[ Started: 2026-07-19 20:28:13 CEST ] [ OmnipathR v3.18.4 for BioC-3.22 from https://git.bioconductor.org/packages/OmnipathR@RELEASE_3_22 (efaae39 2026-01-20 15:40:26) ] [1] "Libraries: " "/home/omnipath/local/R/4.5-3.22" [3] "/home/omnipath/local/R/4.5" "/usr/lib/R/library" trying URL 'https://cran.uni-muenster.de/src/contrib/devtools_2.5.2.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/fs_2.1.0.tar.gz' * installing *source* package ‘fs’ ... ** this is package ‘fs’ version ‘2.1.0’ ** package ‘fs’ successfully unpacked and MD5 sums checked ** using staged installation Package libuv was not found in the pkg-config search path. Perhaps you should add the directory containing `libuv.pc' to the PKG_CONFIG_PATH environment variable Package 'libuv', required by 'virtual:world', not found Using PKG_CFLAGS= Using PKG_LIBS=-luv --------------------------- [CONFIGURE] -------------------------------- Configuration failed because libuv was not found. Try installing: * deb: libuv1-dev (Debian, Ubuntu, etc) * rpm: libuv-devel (Fedora, EPEL) * brew: libuv (OSX) Alternatively set environment variable USE_BUNDLED_LIBUV=1 to build a static version of libuv that is included with this package. -------------------------- [ERROR MESSAGE] --------------------------- :1:10: fatal error: uv.h: No such file or directory compilation terminated. -------------------------------------------------------------------- ERROR: configuration failed for package ‘fs’ * removing ‘/home/omnipath/local/R/4.5-3.22/fs’ * restoring previous ‘/home/omnipath/local/R/4.5-3.22/fs’ * installing *source* package ‘devtools’ ... ** this is package ‘devtools’ version ‘2.5.2’ ** package ‘devtools’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : namespace ‘fs’ 2.0.1 is already loaded, but >= 2.1.0 is required Calls: ... withCallingHandlers -> loadNamespace -> namespaceImport -> loadNamespace Execution halted ERROR: lazy loading failed for package ‘devtools’ * removing ‘/home/omnipath/local/R/4.5-3.22/devtools’ * restoring previous ‘/home/omnipath/local/R/4.5-3.22/devtools’ The downloaded source packages are in ‘/tmp/RtmpbaAhlH/downloaded_packages’ Warning messages: 1: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘fs’ had non-zero exit status 2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘devtools’ had non-zero exit status Bioconductor version '3.22' is out-of-date; the current release version '3.23' is available with R version '4.6'; 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 3.22 (BiocManager 1.30.27), R 4.5.1 (2025-06-13) Old packages: 'devtools', 'fs', 'sp' trying URL 'https://cloud.r-project.org/src/contrib/devtools_2.5.2.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/fs_2.1.0.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/sp_2.2-3.tar.gz' * installing *source* package ‘fs’ ... ** this is package ‘fs’ version ‘2.1.0’ ** package ‘fs’ successfully unpacked and MD5 sums checked ** using staged installation Package libuv was not found in the pkg-config search path. Perhaps you should add the directory containing `libuv.pc' to the PKG_CONFIG_PATH environment variable Package 'libuv', required by 'virtual:world', not found Using PKG_CFLAGS= Using PKG_LIBS=-luv --------------------------- [CONFIGURE] -------------------------------- Configuration failed because libuv was not found. Try installing: * deb: libuv1-dev (Debian, Ubuntu, etc) * rpm: libuv-devel (Fedora, EPEL) * brew: libuv (OSX) Alternatively set environment variable USE_BUNDLED_LIBUV=1 to build a static version of libuv that is included with this package. -------------------------- [ERROR MESSAGE] --------------------------- :1:10: fatal error: uv.h: No such file or directory compilation terminated. -------------------------------------------------------------------- ERROR: configuration failed for package ‘fs’ * removing ‘/home/omnipath/local/R/4.5-3.22/fs’ * restoring previous ‘/home/omnipath/local/R/4.5-3.22/fs’ * installing *source* package ‘sp’ ... ** this is package ‘sp’ version ‘2.2-3’ ** package ‘sp’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 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 Rcentroid.c -o Rcentroid.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 gcdist.c -o gcdist.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 pip.c -o pip.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 pip2.c -o pip2.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 sp_xports.c -o sp_xports.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 surfaceArea.c -o surfaceArea.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 zerodist.c -o zerodist.o gcc -std=gnu2x -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o sp.so Rcentroid.o gcdist.o init.o pip.o pip2.o sp_xports.o surfaceArea.o zerodist.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.5-3.22/00LOCK-sp/00new/sp/libs ** R ** data ** 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 ** 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 (sp) * installing *source* package ‘devtools’ ... ** this is package ‘devtools’ version ‘2.5.2’ ** package ‘devtools’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : namespace ‘fs’ 2.0.1 is already loaded, but >= 2.1.0 is required Calls: ... withCallingHandlers -> loadNamespace -> namespaceImport -> loadNamespace Execution halted ERROR: lazy loading failed for package ‘devtools’ * removing ‘/home/omnipath/local/R/4.5-3.22/devtools’ * restoring previous ‘/home/omnipath/local/R/4.5-3.22/devtools’ The downloaded source packages are in ‘/tmp/RtmpbaAhlH/downloaded_packages’ Warning messages: 1: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘fs’ had non-zero exit status 2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘devtools’ 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 3.22 (BiocManager 1.30.27), R 4.5.1 (2025-06-13) Old packages: 'devtools', 'fs' trying URL 'https://cloud.r-project.org/src/contrib/devtools_2.5.2.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/fs_2.1.0.tar.gz' * installing *source* package ‘fs’ ... ** this is package ‘fs’ version ‘2.1.0’ ** package ‘fs’ successfully unpacked and MD5 sums checked ** using staged installation Package libuv was not found in the pkg-config search path. Perhaps you should add the directory containing `libuv.pc' to the PKG_CONFIG_PATH environment variable Package 'libuv', required by 'virtual:world', not found Using PKG_CFLAGS= Using PKG_LIBS=-luv --------------------------- [CONFIGURE] -------------------------------- Configuration failed because libuv was not found. Try installing: * deb: libuv1-dev (Debian, Ubuntu, etc) * rpm: libuv-devel (Fedora, EPEL) * brew: libuv (OSX) Alternatively set environment variable USE_BUNDLED_LIBUV=1 to build a static version of libuv that is included with this package. -------------------------- [ERROR MESSAGE] --------------------------- :1:10: fatal error: uv.h: No such file or directory compilation terminated. -------------------------------------------------------------------- ERROR: configuration failed for package ‘fs’ * removing ‘/home/omnipath/local/R/4.5-3.22/fs’ * restoring previous ‘/home/omnipath/local/R/4.5-3.22/fs’ * installing *source* package ‘devtools’ ... ** this is package ‘devtools’ version ‘2.5.2’ ** package ‘devtools’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : namespace ‘fs’ 2.0.1 is already loaded, but >= 2.1.0 is required Calls: ... withCallingHandlers -> loadNamespace -> namespaceImport -> loadNamespace Execution halted ERROR: lazy loading failed for package ‘devtools’ * removing ‘/home/omnipath/local/R/4.5-3.22/devtools’ * restoring previous ‘/home/omnipath/local/R/4.5-3.22/devtools’ The downloaded source packages are in ‘/tmp/RtmpbaAhlH/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 ‘fs’ had non-zero exit status 3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘devtools’ had non-zero exit status fs (2.0.1 -> 2.1.0) [CRAN] Installing 1 packages: fs trying URL 'https://cran.uni-muenster.de/src/contrib/fs_2.1.0.tar.gz' Content type 'application/x-gzip' length 1471347 bytes (1.4 MB) ================================================== downloaded 1.4 MB * installing *source* package ‘fs’ ... ** this is package ‘fs’ version ‘2.1.0’ ** package ‘fs’ successfully unpacked and MD5 sums checked ** using staged installation Package libuv was not found in the pkg-config search path. Perhaps you should add the directory containing `libuv.pc' to the PKG_CONFIG_PATH environment variable Package 'libuv', required by 'virtual:world', not found Using PKG_CFLAGS= Using PKG_LIBS=-luv --------------------------- [CONFIGURE] -------------------------------- Configuration failed because libuv was not found. Try installing: * deb: libuv1-dev (Debian, Ubuntu, etc) * rpm: libuv-devel (Fedora, EPEL) * brew: libuv (OSX) Alternatively set environment variable USE_BUNDLED_LIBUV=1 to build a static version of libuv that is included with this package. -------------------------- [ERROR MESSAGE] --------------------------- :1:10: fatal error: uv.h: No such file or directory compilation terminated. -------------------------------------------------------------------- ERROR: configuration failed for package ‘fs’ * removing ‘/home/omnipath/local/R/4.5-3.22/fs’ * restoring previous ‘/home/omnipath/local/R/4.5-3.22/fs’ The downloaded source packages are in ‘/tmp/RtmpbaAhlH/downloaded_packages’ Warning message: In i.p(...) : installation of package ‘fs’ had non-zero exit status [ Finished: 2026-07-19 20:28:42 CEST ]