | ^~~~~~~~~~~~~~~~~~~~~~ src/unix/loop-watcher.c: In function 'uv__run_idle': ./src/queue.h:68:19: warning: storing the address of local variable 'queue' in '((void * (**)[2])MEM[(void *[2] * *)loop_12(D) + 416B])[1]' [-Wdangling-pointer=] 68 | QUEUE_PREV(q) = (n); \ | ^ ./src/queue.h:78:7: note: in expansion of macro 'QUEUE_SPLIT' 78 | QUEUE_SPLIT(h, q, n); \ | ^~~~~~~~~~~ src/unix/loop-watcher.c:52:5: note: in expansion of macro 'QUEUE_MOVE' 52 | QUEUE_MOVE(&loop->name##_handles, &queue); \ | ^~~~~~~~~~ src/unix/loop-watcher.c:68:1: note: in expansion of macro 'UV_LOOP_WATCHER_DEFINE' 68 | UV_LOOP_WATCHER_DEFINE(idle, IDLE) | ^~~~~~~~~~~~~~~~~~~~~~ src/unix/loop-watcher.c:50:11: note: 'queue' declared here 50 | QUEUE queue; \ | ^~~~~ src/unix/loop-watcher.c:68:1: note: in expansion of macro 'UV_LOOP_WATCHER_DEFINE' 68 | UV_LOOP_WATCHER_DEFINE(idle, IDLE) | ^~~~~~~~~~~~~~~~~~~~~~ src/unix/loop-watcher.c:48:34: note: 'loop' declared here 48 | void uv__run_##name(uv_loop_t* loop) { \ | ~~~~~~~~~~~^~~~ src/unix/loop-watcher.c:68:1: note: in expansion of macro 'UV_LOOP_WATCHER_DEFINE' 68 | UV_LOOP_WATCHER_DEFINE(idle, IDLE) | ^~~~~~~~~~~~~~~~~~~~~~ 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 In file included from ./src/uv-common.h:42, from src/unix/internal.h:25, from src/unix/stream.c:23: src/unix/stream.c: In function 'uv__write_callbacks': ./src/queue.h:68:19: warning: storing the address of local variable 'pq' in '((void * (**)[2])MEM[(void *[2] * *)stream_23(D) + 208B])[1]' [-Wdangling-pointer=] 68 | QUEUE_PREV(q) = (n); \ | ^ ./src/queue.h:78:7: note: in expansion of macro 'QUEUE_SPLIT' 78 | QUEUE_SPLIT(h, q, n); \ | ^~~~~~~~~~~ src/unix/stream.c:943:3: note: in expansion of macro 'QUEUE_MOVE' 943 | QUEUE_MOVE(&stream->write_completed_queue, &pq); | ^~~~~~~~~~ src/unix/stream.c:938:9: note: 'pq' declared here 938 | QUEUE pq; | ^~ src/unix/stream.c:935:46: note: 'stream' declared here 935 | static void uv__write_callbacks(uv_stream_t* stream) { | ~~~~~~~~~~~~~^~~~~~ 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 make[1]: Leaving directory '/tmp/RtmpXcVHwl/R.INSTALL23e0b85ba75d40/httpuv/src/libuv' gcc -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -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/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c sha1/sha1.c -o sha1/sha1.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c base64/base64.cpp -o base64/base64.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -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.b ./http-parser/http_parser.o ./sha1/sha1.o ./base64/base64.o -pthread -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.4-3.20/00LOCK-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) The downloaded source packages are in ‘/tmp/RtmpNeE1UU/downloaded_packages’ 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14) 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: 2025-04-16 22:54:09 CEST ]