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This page was generated on 2025-11-12 11:32 -0500 (Wed, 12 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4823
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Package 882/2325HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
glmGamPoi 1.23.0  (landing page)
Constantin Ahlmann-Eltze
Snapshot Date: 2025-11-11 13:40 -0500 (Tue, 11 Nov 2025)
git_url: https://git.bioconductor.org/packages/glmGamPoi
git_branch: devel
git_last_commit: 23ac45d
git_last_commit_date: 2025-10-29 10:58:15 -0500 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped

BUILD results for glmGamPoi on nebbiolo1

To the developers/maintainers of the glmGamPoi package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/glmGamPoi.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: glmGamPoi
Version: 1.23.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data glmGamPoi
StartedAt: 2025-11-11 17:53:43 -0500 (Tue, 11 Nov 2025)
EndedAt: 2025-11-11 18:00:34 -0500 (Tue, 11 Nov 2025)
EllapsedTime: 411.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data glmGamPoi
###
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##############################################################################


* checking for file ‘glmGamPoi/DESCRIPTION’ ... OK
* preparing ‘glmGamPoi’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘glmGamPoi.Rmd’ using rmarkdown

Quitting from glmGamPoi.Rmd:82-91 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! SSL connect error [bioconductor.org]:
OpenSSL SSL_connect: SSL_ERROR_SYSCALL in connection to bioconductor.org:443 
  Consider rerunning with 'localHub=TRUE'
---
Backtrace:
    ▆
 1. └─TENxPBMCData::TENxPBMCData("pbmc4k")
 2.   └─ExperimentHub::ExperimentHub()
 3.     └─AnnotationHub::.Hub(...)
 4.       └─base::tryCatch(...)
 5.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 6.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7.             └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'glmGamPoi.Rmd' failed with diagnostics:
failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! SSL connect error [bioconductor.org]:
OpenSSL SSL_connect: SSL_ERROR_SYSCALL in connection to bioconductor.org:443 
  Consider rerunning with 'localHub=TRUE'
--- failed re-building ‘glmGamPoi.Rmd’

--- re-building ‘pseudobulk.Rmd’ using rmarkdown

warning: solve(): system is singular (rcond: 1.52504e-16); attempting approx solution

warning: solve(): system is singular (rcond: 2.17067e-16); attempting approx solution

warning: solve(): system is singular (rcond: 3.13372e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.30132e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.362e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.38378e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.3915e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.39407e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.39501e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.39538e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.39554e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.39561e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.39564e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.50859e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.70721e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.89268e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.95944e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.98135e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.98845e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.99102e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.99205e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.99248e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.99268e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.99276e-17); attempting approx solution
--- finished re-building ‘pseudobulk.Rmd’

SUMMARY: processing the following file failed:
  ‘glmGamPoi.Rmd’

Error: Vignette re-building failed.
Execution halted