From hp@ge@@on@g|thub @end|ng |rom gm@||@com  Fri Nov  3 23:37:01 2023
From: hp@ge@@on@g|thub @end|ng |rom gm@||@com (=?UTF-8?B?SGVydsOpIFBhZ8Oocw==?=)
Date: Fri, 3 Nov 2023 15:37:01 -0700
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: <0b8bc01b-5f1d-4b21-9c19-09121e35e7c5@gmail.com>

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, Herv? Pag?s wrote:
>
> Hi list,
>
> Here is an example:
>
> ??? hpages at 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 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

-- 
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
=?UTF-8?B?SGVydsOpIFBhZ8Oocw==?=