Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:07:10 -0400 (Fri, 18 Mar 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
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 |
To the developers/maintainers of the ChIPpeakAnno package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPpeakAnno.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 300/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChIPpeakAnno 3.29.4 (landing page) Jianhong Ou
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
riesling1 | Windows Server 2019 Standard / x64 | OK | ERROR | skipped | skipped | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | ERROR | skipped | skipped | |||||||||
Package: ChIPpeakAnno |
Version: 3.29.4 |
Command: chmod a+r ChIPpeakAnno -R && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data ChIPpeakAnno |
StartedAt: 2022-03-17 16:34:07 -0400 (Thu, 17 Mar 2022) |
EndedAt: 2022-03-17 16:39:24 -0400 (Thu, 17 Mar 2022) |
EllapsedTime: 316.7 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r ChIPpeakAnno -R && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data ChIPpeakAnno ### ############################################################################## ############################################################################## * checking for file 'ChIPpeakAnno/DESCRIPTION' ... OK * preparing 'ChIPpeakAnno': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building 'ChIPpeakAnno.Rmd' using rmarkdown duplicated or NA names found. Rename all the names by numbers. If you are importing files downloaded from ensembl, it will be better to import the files into a TxDb object, and then convert to GRanges by toGRanges. Here is the sample code: library(GenomicFeatures) txdb <- makeTxDbFromGFF('D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpS28Vum/Rinst31f83b8a6c0d/ChIPpeakAnno/extdata/GFF_peaks.gff') anno <- toGRanges(txdb, format='gene') duplicated or NA names found. Rename all the names by numbers. Missing totalTest! totalTest is required for HyperG test. If totalTest is missing, pvalue will be calculated by estimating the total binding sites of encoding region of human. totalTest = humanGenomeSize * (2%(codingDNA) + 1%(regulationRegion)) / ( 2 * averagePeakWidth ) = 3.3e+9 * 0.03 / ( 2 * averagePeakWidth) = 5e+7 /averagePeakWidth Warning in (function (seqlevels, genome, new_style) : cannot switch some of GRCh37's seqlevels from NCBI to UCSC style Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene 403 genes were dropped because they have exons located on both strands of the same reference sequence or on more than one reference sequence, so cannot be represented by a single genomic range. Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList object, or use suppressMessages() to suppress this message. --- finished re-building 'ChIPpeakAnno.Rmd' --- re-building 'FAQs.Rmd' using rmarkdown --- finished re-building 'FAQs.Rmd' --- re-building 'pipeline.Rmd' using rmarkdown If you are importing files downloaded from ensembl, it will be better to import the files into a TxDb object, and then convert to GRanges by toGRanges. Here is the sample code: library(GenomicFeatures) txdb <- makeTxDbFromGFF('D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpS28Vum/Rinst31f83b8a6c0d/ChIPpeakAnno/extdata/GFF_peaks.gff') anno <- toGRanges(txdb, format='gene') duplicated or NA names found. Rename all the names by numbers. Missing totalTest! totalTest is required for HyperG test. If totalTest is missing, pvalue will be calculated by estimating the total binding sites of encoding region of human. totalTest = humanGenomeSize * (2%(codingDNA) + 1%(regulationRegion)) / ( 2 * averagePeakWidth ) = 3.3e+9 * 0.03 / ( 2 * averagePeakWidth) = 5e+7 /averagePeakWidth 403 genes were dropped because they have exons located on both strands of the same reference sequence or on more than one reference sequence, so cannot be represented by a single genomic range. Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList object, or use suppressMessages() to suppress this message. Annotate peaks by annoPeaks, see ?annoPeaks for details. maxgap will be ignored. Quitting from lines 163-173 (pipeline.Rmd) Error: processing vignette 'pipeline.Rmd' failed with diagnostics: unimplemented type 'list' in 'EncodeElement' --- failed re-building 'pipeline.Rmd' --- re-building 'quickStart.Rmd' using rmarkdown 403 genes were dropped because they have exons located on both strands of the same reference sequence or on more than one reference sequence, so cannot be represented by a single genomic range. Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList object, or use suppressMessages() to suppress this message. Annotate peaks by annoPeaks, see ?annoPeaks for details. maxgap will be ignored. Annotate peaks by annoPeaks, see ?annoPeaks for details. maxgap will be ignored. --- finished re-building 'quickStart.Rmd' SUMMARY: processing the following file failed: 'pipeline.Rmd' Error: Vignette re-building failed. In addition: Warning messages: 1: In formatStrand(strand) : All the characters for strand, other than '1', '-1', '+', '-' and '*', will be converted into '*'. 2: In formatStrand(strand) : All the characters for strand, other than '1', '-1', '+', '-' and '*', will be converted into '*'. 3: In formatStrand(strand) : All the characters for strand, other than '1', '-1', '+', '-' and '*', will be converted into '*'. 4: In (function (seqlevels, genome, new_style) : cannot switch some of GRCh37's seqlevels from NCBI to UCSC style Execution halted