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

[Martin Maechler]

>>>>> 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]]

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