BioC 3.4: CHECK report for ChIPpeakAnno on malbec1

Package: ChIPpeakAnno

Version: 3.8.9

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.8.9.tar.gz

StartedAt: 2017-04-14 21:30:02 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 21:35:37 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 335.1 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPpeakAnno.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.8.9.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘3.8.9’
* 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 19.5Mb
  sub-directories of 1Mb or more:
    data     12.7Mb
    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 15.94  0.012  15.962
* 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-3.4-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	0.048	0.000	0.048
ChIPpeakAnno-package	0.000	0.000	0.002
ExonPlusUtr.human.GRCh37	4.488	0.024	4.514
GFF2RangedData	0.012	0.000	0.013
HOT.spots	0.128	0.012	0.143
IDRfilter	0.004	0.000	0.001
Peaks.Ste12.Replicate1	0.024	0.000	0.024
Peaks.Ste12.Replicate2	0.024	0.000	0.021
Peaks.Ste12.Replicate3	0.016	0.004	0.021
TSS.human.GRCh37	0.132	0.012	0.145
TSS.human.GRCh38	0.616	0.028	0.647
TSS.human.NCBI36	0.140	0.004	0.144
TSS.mouse.GRCm38	0.808	0.012	0.822
TSS.mouse.NCBIM37	0.152	0.008	0.162
TSS.rat.RGSC3.4	0.136	0.004	0.141
TSS.rat.Rnor_5.0	0.124	0.004	0.130
TSS.zebrafish.Zv8	0.112	0.000	0.109
TSS.zebrafish.Zv9	0.104	0.000	0.103
addAncestors	1.324	0.080	1.405
addGeneIDs	1.168	0.032	1.202
addMetadata	0.760	0.004	0.763
annoGR	0.000	0.000	0.001
annoPeaks	1.412	0.056	1.493
annotatePeakInBatch	2.400	0.032	2.437
annotatedPeak	0.088	0.000	0.090
assignChromosomeRegion	0.000	0.000	0.002
bdp	0.000	0.000	0.001
binOverFeature	0.380	0.000	0.379
condenseMatrixByColnames	0.016	0.000	0.015
convert2EntrezID	0.376	0.000	0.376
countPatternInSeqs	0.080	0.000	0.078
egOrgMap	0	0	0
enrichedGO	0.004	0.000	0.002
estFragmentLength	0.000	0.000	0.001
estLibSize	0.000	0.000	0.001
featureAlignedDistribution	0.392	0.000	0.390
featureAlignedExtentSignal	0.004	0.000	0.003
featureAlignedHeatmap	0.544	0.000	0.543
featureAlignedSignal	0.352	0.016	0.367
findEnhancers	15.940	0.012	15.962
findOverlappingPeaks	0.000	0.000	0.002
findOverlapsOfPeaks	0.384	0.008	0.389
getAllPeakSequence	0.552	0.004	0.663
getAnnotation	0	0	0
getEnrichedGO	0.012	0.000	0.011
getEnrichedPATH	0.000	0.000	0.001
getGeneSeq	0.000	0.000	0.002
getUniqueGOidCount	0.004	0.000	0.001
getVennCounts	0.000	0.000	0.002
hyperGtest	0.000	0.000	0.001
makeVennDiagram	0.004	0.000	0.003
mergePlusMinusPeaks	0.000	0.000	0.001
myPeakList	0.016	0.000	0.018
oligoFrequency	0.004	0.000	0.007
oligoSummary	0.000	0.000	0.001
peakPermTest	0.004	0.000	0.003
peaksNearBDP	0.000	0.000	0.002
pie1	0.016	0.000	0.016
preparePool	0.004	0.000	0.002
reCenterPeaks	0.020	0.000	0.021
summarizeOverlapsByBins	0.192	0.060	3.244
summarizePatternInPeaks	0.516	0.040	0.558
tileCount	0.076	0.040	2.986
tileGRanges	0.044	0.012	0.058
toGRanges	0.016	0.004	0.023
translatePattern	0.000	0.000	0.001
wgEncodeTfbsV3	0.216	0.004	0.224
write2FASTA	0.008	0.000	0.009
xget	0.148	0.004	0.151