BioC 3.5: CHECK report for ChIPpeakAnno on malbec2

Package: ChIPpeakAnno

Version: 3.10.1

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.10.1.tar.gz

StartedAt: 2017-08-15 21:50:58 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 21:57:01 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 362.3 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPpeakAnno.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.10.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-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 ‘3.10.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ChIPpeakAnno’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 19.6Mb
  sub-directories of 1Mb or more:
    data     12.7Mb
    doc       1.1Mb
    extdata   5.2Mb
* 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
findEnhancers 16.068  0.056  16.136
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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
  ‘/home/biocbuild/bbs-3.5-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
** testing if installed package can be loaded
* DONE (ChIPpeakAnno)

name	user	system	elapsed
BED2RangedData	0.168	0.000	0.167
ChIPpeakAnno-package	0.000	0.000	0.001
ExonPlusUtr.human.GRCh37	4.504	0.112	4.618
GFF2RangedData	0.120	0.000	0.121
HOT.spots	0.136	0.004	0.140
IDRfilter	0.000	0.000	0.001
Peaks.Ste12.Replicate1	0.028	0.000	0.027
Peaks.Ste12.Replicate2	0.024	0.000	0.023
Peaks.Ste12.Replicate3	0.024	0.000	0.022
TSS.human.GRCh37	0.140	0.000	0.141
TSS.human.GRCh38	0.804	0.004	0.812
TSS.human.NCBI36	0.172	0.000	0.172
TSS.mouse.GRCm38	0.128	0.000	0.129
TSS.mouse.NCBIM37	0.296	0.012	0.306
TSS.rat.RGSC3.4	0.128	0.008	0.135
TSS.rat.Rnor_5.0	0.092	0.000	0.092
TSS.zebrafish.Zv8	0.088	0.004	0.093
TSS.zebrafish.Zv9	0.760	0.004	0.766
addAncestors	1.272	0.092	1.366
addGeneIDs	1.376	0.080	1.511
addMetadata	1.524	0.028	1.551
annoGR	0	0	0
annoPeaks	2.272	0.108	2.928
annotatePeakInBatch	2.372	0.036	2.409
annotatedPeak	0.104	0.004	0.108
assignChromosomeRegion	0.000	0.004	0.002
bdp	0.000	0.000	0.001
binOverFeature	0.600	0.012	0.612
condenseMatrixByColnames	0.052	0.000	0.050
convert2EntrezID	0.368	0.004	0.372
countPatternInSeqs	0.292	0.000	0.292
cumulativePercentage	0	0	0
egOrgMap	0.016	0.000	0.014
enrichedGO	0.004	0.000	0.003
estFragmentLength	0.000	0.000	0.001
estLibSize	0.000	0.000	0.001
featureAlignedDistribution	0.400	0.004	0.404
featureAlignedExtentSignal	0.004	0.000	0.003
featureAlignedHeatmap	0.632	0.000	0.631
featureAlignedSignal	0.320	0.020	0.338
findEnhancers	16.068	0.056	16.136
findOverlappingPeaks	0.000	0.000	0.002
findOverlapsOfPeaks	0.972	0.000	1.006
getAllPeakSequence	0.720	0.004	0.777
getAnnotation	0.004	0.000	0.001
getEnrichedGO	0.012	0.000	0.013
getEnrichedPATH	0	0	0
getGeneSeq	0.000	0.000	0.002
getUniqueGOidCount	0.000	0.000	0.001
getVennCounts	0.000	0.004	0.002
hyperGtest	0.012	0.000	0.013
makeVennDiagram	0.004	0.000	0.003
mergePlusMinusPeaks	0.004	0.000	0.002
myPeakList	0.020	0.000	0.019
oligoFrequency	0.020	0.000	0.019
oligoSummary	0.004	0.000	0.002
peakPermTest	0.000	0.004	0.002
peaksNearBDP	0.000	0.000	0.001
pie1	0.012	0.000	0.011
preparePool	0.004	0.000	0.001
reCenterPeaks	0.012	0.000	0.014
summarizeOverlapsByBins	0.376	0.156	3.778
summarizePatternInPeaks	0.708	0.032	0.742
tileCount	0.340	0.056	3.698
tileGRanges	0.048	0.000	0.047
toGRanges	0.064	0.000	0.065
translatePattern	0.000	0.000	0.001
wgEncodeTfbsV3	0.256	0.016	0.272
write2FASTA	0.032	0.012	0.042
xget	0.164	0.008	0.172