[ Started: 2025-07-22 18:58:36 CEST ] [ CARNIVAL v2.18.0 for BioC-3.21 from https://git.bioconductor.org/packages/CARNIVAL@RELEASE_3_21 (f97de91 2025-04-15 11:58:07) ] [1] "Libraries: " "/home/omnipath/local/R/4.5-3.21" [3] "/home/omnipath/local/R/4.5" "/usr/lib/R/library" trying URL 'https://cran.uni-muenster.de/src/contrib/httr2_1.2.1.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/spatstat.explore_3.5-2.tar.gz' * installing *source* package ‘httr2’ ... ** this is package ‘httr2’ version ‘1.2.1’ ** 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 ‘spatstat.explore’ ... ** this is package ‘spatstat.explore’ version ‘3.5-2’ ** package ‘spatstat.explore’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c Kborder.c -o Kborder.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c Knone.c -o Knone.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c Krect.c -o Krect.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c call3d.c -o call3d.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c corrections.c -o corrections.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c denspt.c -o denspt.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c densptcross.c -o densptcross.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c digber.c -o digber.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c f3.c -o f3.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c g3.c -o g3.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c idw.c -o idw.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c init.c -o init.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c k3.c -o k3.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c localpcf.c -o localpcf.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c loccum.c -o loccum.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c pcf3.c -o pcf3.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c raster.c -o raster.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c scan.c -o scan.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c segdens.c -o segdens.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c sphefrac.c -o sphefrac.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c sphevol.c -o sphevol.o gcc -std=gnu2x -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o spatstat.explore.so Kborder.o Knone.o Krect.o call3d.o corrections.o denspt.o densptcross.o digber.o f3.o g3.o idw.o init.o k3.o localpcf.o loccum.o pcf3.o raster.o scan.o segdens.o sphefrac.o sphevol.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.5-3.21/00LOCK-spatstat.explore/00new/spatstat.explore/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (spatstat.explore) The downloaded source packages are in ‘/tmp/RtmpxbB65K/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 3.21 (BiocManager 1.30.26), R 4.5.1 (2025-06-13) Old packages: 'enrichplot', 'ggtree', 'wppi' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/enrichplot_1.28.4.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/ggtree_3.16.3.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.16.0.tar.gz' * installing *source* package ‘ggtree’ ... ** this is package ‘ggtree’ version ‘3.16.3’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/ape/libs/ape.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘ggtree’ * removing ‘/home/omnipath/local/R/4.5-3.21/ggtree’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/ggtree’ * installing *source* package ‘wppi’ ... ** this is package ‘wppi’ version ‘1.16.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/igraph/libs/igraph.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘wppi’ * removing ‘/home/omnipath/local/R/4.5-3.21/wppi’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/wppi’ * installing *source* package ‘enrichplot’ ... ** this is package ‘enrichplot’ version ‘1.28.4’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/igraph/libs/igraph.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘enrichplot’ * removing ‘/home/omnipath/local/R/4.5-3.21/enrichplot’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/enrichplot’ The downloaded source packages are in ‘/tmp/RtmpxbB65K/downloaded_packages’ Warning messages: 1: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘ggtree’ had non-zero exit status 2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘wppi’ had non-zero exit status 3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘enrichplot’ had non-zero exit status 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.21 (BiocManager 1.30.26), R 4.5.1 (2025-06-13) Old packages: 'enrichplot', 'ggtree', 'wppi' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/enrichplot_1.28.4.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/ggtree_3.16.3.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.16.0.tar.gz' * installing *source* package ‘ggtree’ ... ** this is package ‘ggtree’ version ‘3.16.3’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/ape/libs/ape.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘ggtree’ * removing ‘/home/omnipath/local/R/4.5-3.21/ggtree’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/ggtree’ * installing *source* package ‘wppi’ ... ** this is package ‘wppi’ version ‘1.16.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/igraph/libs/igraph.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘wppi’ * removing ‘/home/omnipath/local/R/4.5-3.21/wppi’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/wppi’ * installing *source* package ‘enrichplot’ ... ** this is package ‘enrichplot’ version ‘1.28.4’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/igraph/libs/igraph.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘enrichplot’ * removing ‘/home/omnipath/local/R/4.5-3.21/enrichplot’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/enrichplot’ The downloaded source packages are in ‘/tmp/RtmpxbB65K/downloaded_packages’ Warning messages: 1: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' 2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘ggtree’ had non-zero exit status 3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘wppi’ had non-zero exit status 4: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘enrichplot’ had non-zero exit status [ Finished: 2025-07-22 18:59:29 CEST ]