Help with infinite recursion - non-zero exit status in installation of GenomeInfoDbData
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Brandon ▴ 20
@9c8f3a53
Last seen 11 days ago
United States

Hello, I am trying to install GenomeInfoDb in a new renv. I am able to install BiocManager itself as well as the dependencies for some of the other packages. I am having an issue during the installation of GenomeInfoDbData specifically. I'm not sure what to make of it...any insight would be greatly appreciated.


> BiocManager::install("GenomeInfoDbData")
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    BioCsoft: https://bioconductor.org/packages/3.19/bioc
    BioCann: https://bioconductor.org/packages/3.19/data/annotation
    BioCexp: https://bioconductor.org/packages/3.19/data/experiment
    BioCworkflows: https://bioconductor.org/packages/3.19/workflows
    BioCbooks: https://bioconductor.org/packages/3.19/books
    CRAN: https://cloud.r-project.org
Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.0 (2024-04-24 ucrt)
Installing package(s) 'GenomeInfoDbData'
installing the source package 'GenomeInfoDbData'

trying URL 'https://bioconductor.org/packages/3.19/data/annotation/src/contrib/GenomeInfoDbData_1.2.12.tar.gz'
Content type 'application/x-gzip' length 12558310 bytes (12.0 MB)
downloaded 12.0 MB

Error: evaluation nested too deeply: infinite recursion / options(expressions=)?
Execution halted

The downloaded source packages are in
    'C:\Users\userName\AppData\Local\Temp\RtmpUHlYpn\downloaded_packages'
Warning message:
In install.packages(...) :
  installation of package 'GenomeInfoDbData' had non-zero exit status

My session info...


> sessionInfo()
R version 4.4.0 (2024-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] BiocManager_1.30.23

loaded via a namespace (and not attached):
[1] compiler_4.4.0 tools_4.4.0    renv_1.0.7
Install GenomeInfoDbData GenomeInfoDb • 304 views
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Entering edit mode

Hello,

As an update, I am able to install and load GenomeInfoDb successfully in a fresh renv in my WSL distro. However, I'm not sure what is wrong with my Windows installation.

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@james-w-macdonald-5106
Last seen 8 hours ago
United States

Maybe just try again?

> install("GenomeInfoDbData", force = TRUE)
'getOption("repos")' replaces
Bioconductor standard repositories,
see 'help("repositories", package =
"BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.org
Bioconductor version 3.19
  (BiocManager 1.30.23), R 4.4.0
  (2024-04-24 ucrt)
Installing package(s)
  'GenomeInfoDbData'
installing the source package 'GenomeInfoDbData'

trying URL 'https://bioconductor.org/packages/3.19/data/annotation/src/contrib/GenomeInfoDbData_1.2.12.tar.gz'
Content type 'application/x-gzip' length 12558310 bytes (12.0 MB)
downloaded 12.0 MB

* installing *source* package 'GenomeInfoDbData' ...
** using staged installation
** data
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomeInfoDbData)

The downloaded source packages are in
    'C:\Users\jmacdon\AppData\Local\Temp\RtmpIVRQJu\downloaded_packages'
Installation paths not writeable,
  unable to update packages
  path: C:/Program Files/R/R-4.4.0/library
  packages:
    KernSmooth, survival
Old packages: 'S4Arrays',
  'SparseArray'
Update all/some/none? [a/s/n]: n
> sessionInfo()
R version 4.4.0 (2024-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices
[4] utils     datasets  methods  
[7] base     

other attached packages:
[1] BiocManager_1.30.23

loaded via a namespace (and not attached):
[1] compiler_4.4.0 tools_4.4.0   
>
0
Entering edit mode

I did try again...repeatedly...I even tried it on a VM. Thankfully I got it to work on the VM.

I still can't get it to work on windows though.


> BiocManager::install("GenomeInfoDbData")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories",
package = "BiocManager")' for details.
Replacement repositories:
    BioCsoft: https://bioconductor.org/packages/3.19/bioc
    BioCann: https://bioconductor.org/packages/3.19/data/annotation
    BioCexp: https://bioconductor.org/packages/3.19/data/experiment
    BioCworkflows: https://bioconductor.org/packages/3.19/workflows
    BioCbooks: https://bioconductor.org/packages/3.19/books
    CRAN: https://cloud.r-project.org
Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.0 (2024-04-24 ucrt)
Installing package(s) 'GenomeInfoDbData'
installing the source package 'GenomeInfoDbData'

trying URL 'https://bioconductor.org/packages/3.19/data/annotation/src/contrib/GenomeInfoDbData_1.2.12.tar.gz'
Content type 'application/x-gzip' length 12558310 bytes (12.0 MB)
downloaded 12.0 MB

Error: evaluation nested too deeply: infinite recursion / options(expressions=)?
Execution halted

The downloaded source packages are in
    'C:\Users\username\AppData\Local\Temp\RtmpERhM6D\downloaded_packages'
Old packages: 'KernSmooth', 'survival'
Update all/some/none? [a/s/n]: 
n
Warning message:
In install.packages(...) :
  installation of package 'GenomeInfoDbData' had non-zero exit status
> sessionInfo()
R version 4.4.0 (2024-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.4.0      BiocManager_1.30.23 tools_4.4.0         renv_1.0.7
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Entering edit mode

How (why?) are you loading BiocManager via namespace instead of loading the library? Try attaching as normal and see if that helps.

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