[ Started: 2026-04-22 21:48:37 CEST ] [ cosmosR v1.18.1 for BioC-3.22 from https://git.bioconductor.org/packages/cosmosR@RELEASE_3_22 (80dd9b7 2026-02-10 12:59:12) ] [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/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/RtmpZCWZUf/downloaded_packages’ Warning message: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘fs’ 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: 'fs' trying URL 'https://cloud.r-project.org/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/RtmpZCWZUf/downloaded_packages’ Warning message: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘fs’ 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: 'fs' trying URL 'https://cloud.r-project.org/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/RtmpZCWZUf/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 fs (2.0.1 -> 2.1.0 ) [CRAN] limma (ef14858fa... -> 8bfe3ccb0...) [Git] Skipping 6 packages ahead of CRAN: S7, ggplot2, processx, curl, S4Vectors, pkgload 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/RtmpZCWZUf/downloaded_packages’ Downloading git repo https://git.bioconductor.org/packages/limma.git '/usr/bin/git' clone --depth 1 --no-hardlinks https://git.bioconductor.org/packages/limma.git /tmp/RtmpZCWZUf/file15250084ef25f Cloning into '/tmp/RtmpZCWZUf/file15250084ef25f'... ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpZCWZUf/file15250084ef25f/DESCRIPTION’ ... OK * preparing ‘limma’: * checking DESCRIPTION meta-information ... OK * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘limma_3.67.3.tar.gz’ * installing *source* package ‘limma’ ... ** this is package ‘limma’ version ‘3.67.3’ ** 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 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 normexp.c -o normexp.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 weighted_lowess.c -o weighted_lowess.o gcc -std=gnu2x -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o limma.so init.o normexp.o weighted_lowess.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.5-3.22/00LOCK-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) Warning message: In i.p(...) : installation of package ‘fs’ had non-zero exit status [ Finished: 2026-04-22 21:49:08 CEST ]