| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-07-28 11:40 -0400 (Mon, 28 Jul 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| 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 |
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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data annotate
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* 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