[ Started: 2025-07-15 19:14:10 CEST ] [ liana v0.1.14 for BioC-3.22 from https://github.com/saezlab/liana@master (6cab46c 2024-08-07 08:58:01) ] [1] "Libraries: " "/home/omnipath/local/R/4.5-3.22" [3] "/home/omnipath/local/R/4.5" "/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 3.22 (BiocManager 1.30.26), R 4.5.1 (2025-06-13) '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 1.30.26), R 4.5.1 (2025-06-13) 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] decoupleR (2.15.0 -> ee886864d...) [GitHub] BiocNeigh... (NA -> 2.2.0 ) [CRAN] bluster (NA -> 1.18.0 ) [CRAN] scater (NA -> 1.36.0 ) [CRAN] scran (NA -> 1.36.0 ) [CRAN] Downloading GitHub repo sqjin/CellChat@HEAD Skipping 4 packages not available: Biobase, BiocNeighbors, BiocGenerics, ComplexHeatmap ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpyufYVM/remotes100525aa7aed3/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 ‘BiocNeighbors’ is not available for package ‘CellChat’ Perhaps try a variation of: install.packages('BiocNeighbors') * removing ‘/home/omnipath/local/R/4.5-3.22/CellChat’ Skipping 33 packages ahead of CRAN: UCSC.utils, Biobase, XVector, GenomeInfoDb, SparseArray, S4Arrays, IRanges, MatrixGenerics, DelayedArray, GenomicRanges, BiocGenerics, S4Vectors, SummarizedExperiment, Biostrings, KEGGREST, AnnotationDbi, BiocVersion, BiocFileCache, AnnotationHub, dir.expiry, assorthead, beachmat, ScaledMatrix, BiocParallel, SingleCellExperiment, ExperimentHub, BiocSingular, scuttle, metapod, edgeR, muscData, BiocStyle, ComplexHeatmap Installing 4 packages: BiocNeighbors, bluster, scater, scran trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/BiocNeighbors_2.2.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/bluster_1.18.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/scater_1.36.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/scran_1.36.0.tar.gz' * installing *source* package ‘BiocNeighbors’ ... ** this is package ‘BiocNeighbors’ version ‘2.2.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++17 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.22/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.22/assorthead/include' -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 RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: ../inst/include/BiocNeighbors.h:23:48: error: wrong number of template arguments (3, should be 2) 23 | typedef knncolle::SimpleMatrix SimpleMatrix; | ^ In file included from /home/omnipath/local/R/4.5-3.22/assorthead/include/knncolle/Builder.hpp:5, from /home/omnipath/local/R/4.5-3.22/assorthead/include/knncolle/knncolle.hpp:4, from ../inst/include/BiocNeighbors.h:6: /home/omnipath/local/R/4.5-3.22/assorthead/include/knncolle/Matrix.hpp:128:20: note: provided for ‘template class knncolle::SimpleMatrix’ 128 | class SimpleMatrix final : public Matrix { | ^~~~~ ../inst/include/BiocNeighbors.h:28:47: error: wrong number of template arguments (2, should be at least 3) 28 | typedef knncolle::Builder Builder; | ^ /home/omnipath/local/R/4.5-3.22/assorthead/include/knncolle/Builder.hpp:28:7: note: provided for ‘template class knncolle::Builder’ 28 | class Builder { | ^~~~~~~ make: *** [/usr/lib/R/etc/Makeconf:211: RcppExports.o] Error 1 ERROR: compilation failed for package ‘BiocNeighbors’ * removing ‘/home/omnipath/local/R/4.5-3.22/BiocNeighbors’ ERROR: dependency ‘BiocNeighbors’ is not available for package ‘bluster’ Perhaps try a variation of: install.packages('BiocNeighbors') * removing ‘/home/omnipath/local/R/4.5-3.22/bluster’ ERROR: dependency ‘BiocNeighbors’ is not available for package ‘scater’ Perhaps try a variation of: install.packages('BiocNeighbors') * removing ‘/home/omnipath/local/R/4.5-3.22/scater’ ERROR: dependency ‘bluster’ is not available for package ‘scran’ Perhaps try a variation of: install.packages('bluster') * removing ‘/home/omnipath/local/R/4.5-3.22/scran’ The downloaded source packages are in ‘/tmp/RtmpyufYVM/downloaded_packages’ Downloading GitHub repo sqjin/CellChat@HEAD Skipping 4 packages not available: Biobase, BiocNeighbors, BiocGenerics, ComplexHeatmap ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpyufYVM/remotes1005256dde1be5/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 ‘BiocNeighbors’ is not available for package ‘CellChat’ Perhaps try a variation of: install.packages('BiocNeighbors') * removing ‘/home/omnipath/local/R/4.5-3.22/CellChat’ Downloading GitHub repo saezlab/decoupleR@HEAD Skipping 1 packages ahead of CRAN: BiocParallel ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpyufYVM/remotes10052532075617/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) Warning messages: 1: In i.p(...) : installation of package ‘/tmp/RtmpyufYVM/file1005253e892bb2/CellChat_1.6.1.tar.gz’ had non-zero exit status 2: In i.p(...) : installation of package ‘BiocNeighbors’ had non-zero exit status 3: In i.p(...) : installation of package ‘bluster’ had non-zero exit status 4: In i.p(...) : installation of package ‘scater’ had non-zero exit status 5: In i.p(...) : installation of package ‘scran’ had non-zero exit status 6: In i.p(...) : installation of package ‘/tmp/RtmpyufYVM/file10052535f075b6/CellChat_1.6.1.tar.gz’ had non-zero exit status [ Finished: 2025-07-15 19:14:44 CEST ]