From hp@ge@@on@g|thub @end|ng |rom gm@||@com  Sat Nov  4 18:11:24 2023
From: hp@ge@@on@g|thub @end|ng |rom gm@||@com (=?UTF-8?B?SGVydsOpIFBhZ8Oocw==?=)
Date: Sat, 4 Nov 2023 10:11:24 -0700
Subject: [Rd] 'R CMD INSTALL' keeps going on despite serious errors,
 and returns exit code 0
In-Reply-To: <25926.19588.486282.861678@stat.math.ethz.ch>
References: <81945eb7-df8f-446d-b7e7-8f2b591807b4@gmail.com>
 <25926.19588.486282.861678@stat.math.ethz.ch>
Message-ID: <86ad51b1-6736-4e02-a25e-18041eaafdc1@gmail.com>

I see. We'll update soon. Thanks Martin.

On 11/4/23 06:52, Martin Maechler wrote:
>>>>>> 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

-- 
Herv? Pag?s

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

	[[alternative HTML version deleted]]



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