Forgot to mention that the package actually got installed, but is unloadable (not surprisingly):
> "CoreGx" %in% rownames(installed.packages()) [1] TRUE > suppressWarnings(suppressMessages(library(CoreGx))) 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’ Best, H. On 11/3/23 15:10, Hervé Pagès wrote: > > 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 -- 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