From m@ech|er @end|ng |rom @t@t@m@th@ethz@ch  Sat Nov  4 14:52:04 2023
From: m@ech|er @end|ng |rom @t@t@m@th@ethz@ch (Martin Maechler)
Date: Sat, 4 Nov 2023 14:52:04 +0100
Subject: [Rd] 'R CMD INSTALL' keeps going on despite serious errors,
 and returns exit code 0
In-Reply-To: <81945eb7-df8f-446d-b7e7-8f2b591807b4@gmail.com>
References: <81945eb7-df8f-446d-b7e7-8f2b591807b4@gmail.com>
Message-ID: <25926.19588.486282.861678@stat.math.ethz.ch>

>>>>> Herv? Pag?s 
>>>>>     on Fri, 3 Nov 2023 15:10:40 -0700 writes:

    > Hi list,

    > Here is an example:

    >  ??? hpages at XPS15:~$ R CMD INSTALL CoreGx ??? * installing


    > ??? hpages at 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 at 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

    > -- 
    > Herv? Pag?s

    > Bioconductor Core Team
    > hpages.on.github at gmail.com

    > [[alternative HTML version deleted]]

    > ______________________________________________
    > R-devel at r-project.org mailing list
    > https://stat.ethz.ch/mailman/listinfo/r-devel



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