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This page was generated on 2025-04-02 19:29 -0400 (Wed, 02 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4426
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1740/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RGSEA 1.40.0  (landing page)
Chengcheng Ma
Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025)
git_url: https://git.bioconductor.org/packages/RGSEA
git_branch: RELEASE_3_20
git_last_commit: 967e464
git_last_commit_date: 2024-10-29 09:52:48 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

BUILD results for RGSEA on nebbiolo2

To the developers/maintainers of the RGSEA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RGSEA.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: RGSEA
Version: 1.40.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 RGSEA
StartedAt: 2025-03-31 18:47:06 -0400 (Mon, 31 Mar 2025)
EndedAt: 2025-03-31 18:47:17 -0400 (Mon, 31 Mar 2025)
EllapsedTime: 11.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 RGSEA
###
##############################################################################
##############################################################################


* checking for file ‘RGSEA/DESCRIPTION’ ... OK
* preparing ‘RGSEA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘RGSEA.Rnw’ using knitr

Quitting from RGSEA.Rnw:83-87 [RGSEA-DOWNLOAD]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'colnames': error in evaluating the argument 'object' in selecting a method for function 'Table': Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Transferred a partial file [ftp.ncbi.nlm.nih.gov]: transfer closed with 80160 bytes remaining to read
---
Backtrace:
     x
  1. +-GEOquery::GDS2eSet(getGEO("GDS4100"))
  2. | +-base::grep("GSM", colnames(Table(GDS)))
  3. | | \-base::is.factor(x)
  4. | +-BiocGenerics::colnames(Table(GDS))
  5. | \-GEOquery::Table(GDS)
  6. +-GEOquery::getGEO("GDS4100")
  7. | \-GEOquery::getGEOfile(GEO, destdir = destdir, AnnotGPL = AnnotGPL)
  8. |   \-GEOquery:::downloadFile(myurl, destfile, mode)
  9. |     \-base::tryCatch(...)
 10. |       \-base (local) tryCatchList(expr, classes, parentenv, handlers)
 11. |         \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12. |           \-value[[3L]](cond)
 13. |             \-base::message(e)
 14. |               +-base::withRestarts(...)
 15. |               | \-base (local) withOneRestart(expr, restarts[[1L]])
 16. |               |   \-base (local) doWithOneRestart(return(expr), restart)
 17. |               \-base::signalCondition(cond)
 18. +-base (local) `<fn>`(`<httr2_fl>`)
 19. \-base::.handleSimpleError(...)
 20.   \-base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'RGSEA.Rnw' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'colnames': error in evaluating the argument 'object' in selecting a method for function 'Table': Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Transferred a partial file [ftp.ncbi.nlm.nih.gov]: transfer closed with 80160 bytes remaining to read
--- failed re-building ‘RGSEA.Rnw’

SUMMARY: processing the following file failed:
  ‘RGSEA.Rnw’

Error: Vignette re-building failed.
Execution halted