thr3ads.net - R devel - [Rd] 'R CMD INSTALL' keeps going on despite serious errors, and returns exit code 0 [Nov 2023]

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Hervé Pagès

2023-Nov-03 22:10 UTC

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

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

	[[alternative HTML version deleted]]

Hervé Pagès

2023-Nov-03 22:37 UTC

head link

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

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]]

Martin Maechler

2023-Nov-04 13:52 UTC

head link

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

>>>>> 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

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