| Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-22 11:35:47 -0400 (Wed, 22 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 3444 |
| 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 1051/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
InterMine Team
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the InterMineR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/InterMineR.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: InterMineR |
| Version: 1.26.0 |
| Command: chmod a+r InterMineR -R && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data InterMineR |
| StartedAt: 2024-05-21 19:38:09 -0400 (Tue, 21 May 2024) |
| EndedAt: 2024-05-21 19:39:29 -0400 (Tue, 21 May 2024) |
| EllapsedTime: 79.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r InterMineR -R && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data InterMineR ### ############################################################################## ############################################################################## * checking for file 'InterMineR/DESCRIPTION' ... OK * preparing 'InterMineR': * checking DESCRIPTION meta-information ... OK Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:41: unexpected section header '\arguments' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:42: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:50: unexpected section header '\arguments' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:51: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:59: unexpected section header '\arguments' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:60: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:63: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:66: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:69: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:72: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:80: unexpected section header '\arguments' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:81: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:84: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:87: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:90: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:98: unexpected section header '\arguments' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:99: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:102: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:105: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:108: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:116: unexpected section header '\arguments' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:117: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:120: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:123: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:126: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:134: unexpected section header '\arguments' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:135: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:138: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:141: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:144: unknown macro '\item' Warning: F:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpyGXCnW/Rbuild42cc4483503e/InterMineR/man/ListManager-methods.Rd:147: unknown macro '\item' * installing the package to build vignettes * creating vignettes ... ERROR --- re-building 'InterMineR.Rmd' using rmarkdown Quitting from lines 173-177 [run_genepath] (InterMineR.Rmd) Error: processing vignette 'InterMineR.Rmd' failed with diagnostics: Internal Server Error (HTTP 500). Failed to query <query name="Gene_Pathway" model="genomic" view="Gene.primaryIdentifier Gene.symbol Gene.name Gene.pathways.name Gene.pathways.dataSets.name Gene.pathways.identifier Gene.organism.shortName" longDescription="For a given Gene (or List of Genes) show any associated Pathway(s) (Data Source: KEGG or REACTOME). Keywords: pathways, metabolism, cascade " sortOrder="Gene.primaryIdentifier ASC Gene.primaryIdentifier ASC Gene.primaryIdentifier ASC" constraintLogic="B and A"> <constraint path="Gene" value="pparg" code="A" op="LOOKUP" extraValue=""/> <constraint path="Gene.organism.name" value="Homo sapiens" code="B" op="=" extraValue=""/> </query> . --- failed re-building 'InterMineR.Rmd' SUMMARY: processing the following file failed: 'InterMineR.Rmd' Error: Vignette re-building failed. Execution halted