[ Started: 2024-03-29 13:57:23 CET ]
[ liana v0.1.13 for BioC-3.19 from https://github.com/saezlab/liana@master (4c323df 2023-11-03 14:35:54) ]
[1] "Libraries: " "/home/omnipath/local/R/4.4-3.19"
[3] "/home/omnipath/local/R/4.4" "/opt/R-devel/lib/R/library"
Bioconductor version 3.19 (BiocManager 1.30.22), R Under development (unstable)
(2024-03-23 r86179)
Bioconductor version 3.19 (BiocManager 1.30.22), R Under development (unstable)
(2024-03-23 r86179)
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 (3.11.10 -> 582735943...) [GitHub]
Downloading GitHub repo sqjin/CellChat@HEAD
nloptr (NA -> 2.0.3 ) [CRAN]
lme4 (NA -> 1.1-35.2) [CRAN]
pbkrtest (NA -> 0.5.2 ) [CRAN]
car (NA -> 3.1-2 ) [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_2.0.3.tar.gz'
Content type 'application/x-gzip' length 2219877 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
trying URL 'https://cran.uni-muenster.de/src/contrib/lme4_1.1-35.2.tar.gz'
Content type 'application/x-gzip' length 2943611 bytes (2.8 MB)
==================================================
downloaded 2.8 MB
trying URL 'https://cran.uni-muenster.de/src/contrib/pbkrtest_0.5.2.tar.gz'
Content type 'application/x-gzip' length 75295 bytes (73 KB)
==================================================
downloaded 73 KB
trying URL 'https://cran.uni-muenster.de/src/contrib/car_3.1-2.tar.gz'
Content type 'application/x-gzip' length 579829 bytes (566 KB)
==================================================
downloaded 566 KB
trying URL 'https://cran.uni-muenster.de/src/contrib/rstatix_0.7.2.tar.gz'
Content type 'application/x-gzip' length 405256 bytes (395 KB)
==================================================
downloaded 395 KB
trying URL 'https://cran.uni-muenster.de/src/contrib/ggpubr_0.6.0.tar.gz'
Content type 'application/x-gzip' length 1941659 bytes (1.9 MB)
==================================================
downloaded 1.9 MB
* installing *source* package ‘nloptr’ ...
** 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).
- sudo brew install 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/4.4-3.19/nloptr’
ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
* removing ‘/home/omnipath/local/R/4.4-3.19/lme4’
ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
* removing ‘/home/omnipath/local/R/4.4-3.19/pbkrtest’
ERROR: dependencies ‘pbkrtest’, ‘lme4’ are not available for package ‘car’
* removing ‘/home/omnipath/local/R/4.4-3.19/car’
ERROR: dependency ‘car’ is not available for package ‘rstatix’
* removing ‘/home/omnipath/local/R/4.4-3.19/rstatix’
ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’
* removing ‘/home/omnipath/local/R/4.4-3.19/ggpubr’
The downloaded source packages are in
‘/tmp/Rtmp9nOmZl/downloaded_packages’
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/Rtmp9nOmZl/remotes334b57b0f0829/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’
* removing ‘/home/omnipath/local/R/4.4-3.19/CellChat’
Skipping 41 packages ahead of CRAN: zlibbioc, GenomeInfoDbData, Biobase, XVector, GenomeInfoDb, SparseArray, S4Arrays, IRanges, MatrixGenerics, DelayedArray, GenomicRanges, BiocGenerics, S4Vectors, SummarizedExperiment, Biostrings, KEGGREST, interactiveDisplayBase, AnnotationDbi, BiocVersion, BiocFileCache, AnnotationHub, dir.expiry, sparseMatrixStats, beachmat, ScaledMatrix, BiocParallel, DelayedMatrixStats, SingleCellExperiment, BiocNeighbors, limma, ExperimentHub, BiocSingular, scuttle, metapod, bluster, edgeR, muscData, BiocStyle, ComplexHeatmap, scater, scran
Downloading GitHub repo sqjin/CellChat@HEAD
nloptr (NA -> 2.0.3 ) [CRAN]
lme4 (NA -> 1.1-35.2) [CRAN]
pbkrtest (NA -> 0.5.2 ) [CRAN]
car (NA -> 3.1-2 ) [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_2.0.3.tar.gz'
Content type 'application/x-gzip' length 2219877 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
trying URL 'https://cran.uni-muenster.de/src/contrib/lme4_1.1-35.2.tar.gz'
Content type 'application/x-gzip' length 2943611 bytes (2.8 MB)
==================================================
downloaded 2.8 MB
trying URL 'https://cran.uni-muenster.de/src/contrib/pbkrtest_0.5.2.tar.gz'
Content type 'application/x-gzip' length 75295 bytes (73 KB)
==================================================
downloaded 73 KB
trying URL 'https://cran.uni-muenster.de/src/contrib/car_3.1-2.tar.gz'
Content type 'application/x-gzip' length 579829 bytes (566 KB)
==================================================
downloaded 566 KB
trying URL 'https://cran.uni-muenster.de/src/contrib/rstatix_0.7.2.tar.gz'
Content type 'application/x-gzip' length 405256 bytes (395 KB)
==================================================
downloaded 395 KB
trying URL 'https://cran.uni-muenster.de/src/contrib/ggpubr_0.6.0.tar.gz'
Content type 'application/x-gzip' length 1941659 bytes (1.9 MB)
==================================================
downloaded 1.9 MB
* installing *source* package ‘nloptr’ ...
** 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).
- sudo brew install 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/4.4-3.19/nloptr’
ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
* removing ‘/home/omnipath/local/R/4.4-3.19/lme4’
ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
* removing ‘/home/omnipath/local/R/4.4-3.19/pbkrtest’
ERROR: dependencies ‘pbkrtest’, ‘lme4’ are not available for package ‘car’
* removing ‘/home/omnipath/local/R/4.4-3.19/car’
ERROR: dependency ‘car’ is not available for package ‘rstatix’
* removing ‘/home/omnipath/local/R/4.4-3.19/rstatix’
ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’
* removing ‘/home/omnipath/local/R/4.4-3.19/ggpubr’
The downloaded source packages are in
‘/tmp/Rtmp9nOmZl/downloaded_packages’
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/Rtmp9nOmZl/remotes334b55cdd1d30/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’
* removing ‘/home/omnipath/local/R/4.4-3.19/CellChat’
Downloading GitHub repo saezlab/OmnipathR@HEAD
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/Rtmp9nOmZl/remotes334b523238a48/saezlab-OmnipathR-5827359/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
* looking to see if a ‘data/datalist’ file should be added
* building ‘OmnipathR_3.11.10.tar.gz’
* installing *source* package ‘OmnipathR’ ...
** 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
[2024-03-29 13:58:05] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2024-03-29 13:58:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-29 13:58:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-29 13:58:05] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-03-29 13:58:05] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-03-29 13:58:05] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-03-29 13:58:05] [TRACE] [OmnipathR] Contains 1 files.
[2024-03-29 13:58:05] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-03-29 13:58:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-29 13:58:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-29 13:58:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-03-29 13:58:05] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-03-29 13:58:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-29 13:58:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-29 13:58:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-29 13:58:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-29 13:58:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-29 13:58:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-29 13:58:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-29 13:58:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-29 13:58:05] [TRACE] [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-03-29 13:58:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-29 13:58:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-29 13:58:06] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-03-29 13:58:06] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-03-29 13:58:06] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-03-29 13:58:06] [TRACE] [OmnipathR] Contains 1 files.
[2024-03-29 13:58:06] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-03-29 13:58:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-29 13:58:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-29 13:58:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-03-29 13:58:06] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-03-29 13:58:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-29 13:58:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-29 13:58:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-29 13:58:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-29 13:58:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-29 13:58:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-29 13:58:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-29 13:58:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-29 13:58:06] [TRACE] [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)
There were 14 warnings (use warnings() to see them)
[ Finished: 2024-03-29 13:58:07 CET ]