Re: [Rd] 'R CMD INSTALL' keeps going on despite serious errors, and returns exit code 0
I see. We'll update soon. Thanks Martin.
On 11/4/23 06:52, Martin Maechler wrote:
>> Hervé Pagès
>> on Fri, 3 Nov 2023 15:10:40 -0700 writes:
> > Hi list,
>
> > Here is an example:
>
> > hpages@XPS15:~$ R CMD INSTALL CoreGx * installing
>
>
> > hpages@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@XPS15:~$ echo $?
> > 0
>
> > This is with R 4.4, that BioC 3.19 will be based on and that we only
> > started to use recently for our daily builds.
>
> > Strangely, we only see this on Linux. On Windows and Mac, we get the
> > usual hard error, as expected. See:
>
> > -
>
> >https://bioconductor.org/checkResults/3.19/bioc-LATEST/CoreGx/nebbiolo1-install.html
>
> > -
>
> >https://bioconductor.org/checkResults/3.19/bioc-LATEST/CoreGx/palomino3-install.html
>
> > -
>
> >https://bioconductor.org/checkResults/3.19/bioc-LATEST/CoreGx/merida1-install.html
>
> > To reproduce:
>
> > library(remotes)
> > install_git("https://git.bioconductor.org/packages/CoreGx;)
>
> > Thanks,
>
> > H.
>
> >> sessionInfo()
> > R Under development (unstable) (2023-10-22 r85388)
> > Platform: x86_64-pc-linux-gnu
> > Running under: Ubuntu 23.10
>
> > Matrix products: default
> > BLAS: /home/hpages/R/R-4.4.r85388/lib/libRblas.so
> > LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
>
> > locale:
> > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> > [9] LC_ADDRESS=C LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> > time zone: America/Los_Angeles
> > tzcode source: system (glibc)
>
> > attached base packages:
> > [1] stats graphics grDevices utils datasets methods base
>
> > other attached packages:
> > [1] remotes_2.4.2.1
>
> > loaded via a namespace (and not attached):
> > [1] processx_3.8.2 compiler_4.4.0 R6_2.5.1 rprojroot_2.0.3
> > [5] cli_3.6.1 prettyunits_1.2.0 tools_4.4.0 crayon_1.5.2
> > [9] desc_1.4.2 callr_3.7.3
Re: [Rd] 'R CMD INSTALL' keeps going on despite serious errors, and returns exit code 0
> Hervé Pagès
> on Fri, 3 Nov 2023 15:10:40 -0700 writes:
> Hi list,
> Here is an example:
> hpages@XPS15:~$ R CMD INSTALL CoreGx * installing
> hpages@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@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.git...@gmail.com
> [[alternative HTML version deleted]]
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
__
R-devel@r-project.org mailing
Re: [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, Hervé Pagès wrote:
>
> Hi list,
>
> Here is an example:
>
> hpages@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@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.git...@gmail.com
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
[[alternative HTML version deleted]]
__
R-devel@r-project.org mailing list
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[Rd] 'R CMD INSTALL' keeps going on despite serious errors, and returns exit code 0
Hi list,
Here is an example:
hpages@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@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.git...@gmail.com
[[alternative HTML version deleted]]
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