Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-07-28 11:40 -0400 (Mon, 28 Jul 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 71/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
annotate 1.86.1 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the annotate package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/annotate.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. |
Package: annotate |
Version: 1.86.1 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data annotate |
StartedAt: 2025-07-27 16:07:27 -0400 (Sun, 27 Jul 2025) |
EndedAt: 2025-07-27 16:08:19 -0400 (Sun, 27 Jul 2025) |
EllapsedTime: 52.1 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data annotate ### ############################################################################## ############################################################################## * checking for file ‘annotate/DESCRIPTION’ ... OK * preparing ‘annotate’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘chromLOC.Rmd’ using rmarkdown --- finished re-building ‘chromLOC.Rmd’ --- re-building ‘useDataPkgs.Rmd’ using rmarkdown --- finished re-building ‘useDataPkgs.Rmd’ --- re-building ‘GOusage.Rnw’ using Sweave Attaching package: ‘graph’ The following object is masked from ‘package:XML’: addNode Attaching package: ‘Rgraphviz’ The following object is masked from ‘package:annotate’: toFile The following objects are masked from ‘package:IRanges’: from, to The following objects are masked from ‘package:S4Vectors’: from, to --- finished re-building ‘GOusage.Rnw’ --- re-building ‘annotate.Rnw’ using Sweave --- finished re-building ‘annotate.Rnw’ --- re-building ‘prettyOutput.Rnw’ using Sweave --- finished re-building ‘prettyOutput.Rnw’ --- re-building ‘query.Rnw’ using Sweave Error: processing vignette 'query.Rnw' failed with diagnostics: chunk 3 (label = getabsts) Error in file(file, "r") : cannot open the connection to 'https://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?tool=bioconductor&rettype=xml&retmode=text&db=PubMed&id=1939271%2c2449431%2c7729427%2c7835343%2c7836461%2c7933101%2c8121496%2c8680883%2c8764009%2c8764062' --- failed re-building ‘query.Rnw’ --- re-building ‘useProbeInfo.Rnw’ using Sweave Loading required package: org.Rn.eg.db Error: processing vignette 'useProbeInfo.Rnw' failed with diagnostics: chunk 3 (label = getACC) Error in file(con, "r") : cannot open the connection to 'https://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&rettype=fasta&id=NM_031013' --- failed re-building ‘useProbeInfo.Rnw’ SUMMARY: processing the following files failed: ‘query.Rnw’ ‘useProbeInfo.Rnw’ Error: Vignette re-building failed. In addition: Warning messages: 1: In file(file, "r") : cannot open URL 'https://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?tool=bioconductor&rettype=xml&retmode=text&db=PubMed&id=1939271%2c2449431%2c7729427%2c7835343%2c7836461%2c7933101%2c8121496%2c8680883%2c8764009%2c8764062': HTTP status was '500 Internal Server Error' 2: In file(con, "r") : cannot open URL 'https://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&rettype=fasta&id=NM_031013': HTTP status was '500 Internal Server Error' Execution halted