Back to Multiple platform build/check report for BioC 3.18:   simplified   long
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-02-22 11:35:45 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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 111/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.10.2  (landing page)
Aditya Bhagwat
Snapshot Date: 2024-02-21 14:05:05 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: RELEASE_3_18
git_last_commit: 230045c
git_last_commit_date: 2023-11-08 04:08:57 -0500 (Wed, 08 Nov 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

BUILD results for autonomics on nebbiolo2


To the developers/maintainers of the autonomics package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/autonomics.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: autonomics
Version: 1.10.2
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data autonomics
StartedAt: 2024-02-21 15:57:35 -0500 (Wed, 21 Feb 2024)
EndedAt: 2024-02-21 16:00:22 -0500 (Wed, 21 Feb 2024)
EllapsedTime: 166.8 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data autonomics
###
##############################################################################
##############################################################################


* checking for file ‘autonomics/DESCRIPTION’ ... OK
* preparing ‘autonomics’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘using_autonomics.Rmd’ using rmarkdown
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE161nnn/GSE161731/suppl//GSE161731_counts.csv.gz?tool=geoquery'
Content type 'application/x-gzip' length 8347405 bytes (8.0 MB)
==================================================
downloaded 8.0 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE161nnn/GSE161731/suppl//GSE161731_counts_key.csv.gz?tool=geoquery'
Content type 'application/x-gzip' length 2443 bytes
==================================================
downloaded 2443 bytes

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE161nnn/GSE161731/suppl//GSE161731_key.csv.gz?tool=geoquery'
Content type 'application/x-gzip' length 2398 bytes
==================================================
downloaded 2398 bytes

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE161nnn/GSE161731/suppl//GSE161731_xpr_nlcpm.csv.gz?tool=geoquery'
Content type 'application/x-gzip' length 16839511 bytes (16.1 MB)
==================================================
downloaded 16.1 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE161nnn/GSE161731/suppl//GSE161731_xpr_tpm_geo.txt.gz?tool=geoquery'
Content type 'application/x-gzip' length 23859414 bytes (22.8 MB)
==================================================
downloaded 22.8 MB


Quitting from lines 199-202 [unnamed-chunk-11] (using_autonomics.Rmd)
Error: processing vignette 'using_autonomics.Rmd' failed with diagnostics:
NA/NaN argument
--- failed re-building ‘using_autonomics.Rmd’

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

Error: Vignette re-building failed.
Execution halted