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This page was generated on 2022-03-18 11:07:10 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R 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

BUILD results for ChIPpeakAnno on riesling1


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.

raw results

Package 300/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.29.4  (landing page)
Jianhong Ou
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/ChIPpeakAnno
git_branch: master
git_last_commit: 84091f2
git_last_commit_date: 2022-02-04 15:03:54 -0400 (Fri, 04 Feb 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  skipped
riesling1Windows Server 2019 Standard / x64  OK    ERROR  skippedskipped
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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