[ Started: 2025-03-30 01:08:25 CET ]
[ liana v0.1.14 for BioC-3.21 from https://github.com/saezlab/liana@master (6cab46c 2024-08-07 08:58:01) ]
[1] "Libraries: " "/home/omnipath/local/R/4.5-3.21"
[3] "/home/omnipath/local/R/4.5" "/opt/R-devel/lib/R/library"
Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable)
(2025-02-12 r87715)
Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable)
(2025-02-12 r87715)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
`force = TRUE` to re-install: 'BiocCheck'
CellChat (NA -> e4f68625b...) [GitHub]
OmnipathR (3.15.12 -> b71fb21d9...) [GitHub]
decoupleR (2.13.0 -> ee886864d...) [GitHub]
basilisk (1.19.3 -> d962fd4f4...) [GitHub]
Downloading GitHub repo sqjin/CellChat@HEAD
nloptr (NA -> 2.2.1 ) [CRAN]
lme4 (NA -> 1.1-37) [CRAN]
pbkrtest (NA -> 0.5.3 ) [CRAN]
car (NA -> 3.1-3 ) [CRAN]
rstatix (NA -> 0.7.2 ) [CRAN]
ggpubr (NA -> 0.6.0 ) [CRAN]
Skipping 4 packages not available: Biobase, BiocNeighbors, BiocGenerics, ComplexHeatmap
Installing 6 packages: nloptr, lme4, pbkrtest, car, rstatix, ggpubr
trying URL 'https://cran.uni-muenster.de/src/contrib/nloptr_2.2.1.tar.gz'
trying URL 'https://cran.uni-muenster.de/src/contrib/lme4_1.1-37.tar.gz'
trying URL 'https://cran.uni-muenster.de/src/contrib/pbkrtest_0.5.3.tar.gz'
trying URL 'https://cran.uni-muenster.de/src/contrib/car_3.1-3.tar.gz'
trying URL 'https://cran.uni-muenster.de/src/contrib/rstatix_0.7.2.tar.gz'
trying URL 'https://cran.uni-muenster.de/src/contrib/ggpubr_0.6.0.tar.gz'
* installing *source* package ‘nloptr’ ...
** this is package ‘nloptr’ version ‘2.2.1’
** package ‘nloptr’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++17 accepts -g... yes
checking for g++ -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++ -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ -std=gnu++17 accepts -g... (cached) yes
checking for g++ -std=gnu++17 option to enable C++11 features... (cached) none needed
checking for pkg-config... /usr/bin/pkg-config
checking if pkg-config knows NLopt... no
checking for cmake... no
------------------ CMAKE NOT FOUND --------------------
CMake was not found on the PATH. Please install CMake:
- sudo yum install cmake (Fedora/CentOS; inside a terminal)
- sudo apt install cmake (Debian/Ubuntu; inside a terminal).
- sudo pacman -S cmake (Arch Linux; inside a terminal).
- brew install --cask cmake (MacOS; inside a terminal with Homebrew)
- sudo port install cmake (MacOS; inside a terminal with MacPorts)
Alternatively install CMake from:
-------------------------------------------------------
ERROR: configuration failed for package ‘nloptr’
* removing ‘/home/omnipath/local/R/4.5-3.21/nloptr’
ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
Perhaps try a variation of:
install.packages('nloptr')
* removing ‘/home/omnipath/local/R/4.5-3.21/lme4’
ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
Perhaps try a variation of:
install.packages('lme4')
* removing ‘/home/omnipath/local/R/4.5-3.21/pbkrtest’
ERROR: dependencies ‘pbkrtest’, ‘lme4’ are not available for package ‘car’
Perhaps try a variation of:
install.packages(c('pbkrtest', 'lme4'))
* removing ‘/home/omnipath/local/R/4.5-3.21/car’
ERROR: dependency ‘car’ is not available for package ‘rstatix’
Perhaps try a variation of:
install.packages('car')
* removing ‘/home/omnipath/local/R/4.5-3.21/rstatix’
ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’
Perhaps try a variation of:
install.packages('rstatix')
* removing ‘/home/omnipath/local/R/4.5-3.21/ggpubr’
The downloaded source packages are in
‘/tmp/RtmpuJxHCn/downloaded_packages’
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpuJxHCn/remotes1466dc7d6130a0/sqjin-CellChat-e4f6862/DESCRIPTION’ ... OK
* preparing ‘CellChat’:
* 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 ‘CellChat_1.6.1.tar.gz’
ERROR: dependency ‘ggpubr’ is not available for package ‘CellChat’
Perhaps try a variation of:
install.packages('ggpubr')
* removing ‘/home/omnipath/local/R/4.5-3.21/CellChat’
Downloading GitHub repo sqjin/CellChat@HEAD
nloptr (NA -> 2.2.1 ) [CRAN]
lme4 (NA -> 1.1-37) [CRAN]
pbkrtest (NA -> 0.5.3 ) [CRAN]
car (NA -> 3.1-3 ) [CRAN]
rstatix (NA -> 0.7.2 ) [CRAN]
ggpubr (NA -> 0.6.0 ) [CRAN]
Skipping 4 packages not available: Biobase, BiocNeighbors, BiocGenerics, ComplexHeatmap
Installing 6 packages: nloptr, lme4, pbkrtest, car, rstatix, ggpubr
trying URL 'https://cran.uni-muenster.de/src/contrib/nloptr_2.2.1.tar.gz'
trying URL 'https://cran.uni-muenster.de/src/contrib/lme4_1.1-37.tar.gz'
trying URL 'https://cran.uni-muenster.de/src/contrib/pbkrtest_0.5.3.tar.gz'
trying URL 'https://cran.uni-muenster.de/src/contrib/car_3.1-3.tar.gz'
trying URL 'https://cran.uni-muenster.de/src/contrib/rstatix_0.7.2.tar.gz'
trying URL 'https://cran.uni-muenster.de/src/contrib/ggpubr_0.6.0.tar.gz'
* installing *source* package ‘nloptr’ ...
** this is package ‘nloptr’ version ‘2.2.1’
** package ‘nloptr’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++17 accepts -g... yes
checking for g++ -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++ -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ -std=gnu++17 accepts -g... (cached) yes
checking for g++ -std=gnu++17 option to enable C++11 features... (cached) none needed
checking for pkg-config... /usr/bin/pkg-config
checking if pkg-config knows NLopt... no
checking for cmake... no
------------------ CMAKE NOT FOUND --------------------
CMake was not found on the PATH. Please install CMake:
- sudo yum install cmake (Fedora/CentOS; inside a terminal)
- sudo apt install cmake (Debian/Ubuntu; inside a terminal).
- sudo pacman -S cmake (Arch Linux; inside a terminal).
- brew install --cask cmake (MacOS; inside a terminal with Homebrew)
- sudo port install cmake (MacOS; inside a terminal with MacPorts)
Alternatively install CMake from:
-------------------------------------------------------
ERROR: configuration failed for package ‘nloptr’
* removing ‘/home/omnipath/local/R/4.5-3.21/nloptr’
ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
Perhaps try a variation of:
install.packages('nloptr')
* removing ‘/home/omnipath/local/R/4.5-3.21/lme4’
ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
Perhaps try a variation of:
install.packages('lme4')
* removing ‘/home/omnipath/local/R/4.5-3.21/pbkrtest’
ERROR: dependencies ‘pbkrtest’, ‘lme4’ are not available for package ‘car’
Perhaps try a variation of:
install.packages(c('pbkrtest', 'lme4'))
* removing ‘/home/omnipath/local/R/4.5-3.21/car’
ERROR: dependency ‘car’ is not available for package ‘rstatix’
Perhaps try a variation of:
install.packages('car')
* removing ‘/home/omnipath/local/R/4.5-3.21/rstatix’
ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’
Perhaps try a variation of:
install.packages('rstatix')
* removing ‘/home/omnipath/local/R/4.5-3.21/ggpubr’
The downloaded source packages are in
‘/tmp/RtmpuJxHCn/downloaded_packages’
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpuJxHCn/remotes1466dc6ab38e8c/sqjin-CellChat-e4f6862/DESCRIPTION’ ... OK
* preparing ‘CellChat’:
* 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 ‘CellChat_1.6.1.tar.gz’
ERROR: dependency ‘ggpubr’ is not available for package ‘CellChat’
Perhaps try a variation of:
install.packages('ggpubr')
* removing ‘/home/omnipath/local/R/4.5-3.21/CellChat’
Downloading GitHub repo saezlab/OmnipathR@HEAD
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpuJxHCn/remotes1466dc72cc88c/saezlab-OmnipathR-b71fb21/DESCRIPTION’ ... OK
* preparing ‘OmnipathR’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Removed empty directory ‘OmnipathR/.github’
* looking to see if a ‘data/datalist’ file should be added
* building ‘OmnipathR_3.15.12.tar.gz’
* installing *source* package ‘OmnipathR’ ...
** this is package ‘OmnipathR’ version ‘3.15.12’
** using staged installation
** 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
[2025-03-30 01:09:08] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2025-03-30 01:09:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-30 01:09:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-30 01:09:08] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-03-30 01:09:08] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-03-30 00:08:58 UTC; omnipath
[2025-03-30 01:09:08] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-03-30 01:09:08] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-30 00:08:59 UTC; unix
[2025-03-30 01:09:08] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.12
[2025-03-30 01:09:08] [INFO] [OmnipathR] Package `OmnipathR` repository: NA
[2025-03-30 01:09:08] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-03-30; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-03-30 01:09:08] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-03-30 01:09:08] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.1(2024-11-27); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.12(2025-03-30); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-30 01:09:08] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-03-30 01:09:08] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-03-30 01:09:08] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-03-30 01:09:08] [TRACE] [OmnipathR] Contains 1 files.
[2025-03-30 01:09:08] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-03-30 01:09:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-30 01:09:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-30 01:09:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-03-30 01:09:08] [TRACE] [OmnipathR] Pandoc version: `3.1.3`.
[2025-03-30 01:09:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-30 01:09:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-30 01:09:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-30 01:09:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-30 01:09:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-30 01:09:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-30 01:09:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-30 01:09:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-30 01:09:09] [TRACE] [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-03-30 01:09:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-30 01:09:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-30 01:09:10] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-03-30 01:09:10] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-03-30 00:08:58 UTC; omnipath
[2025-03-30 01:09:10] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-03-30 01:09:10] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-30 00:08:59 UTC; unix
[2025-03-30 01:09:10] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.12
[2025-03-30 01:09:10] [INFO] [OmnipathR] Package `OmnipathR` repository: NA
[2025-03-30 01:09:10] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-03-30; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-03-30 01:09:10] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-03-30 01:09:10] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.1(2024-11-27); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.12(2025-03-30); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-30 01:09:10] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-03-30 01:09:10] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-03-30 01:09:10] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-03-30 01:09:10] [TRACE] [OmnipathR] Contains 1 files.
[2025-03-30 01:09:10] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-03-30 01:09:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-30 01:09:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-30 01:09:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-03-30 01:09:10] [TRACE] [OmnipathR] Pandoc version: `3.1.3`.
[2025-03-30 01:09:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-30 01:09:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-30 01:09:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-30 01:09:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-30 01:09:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-30 01:09:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-30 01:09:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-30 01:09:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-30 01:09:10] [TRACE] [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)
Downloading GitHub repo saezlab/decoupleR@HEAD
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpuJxHCn/remotes1466dc1aeaee95/saezlab-decoupleR-ee88686/DESCRIPTION’ ... OK
* preparing ‘decoupleR’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘decoupleR_2.9.7.tar.gz’
* installing *source* package ‘decoupleR’ ...
** this is package ‘decoupleR’ version ‘2.9.7’
** 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 (decoupleR)
Downloading GitHub repo LTLA/basilisk@HEAD
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpuJxHCn/remotes1466dc4731db7b/LTLA-basilisk-d962fd4/DESCRIPTION’ ... OK
* preparing ‘basilisk’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘basilisk_1.19.1.tar.gz’
* installing *source* package ‘basilisk’ ...
** this is package ‘basilisk’ version ‘1.19.1’
** using non-staged installation via StagedInstall field
** 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
* DONE (basilisk)
There were 14 warnings (use warnings() to see them)
[ Finished: 2025-03-30 01:09:23 CET ]