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Package 100/553HostnameOS / ArchBUILDCHECKBUILD BIN
ChIPpeakAnno 2.4.0
Lihua Julie Zhu
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/ChIPpeakAnno
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK [ WARNINGS ] OK 

Summary

Package: ChIPpeakAnno
Version: 2.4.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChIPpeakAnno_2.4.0.tar.gz
StartedAt: 2012-09-23 23:40:14 -0700 (Sun, 23 Sep 2012)
EndedAt: 2012-09-23 23:45:02 -0700 (Sun, 23 Sep 2012)
EllapsedTime: 287.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/ChIPpeakAnno.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ChIPpeakAnno/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPpeakAnno' version '2.4.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'ChIPpeakAnno' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.4Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotatePeakInBatch: warning in getAnnotation(mart, feature =
  featureType): partial argument match of 'feature' to 'featureType'
getAnnotation: warning in getBM(c("ensembl_gene_id", "chromosome_name",
  "start_position", "end_position", "strand", "description",
  "gene_biotype"), filter = c("biotype"), values = "miRNA", mart =
  mart): partial argument match of 'filter' to 'filters'
peaksNearBDP: warning in getAnnotation(mart, feature = "TSS"): partial
  argument match of 'feature' to 'featureType'
* checking Rd files ... NOTE
prepare_Rd: BED2RangedData.Rd:15-17: Dropping empty section \details
prepare_Rd: BED2RangedData.Rd:22: Dropping empty section \references
prepare_Rd: BED2RangedData.Rd:27: Dropping empty section \seealso
prepare_Rd: ExonPlusUtr.human.GRCh37.Rd:28-30: Dropping empty section \source
prepare_Rd: ExonPlusUtr.human.GRCh37.Rd:31-32: Dropping empty section \references
prepare_Rd: GFF2RangedData.Rd:15-17: Dropping empty section \details
prepare_Rd: GFF2RangedData.Rd:22: Dropping empty section \references
prepare_Rd: GFF2RangedData.Rd:27: Dropping empty section \seealso
prepare_Rd: Peaks.Ste12.Replicate1.Rd:14-16: Dropping empty section \details
prepare_Rd: Peaks.Ste12.Replicate1.Rd:17-18: Dropping empty section \source
prepare_Rd: Peaks.Ste12.Replicate2.Rd:14-16: Dropping empty section \details
prepare_Rd: Peaks.Ste12.Replicate3.Rd:14-16: Dropping empty section \details
prepare_Rd: TSS.human.GRCh37.Rd:25-27: Dropping empty section \source
prepare_Rd: TSS.human.GRCh37.Rd:28-29: Dropping empty section \references
prepare_Rd: TSS.human.NCBI36.Rd:26-28: Dropping empty section \source
prepare_Rd: TSS.human.NCBI36.Rd:29-30: Dropping empty section \references
prepare_Rd: TSS.mouse.NCBIM37.Rd:26-28: Dropping empty section \source
prepare_Rd: TSS.mouse.NCBIM37.Rd:29-30: Dropping empty section \references
prepare_Rd: TSS.rat.RGSC3.4.Rd:25-27: Dropping empty section \source
prepare_Rd: TSS.rat.RGSC3.4.Rd:28-29: Dropping empty section \references
prepare_Rd: TSS.zebrafish.Zv8.Rd:26-28: Dropping empty section \source
prepare_Rd: TSS.zebrafish.Zv8.Rd:29-31: Dropping empty section \references
prepare_Rd: addAncestors.Rd:23-25: Dropping empty section \details
prepare_Rd: addAncestors.Rd:34-36: Dropping empty section \note
prepare_Rd: addAncestors.Rd:29-30: Dropping empty section \references
prepare_Rd: addAncestors.Rd:38-40: Dropping empty section \seealso
prepare_Rd: addGeneIDs.Rd:67-68: Dropping empty section \note
prepare_Rd: addGeneIDs.Rd:70-72: Dropping empty section \seealso
prepare_Rd: annotatePeakInBatch.Rd:31-32: Dropping empty section \details
prepare_Rd: annotatePeakInBatch.Rd:48-49: Dropping empty section \note
prepare_Rd: annotatedPeak.Rd:26-28: Dropping empty section \source
prepare_Rd: annotatedPeak.Rd:29-31: Dropping empty section \references
prepare_Rd: condenseMatrixByColnames.Rd:19-21: Dropping empty section \details
prepare_Rd: condenseMatrixByColnames.Rd:30-31: Dropping empty section \note
prepare_Rd: condenseMatrixByColnames.Rd:25-26: Dropping empty section \references
prepare_Rd: condenseMatrixByColnames.Rd:33-35: Dropping empty section \seealso
prepare_Rd: convert2EntrezID.Rd:20-22: Dropping empty section \details
prepare_Rd: convert2EntrezID.Rd:31-32: Dropping empty section \note
prepare_Rd: convert2EntrezID.Rd:26-27: Dropping empty section \references
prepare_Rd: convert2EntrezID.Rd:34-36: Dropping empty section \seealso
prepare_Rd: countPatternInSeqs.Rd:22-24: Dropping empty section \details
prepare_Rd: countPatternInSeqs.Rd:34-36: Dropping empty section \note
prepare_Rd: countPatternInSeqs.Rd:28-30: Dropping empty section \references
prepare_Rd: enrichedGO.Rd:79-81: Dropping empty section \details
prepare_Rd: enrichedGO.Rd:88-90: Dropping empty section \note
prepare_Rd: enrichedGO.Rd:82-83: Dropping empty section \source
prepare_Rd: enrichedGO.Rd:84-86: Dropping empty section \references
prepare_Rd: findOverlappingPeaks.Rd:53-55: Dropping empty section \note
prepare_Rd: findVennCounts.Rd:29-31: Dropping empty section \details
prepare_Rd: findVennCounts.Rd:37-39: Dropping empty section \references
prepare_Rd: findVennCounts.Rd:58-59: Dropping empty section \examples
prepare_Rd: getAllPeakSequence.Rd:20-22: Dropping empty section \details
prepare_Rd: getAllPeakSequence.Rd:31-34: Dropping empty section \note
prepare_Rd: getAllPeakSequence.Rd:35: Dropping empty section \seealso
prepare_Rd: getAnnotation.Rd:17-19: Dropping empty section \details
prepare_Rd: getAnnotation.Rd:31: Dropping empty section \seealso
prepare_Rd: getEnrichedGO.Rd:22-23: Dropping empty section \details
prepare_Rd: getEnrichedGO.Rd:92-95: Dropping empty section \note
prepare_Rd: getGeneSeq.Rd:15-17: Dropping empty section \details
prepare_Rd: getGeneSeq.Rd:26: Dropping empty section \references
prepare_Rd: getGeneSeq.Rd:31: Dropping empty section \seealso
prepare_Rd: getUniqueGOidCount.Rd:15-17: Dropping empty section \details
prepare_Rd: getUniqueGOidCount.Rd:23: Dropping empty section \references
prepare_Rd: makeVennDiagram.Rd:36-38: Dropping empty section \details
prepare_Rd: makeVennDiagram.Rd:47-49: Dropping empty section \note
prepare_Rd: makeVennDiagram.Rd:42-43: Dropping empty section \references
prepare_Rd: myPeakList.Rd:14-15: Dropping empty section \details
prepare_Rd: myPeakList.Rd:19-20: Dropping empty section \references
prepare_Rd: peaksNearBDP.Rd:21-22: Dropping empty section \details
prepare_Rd: peaksNearBDP.Rd:52-53: Dropping empty section \note
prepare_Rd: summarizePatternInPeaks.Rd:36-38: Dropping empty section \details
prepare_Rd: summarizePatternInPeaks.Rd:48-50: Dropping empty section \note
prepare_Rd: summarizePatternInPeaks.Rd:42-44: Dropping empty section \references
prepare_Rd: summarizePatternInPeaks.Rd:54-56: Dropping empty section \seealso
prepare_Rd: translatePattern.Rd:21-23: Dropping empty section \details
prepare_Rd: translatePattern.Rd:33-35: Dropping empty section \note
prepare_Rd: translatePattern.Rd:27-29: Dropping empty section \references
prepare_Rd: write2FASTA.Rd:17-18: Dropping empty section \details
prepare_Rd: write2FASTA.Rd:24-26: Dropping empty section \note
prepare_Rd: write2FASTA.Rd:22: Dropping empty section \references
prepare_Rd: write2FASTA.Rd:27: Dropping empty section \seealso
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'writeFASTA' is deprecated.
  Warning: 'writeFASTA' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.10-bioc/meat/ChIPpeakAnno.Rcheck/00check.log'
for details.

ChIPpeakAnno.Rcheck/00install.out:

* installing *source* package 'ChIPpeakAnno' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'space' when loading 'IRanges'
** help
*** installing help indices
** building package indices
** installing vignettes
   'ChIPpeakAnno.Rnw' 
** testing if installed package can be loaded
Warning: replacing previous import 'space' when loading 'IRanges'

* DONE (ChIPpeakAnno)

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings:

nameusersystemelapsed
BED2RangedData0.0470.0000.048
ChIPpeakAnno-package0.0030.0000.003
ExonPlusUtr.human.GRCh377.1870.1897.409
GFF2RangedData0.0240.0000.025
Peaks.Ste12.Replicate10.0380.0040.041
Peaks.Ste12.Replicate20.0800.0030.083
Peaks.Ste12.Replicate30.0300.0020.032
TSS.human.GRCh370.3290.0110.340
TSS.human.NCBI360.5130.0190.533
TSS.mouse.NCBIM370.2130.0130.227
TSS.rat.RGSC3.40.1700.0100.182
TSS.zebrafish.Zv80.1580.0080.167
addAncestors2.6000.2062.814
addGeneIDs1.3930.0421.437
annotatePeakInBatch0.0030.0000.004
annotatedPeak0.2160.0450.262
condenseMatrixByColnames0.0360.0000.035
convert2EntrezID0.5850.0150.601
countPatternInSeqs0.0970.0020.100
enrichedGO0.0030.0010.004
findOverlappingPeaks0.0010.0000.002
getAllPeakSequence0.6030.0260.657
getAnnotation0.0010.0000.000
getEnrichedGO0.0170.0020.020
getEnrichedPATH0.0010.0000.000
getGeneSeq0.0010.0000.002
getUniqueGOidCount0.0010.0010.002
hyperGtest0.0020.0010.002
makeVennDiagram0.0020.0000.002
myPeakList0.0380.0020.041
peaksNearBDP0.0000.0000.001
summarizePatternInPeaks0.4690.0300.506
translatePattern0.0000.0000.001
write2FASTA0.0690.0000.071