>>>>> 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
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