Package: ChIPpeakAnno

Version: 2.7.3

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_2.7.3.tar.gz

StartedAt: 2013-03-25 00:41:44 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:49:51 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 487.2 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPpeakAnno.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPpeakAnno’ version ‘2.7.3’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ChIPpeakAnno’ can be installed ... [42s/42s] 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 DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... OK
* checking Rd files ... NOTE
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:16-18: Dropping empty section \details
prepare_Rd: GFF2RangedData.Rd:23: Dropping empty section \references
prepare_Rd: GFF2RangedData.Rd:28: 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: 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: assignChromosomeRegion.Rd:45-47: Dropping empty section \details
prepare_Rd: assignChromosomeRegion.Rd:61-62: Dropping empty section \note
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:59-61: Dropping empty section \note
prepare_Rd: findVennCounts.Rd:31-33: Dropping empty section \details
prepare_Rd: findVennCounts.Rd:39-41: Dropping empty section \references
prepare_Rd: findVennCounts.Rd:60-61: 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:44-46: Dropping empty section \note
prepare_Rd: makeVennDiagram.Rd:39-40: 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [57s/62s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
ExonPlusUtr.human.GRCh37 15.069  0.252  16.086
addAncestors              9.792  0.192  10.597
addGeneIDs                4.661  0.056   7.342
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.

* installing *source* package ‘ChIPpeakAnno’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘ChIPpeakAnno.Rnw’ 
** testing if installed package can be loaded
* DONE (ChIPpeakAnno)

name	user	system	elapsed
BED2RangedData	0.148	0.000	0.161
ChIPpeakAnno-package	0.084	0.008	0.093
ExonPlusUtr.human.GRCh37	15.069	0.252	16.086
GFF2RangedData	0.060	0.004	0.158
Peaks.Ste12.Replicate1	0.044	0.012	0.053
Peaks.Ste12.Replicate2	0.028	0.012	0.042
Peaks.Ste12.Replicate3	0.048	0.012	0.059
TSS.human.GRCh37	0.232	0.004	0.234
TSS.human.NCBI36	0.280	0.004	0.283
TSS.mouse.NCBIM37	0.320	0.016	0.338
TSS.rat.RGSC3.4	0.148	0.004	0.155
TSS.zebrafish.Zv8	0.136	0.016	0.165
addAncestors	9.792	0.192	10.597
addGeneIDs	4.661	0.056	7.342
annotatePeakInBatch	0.052	0.008	0.061
annotatedPeak	0.324	0.024	0.345
assignChromosomeRegion	0.012	0.000	0.014
condenseMatrixByColnames	0.056	0.000	0.056
convert2EntrezID	0.640	0.000	0.643
countPatternInSeqs	0.152	0.004	0.155
enrichedGO	0.012	0.004	0.015
findOverlappingPeaks	0.016	0.000	0.016
getAllPeakSequence	1.016	0.028	1.059
getAnnotation	0.004	0.008	0.012
getEnrichedGO	0.048	0.008	0.055
getEnrichedPATH	0.056	0.000	0.054
getGeneSeq	0.060	0.004	0.064
getUniqueGOidCount	0.056	0.000	0.055
hyperGtest	0.016	0.000	0.013
makeVennDiagram	0.016	0.000	0.018
myPeakList	0.044	0.000	0.043
peaksNearBDP	0.040	0.012	0.052
summarizePatternInPeaks	0.988	0.016	1.005
translatePattern	0.052	0.000	0.053
write2FASTA	0.140	0.000	0.141