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

[Hervé Pagès]

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 using XPS15:~$ R CMD INSTALL CoreGx     * installing
>
>
>      >     hpages using 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 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
>
>      > [[alternative HTML version deleted]]
>
>      > ______________________________________________
>      >R-devel using r-project.org  mailing list
>      >https://stat.ethz.ch/mailman/listinfo/r-devel

-- 
Hervé Pagès

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

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