| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-24 11:39 -0400 (Wed, 24 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4284 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
| 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 69/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| annotate 1.83.0 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | 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: 1.83.0 |
| Command: chmod a+r annotate -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data annotate |
| StartedAt: 2024-07-23 16:52:10 -0400 (Tue, 23 Jul 2024) |
| EndedAt: 2024-07-23 16:54:09 -0400 (Tue, 23 Jul 2024) |
| EllapsedTime: 119.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### chmod a+r annotate -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe 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
texify: major issue: So far, you have not checked for updates as a MiKTeX user.
--- finished re-building 'GOusage.Rnw'
--- re-building 'annotate.Rnw' using Sweave
texify: major issue: So far, you have not checked for updates as a MiKTeX user.
--- finished re-building 'annotate.Rnw'
--- re-building 'prettyOutput.Rnw' using Sweave
texify: major issue: So far, you have not checked for updates as a MiKTeX user.
--- finished re-building 'prettyOutput.Rnw'
--- re-building 'query.Rnw' using Sweave
Read 4 items
Error: processing vignette 'query.Rnw' failed with diagnostics:
chunk 6
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=gene&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
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: 'Biostrings'
The following object is masked from 'package:grid':
pattern
The following object is masked from 'package:graph':
complement
The following object is masked from 'package:base':
strsplit
texify: major issue: So far, you have not checked for updates as a MiKTeX user.
--- finished re-building 'useProbeInfo.Rnw'
SUMMARY: processing the following file failed:
'query.Rnw'
Error: Vignette re-building failed.
In addition: Warning message:
In file(file, "r") :
cannot open URL 'https://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?tool=bioconductor&rettype=xml&retmode=text&db=gene&id=1939271%2c2449431%2c7729427%2c7835343%2c7836461%2c7933101%2c8121496%2c8680883%2c8764009%2c8764062': HTTP status was '400 Bad Request'
Execution halted