BioC 3.3: CHECK report for ChIPpeakAnno on windows2.bioconductor.org

Package: ChIPpeakAnno

Version: 3.5.0

Command: rm -rf ChIPpeakAnno.buildbin-libdir ChIPpeakAnno.Rcheck && mkdir ChIPpeakAnno.buildbin-libdir ChIPpeakAnno.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPpeakAnno.buildbin-libdir ChIPpeakAnno_3.5.0.tar.gz >ChIPpeakAnno.Rcheck\00install.out 2>&1 && cp ChIPpeakAnno.Rcheck\00install.out ChIPpeakAnno-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=ChIPpeakAnno.buildbin-libdir --install="check:ChIPpeakAnno-install.out" --force-multiarch --no-vignettes --timings ChIPpeakAnno_3.5.0.tar.gz

StartedAt: 2015-10-27 01:15:46 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:22:07 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 380.9 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPpeakAnno.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf ChIPpeakAnno.buildbin-libdir ChIPpeakAnno.Rcheck && mkdir ChIPpeakAnno.buildbin-libdir ChIPpeakAnno.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPpeakAnno.buildbin-libdir ChIPpeakAnno_3.5.0.tar.gz >ChIPpeakAnno.Rcheck\00install.out 2>&1 && cp ChIPpeakAnno.Rcheck\00install.out ChIPpeakAnno-install.out  && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=ChIPpeakAnno.buildbin-libdir --install="check:ChIPpeakAnno-install.out" --force-multiarch --no-vignettes --timings ChIPpeakAnno_3.5.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/ChIPpeakAnno.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChIPpeakAnno/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPpeakAnno' version '3.5.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'grid' 'IRanges' 'Biostrings' 'GenomicRanges' 'S4Vectors'
  'VennDiagram'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 whether package 'ChIPpeakAnno' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 18.2Mb
  sub-directories of 1Mb or more:
    data     12.7Mb
    extdata   4.7Mb
* checking package directory ... OK
* checking 'build' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [24s] OK
** running examples for arch 'x64' ... [27s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [48s]
 [48s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [50s]
 [50s] OK
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'c:/biocbld/bbs-3.3-bioc/meat/ChIPpeakAnno.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'ChIPpeakAnno' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'ChIPpeakAnno' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChIPpeakAnno' as ChIPpeakAnno_3.5.0.zip
* DONE (ChIPpeakAnno)

name	user	system	elapsed
BED2RangedData	0.04	0.00	0.03
ChIPpeakAnno-package	0.01	0.00	0.01
ExonPlusUtr.human.GRCh37	3.69	0.16	3.85
GFF2RangedData	0.01	0.00	0.01
HOT.spots	0.47	0.01	0.49
Peaks.Ste12.Replicate1	0.02	0.00	0.02
Peaks.Ste12.Replicate2	0.03	0.00	0.03
Peaks.Ste12.Replicate3	0.02	0.00	0.02
TSS.human.GRCh37	0.15	0.00	0.15
TSS.human.GRCh38	0.45	0.00	0.45
TSS.human.NCBI36	0.16	0.00	0.16
TSS.mouse.GRCm38	0.13	0.00	0.13
TSS.mouse.NCBIM37	0.10	0.03	0.13
TSS.rat.RGSC3.4	0.09	0.02	0.11
TSS.rat.Rnor_5.0	0.1	0.0	0.1
TSS.zebrafish.Zv8	0.06	0.04	0.10
TSS.zebrafish.Zv9	0.17	0.00	0.18
addAncestors	1.35	0.10	1.43
addGeneIDs	1.70	0.25	1.96
annoGR	0	0	0
annotatePeakInBatch	0.86	0.06	0.92
annotatedPeak	0.09	0.00	0.09
assignChromosomeRegion	0	0	0
binOverFeature	0.35	0.00	0.34
condenseMatrixByColnames	0.01	0.00	0.01
convert2EntrezID	0.31	0.02	0.33
countPatternInSeqs	0.1	0.0	0.1
egOrgMap	0	0	0
enrichedGO	0	0	0
featureAlignedDistribution	0.84	0.00	0.84
featureAlignedHeatmap	0.96	0.00	0.95
featureAlignedSignal	0.80	0.03	0.83
findOverlappingPeaks	0	0	0
findOverlapsOfPeaks	0.44	0.00	0.43
getAllPeakSequence	0.48	0.03	0.63
getAnnotation	0	0	0
getEnrichedGO	0.02	0.00	0.01
getEnrichedPATH	0.01	0.00	0.02
getGeneSeq	0	0	0
getUniqueGOidCount	0	0	0
getVennCounts	0	0	0
hyperGtest	0	0	0
makeVennDiagram	0.02	0.00	0.02
mergePlusMinusPeaks	0	0	0
myPeakList	0.03	0.03	0.06
peakPermTest	0	0	0
peaksNearBDP	0	0	0
pie1	0.01	0.00	0.01
preparePool	0	0	0
summarizePatternInPeaks	0.46	0.00	0.46
toGRanges	0.02	0.00	0.02
translatePattern	0	0	0
wgEncodeTfbsV3	0.25	0.00	0.25
write2FASTA	0	0	0

name	user	system	elapsed
BED2RangedData	0.03	0.00	0.03
ChIPpeakAnno-package	0	0	0
ExonPlusUtr.human.GRCh37	3.83	0.03	3.86
GFF2RangedData	0.01	0.00	0.01
HOT.spots	0.13	0.00	0.12
Peaks.Ste12.Replicate1	0.03	0.00	0.03
Peaks.Ste12.Replicate2	0.03	0.00	0.04
Peaks.Ste12.Replicate3	0.02	0.00	0.01
TSS.human.GRCh37	0.17	0.00	0.17
TSS.human.GRCh38	0.8	0.0	0.8
TSS.human.NCBI36	0.26	0.01	0.28
TSS.mouse.GRCm38	0.63	0.00	0.62
TSS.mouse.NCBIM37	0.09	0.00	0.10
TSS.rat.RGSC3.4	0.08	0.02	0.09
TSS.rat.Rnor_5.0	0.08	0.00	0.08
TSS.zebrafish.Zv8	0.07	0.00	0.08
TSS.zebrafish.Zv9	0.1	0.0	0.1
addAncestors	1.36	0.10	1.45
addGeneIDs	2.11	0.28	2.39
annoGR	0	0	0
annotatePeakInBatch	0.88	0.08	0.96
annotatedPeak	0.14	0.00	0.14
assignChromosomeRegion	0	0	0
binOverFeature	0.54	0.03	0.57
condenseMatrixByColnames	0.03	0.00	0.03
convert2EntrezID	0.57	0.00	0.58
countPatternInSeqs	0.14	0.00	0.14
egOrgMap	0.02	0.00	0.02
enrichedGO	0	0	0
featureAlignedDistribution	1.12	0.00	1.12
featureAlignedHeatmap	1.19	0.00	1.19
featureAlignedSignal	1.31	0.01	1.33
findOverlappingPeaks	0.02	0.00	0.01
findOverlapsOfPeaks	0.79	0.02	0.82
getAllPeakSequence	0.61	0.01	0.62
getAnnotation	0	0	0
getEnrichedGO	0.02	0.00	0.02
getEnrichedPATH	0	0	0
getGeneSeq	0	0	0
getUniqueGOidCount	0	0	0
getVennCounts	0	0	0
hyperGtest	0	0	0
makeVennDiagram	0	0	0
mergePlusMinusPeaks	0	0	0
myPeakList	0.06	0.00	0.06
peakPermTest	0	0	0
peaksNearBDP	0	0	0
pie1	0.02	0.00	0.02
preparePool	0	0	0
summarizePatternInPeaks	0.50	0.02	0.51
toGRanges	0.03	0.00	0.03
translatePattern	0	0	0
wgEncodeTfbsV3	0.22	0.00	0.22
write2FASTA	0.01	0.00	0.02