[Rd] 'R CMD INSTALL' keeps going on despite serious errors, and returns exit code 0

[Hervé Pagès]

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 using 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 using 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.github using gmail.com

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

	[[alternative HTML version deleted]]