Hi list, Here is an example:
hpages@XPS15:~$ R CMD INSTALL CoreGx * installing to library ‘/home/hpages/R/R-4.4.r85388/site-library’ * installing *source* package ‘CoreGx’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error : in method for ‘updateObject’ with signature ‘object="CoreSet"’: arguments (‘verbose’) after ‘...’ in the generic must appear in the method, in the same place at the end of the argument list Error: unable to load R code in package ‘CoreGx’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Error : in method for ‘updateObject’ with signature ‘object="CoreSet"’: arguments (‘verbose’) after ‘...’ in the generic must appear in the method, in the same place at the end of the argument list Error: package or namespace load failed for ‘CoreGx’: unable to load R code in package ‘CoreGx’ Error: loading failed ** testing if installed package can be loaded from final location Error : in method for ‘updateObject’ with signature ‘object="CoreSet"’: arguments (‘verbose’) after ‘...’ in the generic must appear in the method, in the same place at the end of the argument list Error: package or namespace load failed for ‘CoreGx’: unable to load R code in package ‘CoreGx’ Error: loading failed Error : in method for ‘updateObject’ with signature ‘object="CoreSet"’: arguments (‘verbose’) after ‘...’ in the generic must appear in the method, in the same place at the end of the argument list Error: unable to load R code in package ‘CoreGx’ ** testing if installed package keeps a record of temporary installation path * DONE (CoreGx) Many serious errors were ignored. Plus the command returned exit code 0: hpages@XPS15:~$ echo $? 0 This is with R 4.4, that BioC 3.19 will be based on and that we only started to use recently for our daily builds. Strangely, we only see this on Linux. On Windows and Mac, we get the usual hard error, as expected. See: - https://bioconductor.org/checkResults/3.19/bioc-LATEST/CoreGx/nebbiolo1-install.html - https://bioconductor.org/checkResults/3.19/bioc-LATEST/CoreGx/palomino3-install.html - https://bioconductor.org/checkResults/3.19/bioc-LATEST/CoreGx/merida1-install.html To reproduce: library(remotes) install_git("https://git.bioconductor.org/packages/CoreGx";) Thanks, H. > sessionInfo() R Under development (unstable) (2023-10-22 r85388) Platform: x86_64-pc-linux-gnu Running under: Ubuntu 23.10 Matrix products: default BLAS: /home/hpages/R/R-4.4.r85388/lib/libRblas.so LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C time zone: America/Los_Angeles tzcode source: system (glibc) attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] remotes_2.4.2.1 loaded via a namespace (and not attached): [1] processx_3.8.2 compiler_4.4.0 R6_2.5.1 rprojroot_2.0.3 [5] cli_3.6.1 prettyunits_1.2.0 tools_4.4.0 crayon_1.5.2 [9] desc_1.4.2 callr_3.7.3 pkgbuild_1.4.2 ps_1.7.5 -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
