[ Started: 2024-10-02 16:38:54 CEST ]
[ liana v0.1.14 for BioC-3.20 from https://github.com/saezlab/liana@master (6cab46c 2024-08-07 08:58:01) ]
[1] "Libraries: " "/home/omnipath/local/R/4.4-3.20"
[3] "/home/omnipath/local/R/4.4" "/usr/lib/R/library"
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14)
Old packages: 'dorothea'
trying URL 'https://bioconductor.org/packages/3.20/data/experiment/src/contrib/dorothea_1.17.0.tar.gz'
Content type 'application/x-gzip' length 34631571 bytes (33.0 MB)
==================================================
downloaded 33.0 MB
* installing *source* package ‘dorothea’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (dorothea)
The downloaded source packages are in
‘/tmp/Rtmptvsv79/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 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14)
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 (3.13.26 -> 662c4c8b7...) [GitHub]
decoupleR (2.11.0 -> 8716d1a7f...) [GitHub]
XVector (NA -> 0.42.0 ) [CRAN]
GenomeInfoDb (NA -> 1.38.8 ) [CRAN]
SparseArray (NA -> 1.2.4 ) [CRAN]
S4Arrays (NA -> 1.2.1 ) [CRAN]
IRanges (NA -> 2.36.0 ) [CRAN]
DelayedArray (NA -> 0.28.0 ) [CRAN]
GenomicRa... (NA -> 1.54.1 ) [CRAN]
S4Vectors (NA -> 0.40.2 ) [CRAN]
Summarize... (NA -> 1.32.0 ) [CRAN]
Biostrings (NA -> 2.70.3 ) [CRAN]
KEGGREST (NA -> 1.42.0 ) [CRAN]
Annotatio... (NA -> 1.64.1 ) [CRAN]
Annotatio... (NA -> 3.10.1 ) [CRAN]
beachmat (NA -> 2.18.1 ) [CRAN]
ScaledMatrix (NA -> 1.10.0 ) [CRAN]
DelayedMa... (NA -> 1.24.0 ) [CRAN]
SingleCel... (NA -> 1.24.0 ) [CRAN]
BiocNeigh... (NA -> 1.20.2 ) [CRAN]
Experimen... (NA -> 2.10.0 ) [CRAN]
BiocSingular (NA -> 1.18.0 ) [CRAN]
scuttle (NA -> 1.12.0 ) [CRAN]
bluster (NA -> 1.12.0 ) [CRAN]
muscData (NA -> 1.16.0 ) [CRAN]
ComplexHe... (NA -> 2.18.0 ) [CRAN]
scater (NA -> 1.30.1 ) [CRAN]
scran (NA -> 1.30.2 ) [CRAN]
Downloading GitHub repo sqjin/CellChat@HEAD
nloptr (NA -> 2.1.1 ) [CRAN]
lme4 (NA -> 1.1-35.5) [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 8 packages: nloptr, lme4, pbkrtest, car, rstatix, BiocNeighbors, ggpubr, ComplexHeatmap
trying URL 'https://cran.uni-muenster.de/src/contrib/nloptr_2.1.1.tar.gz'
Content type 'application/x-gzip' length 2236635 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
trying URL 'https://cran.uni-muenster.de/src/contrib/lme4_1.1-35.5.tar.gz'
Content type 'application/x-gzip' length 3300116 bytes (3.1 MB)
==================================================
downloaded 3.1 MB
trying URL 'https://cran.uni-muenster.de/src/contrib/pbkrtest_0.5.3.tar.gz'
Content type 'application/x-gzip' length 59013 bytes (57 KB)
==================================================
downloaded 57 KB
trying URL 'https://cran.uni-muenster.de/src/contrib/car_3.1-3.tar.gz'
Content type 'application/x-gzip' length 384407 bytes (375 KB)
==================================================
downloaded 375 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).
- 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/4.4-3.20/nloptr’
ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
* removing ‘/home/omnipath/local/R/4.4-3.20/lme4’
ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
* removing ‘/home/omnipath/local/R/4.4-3.20/pbkrtest’
ERROR: dependencies ‘pbkrtest’, ‘lme4’ are not available for package ‘car’
* removing ‘/home/omnipath/local/R/4.4-3.20/car’
ERROR: dependency ‘car’ is not available for package ‘rstatix’
* removing ‘/home/omnipath/local/R/4.4-3.20/rstatix’
ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’
* removing ‘/home/omnipath/local/R/4.4-3.20/ggpubr’
The downloaded source packages are in
‘/tmp/Rtmptvsv79/downloaded_packages’
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/Rtmptvsv79/remotes3b7bf239394d51/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: dependencies ‘ComplexHeatmap’, ‘ggpubr’, ‘BiocNeighbors’ are not available for package ‘CellChat’
* removing ‘/home/omnipath/local/R/4.4-3.20/CellChat’
Skipping 15 packages ahead of CRAN: zlibbioc, GenomeInfoDbData, Biobase, MatrixGenerics, BiocGenerics, interactiveDisplayBase, BiocVersion, BiocFileCache, dir.expiry, sparseMatrixStats, BiocParallel, limma, metapod, edgeR, BiocStyle
Installing 26 packages: XVector, GenomeInfoDb, SparseArray, S4Arrays, IRanges, DelayedArray, GenomicRanges, S4Vectors, SummarizedExperiment, Biostrings, KEGGREST, AnnotationDbi, AnnotationHub, beachmat, ScaledMatrix, DelayedMatrixStats, SingleCellExperiment, BiocNeighbors, ExperimentHub, BiocSingular, scuttle, bluster, muscData, ComplexHeatmap, scater, scran
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/XVector_0.42.0.tar.gz'
Content type 'application/gzip' length 67825 bytes (66 KB)
==================================================
downloaded 66 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/GenomeInfoDb_1.38.8.tar.gz'
Content type 'application/gzip' length 3581806 bytes (3.4 MB)
==================================================
downloaded 3.4 MB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/SparseArray_1.2.4.tar.gz'
Content type 'application/gzip' length 367778 bytes (359 KB)
==================================================
downloaded 359 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/S4Arrays_1.2.1.tar.gz'
Content type 'application/gzip' length 282089 bytes (275 KB)
==================================================
downloaded 275 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/IRanges_2.36.0.tar.gz'
Content type 'application/gzip' length 481055 bytes (469 KB)
==================================================
downloaded 469 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/DelayedArray_0.28.0.tar.gz'
Content type 'application/gzip' length 624166 bytes (609 KB)
==================================================
downloaded 609 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/GenomicRanges_1.54.1.tar.gz'
Content type 'application/gzip' length 1140246 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/S4Vectors_0.40.2.tar.gz'
Content type 'application/gzip' length 838187 bytes (818 KB)
==================================================
downloaded 818 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/SummarizedExperiment_1.32.0.tar.gz'
Content type 'application/gzip' length 686052 bytes (669 KB)
==================================================
downloaded 669 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/Biostrings_2.70.3.tar.gz'
Content type 'application/gzip' length 12740728 bytes (12.2 MB)
==================================================
downloaded 12.2 MB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/KEGGREST_1.42.0.tar.gz'
Content type 'application/gzip' length 22412 bytes (21 KB)
==================================================
downloaded 21 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/AnnotationDbi_1.64.1.tar.gz'
Content type 'application/gzip' length 4359564 bytes (4.2 MB)
==================================================
downloaded 4.2 MB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/AnnotationHub_3.10.1.tar.gz'
Content type 'application/gzip' length 994797 bytes (971 KB)
==================================================
downloaded 971 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/beachmat_2.18.1.tar.gz'
Content type 'application/gzip' length 512143 bytes (500 KB)
==================================================
downloaded 500 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/ScaledMatrix_1.10.0.tar.gz'
Content type 'application/gzip' length 313034 bytes (305 KB)
==================================================
downloaded 305 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/DelayedMatrixStats_1.24.0.tar.gz'
Content type 'application/gzip' length 271120 bytes (264 KB)
==================================================
downloaded 264 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/SingleCellExperiment_1.24.0.tar.gz'
Content type 'application/gzip' length 985002 bytes (961 KB)
==================================================
downloaded 961 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/BiocNeighbors_1.20.2.tar.gz'
Content type 'application/gzip' length 1039738 bytes (1015 KB)
==================================================
downloaded 1015 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/ExperimentHub_2.10.0.tar.gz'
Content type 'application/gzip' length 497004 bytes (485 KB)
==================================================
downloaded 485 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/BiocSingular_1.18.0.tar.gz'
Content type 'application/gzip' length 616448 bytes (602 KB)
==================================================
downloaded 602 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/scuttle_1.12.0.tar.gz'
Content type 'application/gzip' length 1029515 bytes (1005 KB)
==================================================
downloaded 1005 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/bluster_1.12.0.tar.gz'
Content type 'application/gzip' length 2995786 bytes (2.9 MB)
==================================================
downloaded 2.9 MB
trying URL 'https://bioconductor.org/packages/3.18/data/experiment/src/contrib/muscData_1.16.0.tar.gz'
Content type 'application/gzip' length 236236 bytes (230 KB)
==================================================
downloaded 230 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/ComplexHeatmap_2.18.0.tar.gz'
Content type 'application/gzip' length 1455170 bytes (1.4 MB)
==================================================
downloaded 1.4 MB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/scater_1.30.1.tar.gz'
Content type 'application/gzip' length 4123647 bytes (3.9 MB)
==================================================
downloaded 3.9 MB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/scran_1.30.2.tar.gz'
Content type 'application/gzip' length 1802446 bytes (1.7 MB)
==================================================
downloaded 1.7 MB
* installing *source* package ‘S4Vectors’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c AEbufs.c -o AEbufs.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c DataFrame_class.c -o DataFrame_class.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c Hits_class.c -o Hits_class.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c LLint_class.c -o LLint_class.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c List_class.c -o List_class.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c Rle_class.c -o Rle_class.o
Rle_class.c: In function ‘_subset_Rle_by_ranges’:
Rle_class.c:1136:17: error: format not a string literal and no format arguments [-Werror=format-security]
1136 | error(errmsg);
| ^~~~~
Rle_class.c: In function ‘_subset_Rle_by_positions’:
Rle_class.c:1161:17: error: format not a string literal and no format arguments [-Werror=format-security]
1161 | error(errmsg);
| ^~~~~
Rle_class.c: In function ‘Rle_extract_range’:
Rle_class.c:1190:17: error: format not a string literal and no format arguments [-Werror=format-security]
1190 | error(errmsg);
| ^~~~~
cc1: some warnings being treated as errors
make: *** [/usr/lib/R/etc/Makeconf:195: Rle_class.o] Error 1
ERROR: compilation failed for package ‘S4Vectors’
* removing ‘/home/omnipath/local/R/4.4-3.20/S4Vectors’
ERROR: dependency ‘S4Vectors’ is not available for package ‘IRanges’
* removing ‘/home/omnipath/local/R/4.4-3.20/IRanges’
ERROR: dependency ‘S4Vectors’ is not available for package ‘BiocNeighbors’
* removing ‘/home/omnipath/local/R/4.4-3.20/BiocNeighbors’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘XVector’
* removing ‘/home/omnipath/local/R/4.4-3.20/XVector’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘GenomeInfoDb’
* removing ‘/home/omnipath/local/R/4.4-3.20/GenomeInfoDb’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘S4Arrays’
* removing ‘/home/omnipath/local/R/4.4-3.20/S4Arrays’
ERROR: dependencies ‘S4Vectors’, ‘BiocNeighbors’ are not available for package ‘bluster’
* removing ‘/home/omnipath/local/R/4.4-3.20/bluster’
ERROR: dependency ‘IRanges’ is not available for package ‘ComplexHeatmap’
* removing ‘/home/omnipath/local/R/4.4-3.20/ComplexHeatmap’
ERROR: dependencies ‘S4Vectors’, ‘S4Arrays’, ‘IRanges’, ‘XVector’ are not available for package ‘SparseArray’
* removing ‘/home/omnipath/local/R/4.4-3.20/SparseArray’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘GenomeInfoDb’, ‘XVector’ are not available for package ‘GenomicRanges’
* removing ‘/home/omnipath/local/R/4.4-3.20/GenomicRanges’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘XVector’, ‘GenomeInfoDb’ are not available for package ‘Biostrings’
* removing ‘/home/omnipath/local/R/4.4-3.20/Biostrings’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘S4Arrays’, ‘SparseArray’ are not available for package ‘DelayedArray’
* removing ‘/home/omnipath/local/R/4.4-3.20/DelayedArray’
ERROR: dependency ‘Biostrings’ is not available for package ‘KEGGREST’
* removing ‘/home/omnipath/local/R/4.4-3.20/KEGGREST’
ERROR: dependencies ‘GenomicRanges’, ‘S4Vectors’, ‘IRanges’, ‘GenomeInfoDb’, ‘S4Arrays’, ‘DelayedArray’ are not available for package ‘SummarizedExperiment’
* removing ‘/home/omnipath/local/R/4.4-3.20/SummarizedExperiment’
ERROR: dependencies ‘IRanges’, ‘S4Vectors’, ‘KEGGREST’ are not available for package ‘AnnotationDbi’
* removing ‘/home/omnipath/local/R/4.4-3.20/AnnotationDbi’
ERROR: dependencies ‘DelayedArray’, ‘SparseArray’ are not available for package ‘beachmat’
* removing ‘/home/omnipath/local/R/4.4-3.20/beachmat’
ERROR: dependencies ‘S4Vectors’, ‘DelayedArray’ are not available for package ‘ScaledMatrix’
* removing ‘/home/omnipath/local/R/4.4-3.20/ScaledMatrix’
ERROR: dependencies ‘DelayedArray’, ‘S4Vectors’, ‘IRanges’ are not available for package ‘DelayedMatrixStats’
* removing ‘/home/omnipath/local/R/4.4-3.20/DelayedMatrixStats’
ERROR: dependencies ‘AnnotationDbi’, ‘S4Vectors’ are not available for package ‘AnnotationHub’
* removing ‘/home/omnipath/local/R/4.4-3.20/AnnotationHub’
ERROR: dependencies ‘SummarizedExperiment’, ‘S4Vectors’, ‘GenomicRanges’, ‘DelayedArray’ are not available for package ‘SingleCellExperiment’
* removing ‘/home/omnipath/local/R/4.4-3.20/SingleCellExperiment’
ERROR: dependencies ‘S4Vectors’, ‘DelayedArray’, ‘ScaledMatrix’, ‘beachmat’ are not available for package ‘BiocSingular’
* removing ‘/home/omnipath/local/R/4.4-3.20/BiocSingular’
ERROR: dependencies ‘AnnotationHub’, ‘S4Vectors’ are not available for package ‘ExperimentHub’
* removing ‘/home/omnipath/local/R/4.4-3.20/ExperimentHub’
ERROR: dependencies ‘SingleCellExperiment’, ‘S4Vectors’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘DelayedArray’, ‘DelayedMatrixStats’, ‘beachmat’ are not available for package ‘scuttle’
* removing ‘/home/omnipath/local/R/4.4-3.20/scuttle’
ERROR: dependencies ‘ExperimentHub’, ‘SingleCellExperiment’ are not available for package ‘muscData’
* removing ‘/home/omnipath/local/R/4.4-3.20/muscData’
ERROR: dependencies ‘SingleCellExperiment’, ‘scuttle’, ‘S4Vectors’, ‘SummarizedExperiment’, ‘DelayedArray’, ‘beachmat’, ‘BiocNeighbors’, ‘BiocSingular’ are not available for package ‘scater’
* removing ‘/home/omnipath/local/R/4.4-3.20/scater’
ERROR: dependencies ‘SingleCellExperiment’, ‘scuttle’, ‘SummarizedExperiment’, ‘S4Vectors’, ‘DelayedArray’, ‘DelayedMatrixStats’, ‘BiocSingular’, ‘bluster’, ‘beachmat’ are not available for package ‘scran’
* removing ‘/home/omnipath/local/R/4.4-3.20/scran’
The downloaded source packages are in
‘/tmp/Rtmptvsv79/downloaded_packages’
Downloading GitHub repo sqjin/CellChat@HEAD
nloptr (NA -> 2.1.1 ) [CRAN]
lme4 (NA -> 1.1-35.5) [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 8 packages: nloptr, lme4, pbkrtest, car, rstatix, BiocNeighbors, ggpubr, ComplexHeatmap
trying URL 'https://cran.uni-muenster.de/src/contrib/nloptr_2.1.1.tar.gz'
Content type 'application/x-gzip' length 2236635 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
trying URL 'https://cran.uni-muenster.de/src/contrib/lme4_1.1-35.5.tar.gz'
Content type 'application/x-gzip' length 3300116 bytes (3.1 MB)
==================================================
downloaded 3.1 MB
trying URL 'https://cran.uni-muenster.de/src/contrib/pbkrtest_0.5.3.tar.gz'
Content type 'application/x-gzip' length 59013 bytes (57 KB)
==================================================
downloaded 57 KB
trying URL 'https://cran.uni-muenster.de/src/contrib/car_3.1-3.tar.gz'
Content type 'application/x-gzip' length 384407 bytes (375 KB)
==================================================
downloaded 375 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).
- 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/4.4-3.20/nloptr’
ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
* removing ‘/home/omnipath/local/R/4.4-3.20/lme4’
ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
* removing ‘/home/omnipath/local/R/4.4-3.20/pbkrtest’
ERROR: dependencies ‘pbkrtest’, ‘lme4’ are not available for package ‘car’
* removing ‘/home/omnipath/local/R/4.4-3.20/car’
ERROR: dependency ‘car’ is not available for package ‘rstatix’
* removing ‘/home/omnipath/local/R/4.4-3.20/rstatix’
ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’
* removing ‘/home/omnipath/local/R/4.4-3.20/ggpubr’
The downloaded source packages are in
‘/tmp/Rtmptvsv79/downloaded_packages’
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/Rtmptvsv79/remotes3b7bf22f2a1a5e/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: dependencies ‘ComplexHeatmap’, ‘ggpubr’, ‘BiocNeighbors’ are not available for package ‘CellChat’
* removing ‘/home/omnipath/local/R/4.4-3.20/CellChat’
Downloading GitHub repo saezlab/OmnipathR@HEAD
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/Rtmptvsv79/remotes3b7bf233877af0/saezlab-OmnipathR-662c4c8/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_3.13.26.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
[2024-10-02 16:40:57] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2024-10-02 16:40:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-02 16:40:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-02 16:40:57] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-10-02 16:40:57] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-10-02 16:40:57] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-10-02 16:40:57] [TRACE] [OmnipathR] Contains 1 files.
[2024-10-02 16:40:57] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-10-02 16:40:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-02 16:40:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-02 16:40:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-10-02 16:40:57] [TRACE] [OmnipathR] Pandoc version: `3.1.3`.
[2024-10-02 16:40:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-02 16:40:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-02 16:40:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-02 16:40:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-02 16:40:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-02 16:40:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-02 16:40:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-02 16:40:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-02 16:40:57] [TRACE] [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-10-02 16:40:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-02 16:40:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-02 16:40:59] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-10-02 16:40:59] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-10-02 16:40:59] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-10-02 16:40:59] [TRACE] [OmnipathR] Contains 1 files.
[2024-10-02 16:40:59] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-10-02 16:40:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-02 16:40:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-02 16:40:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-10-02 16:40:59] [TRACE] [OmnipathR] Pandoc version: `3.1.3`.
[2024-10-02 16:40:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-02 16:40:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-02 16:40:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-02 16:40:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-02 16:40:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-02 16:40:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-02 16:40:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-02 16:40:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-02 16:40:59] [TRACE] [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)
Downloading GitHub repo saezlab/decoupleR@HEAD
Skipping 1 packages ahead of CRAN: BiocParallel
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/Rtmptvsv79/remotes3b7bf25511913e/saezlab-decoupleR-8716d1a/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’ ...
** 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)
There were 42 warnings (use warnings() to see them)
[ Finished: 2024-10-02 16:41:06 CEST ]