I see. We'll update soon. Thanks Martin. On 11/4/23 06:52, Martin Maechler wrote: >>>>>> Hervé Pagès >>>>>> on Fri, 3 Nov 2023 15:10:40 -0700 writes: > > Hi list, > > > Here is an example: > > > hpages@XPS15:~$ R CMD INSTALL CoreGx * installing > > > > hpages@XPS15:~$ R CMD INSTALL CoreGx > > * installing to library ‘/home/hpages/R/R-4.4.r85388/site-library’ > ^^^^^^^ > > Yes, this was bad behavior was the case for a short time (too > long, my fault !!) in R-devel. > > But that, svn rev 85388 , was *long* ago (close to 2 weeks): > Current R-devel is 85471 > (The bug was "only" in 382--388, fixed in 389 -- you were really unlucky!) > > Still, I'm sorry that you were accidentally affected, too. > Martin > > > > * 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
-- 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