BioC 3.4: CHECK report for ChIPpeakAnno on morelia

Package: ChIPpeakAnno

Version: 3.8.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.8.9.tar.gz

StartedAt: 2017-04-14 23:45:45 -0700 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:52:46 -0700 (Fri, 14 Apr 2017)

EllapsedTime: 421.2 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPpeakAnno.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.8.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 20.1Mb
  sub-directories of 1Mb or more:
    data     12.7Mb
    doc       1.6Mb
    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 22.890  0.167  23.091
addGeneIDs     1.392  0.140  12.161
* 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
  ‘/Users/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	0.047	0.000	0.048
ChIPpeakAnno-package	0.002	0.000	0.002
ExonPlusUtr.human.GRCh37	4.692	0.115	4.845
GFF2RangedData	0.013	0.001	0.013
HOT.spots	0.169	0.028	0.207
IDRfilter	0.002	0.000	0.003
Peaks.Ste12.Replicate1	0.036	0.003	0.040
Peaks.Ste12.Replicate2	0.027	0.002	0.030
Peaks.Ste12.Replicate3	0.028	0.002	0.031
TSS.human.GRCh37	0.181	0.028	0.210
TSS.human.GRCh38	0.763	0.013	0.779
TSS.human.NCBI36	0.181	0.030	0.222
TSS.mouse.GRCm38	0.693	0.044	0.739
TSS.mouse.NCBIM37	0.149	0.027	0.208
TSS.rat.RGSC3.4	0.121	0.025	0.147
TSS.rat.Rnor_5.0	0.107	0.027	0.133
TSS.zebrafish.Zv8	0.111	0.024	0.134
TSS.zebrafish.Zv9	0.138	0.028	0.167
addAncestors	2.186	0.215	2.690
addGeneIDs	1.392	0.140	12.161
addMetadata	0.994	0.022	1.015
annoGR	0.001	0.000	0.001
annoPeaks	1.630	0.160	2.577
annotatePeakInBatch	2.628	0.176	2.805
annotatedPeak	0.122	0.011	0.134
assignChromosomeRegion	0.006	0.000	0.005
bdp	0.001	0.000	0.001
binOverFeature	0.505	0.032	0.546
condenseMatrixByColnames	0.023	0.000	0.022
convert2EntrezID	0.503	0.006	0.509
countPatternInSeqs	0.113	0.001	0.161
egOrgMap	0.002	0.000	0.001
enrichedGO	0.003	0.001	0.074
estFragmentLength	0.002	0.000	0.002
estLibSize	0.002	0.000	0.002
featureAlignedDistribution	0.564	0.001	0.584
featureAlignedExtentSignal	0.005	0.001	0.006
featureAlignedHeatmap	0.716	0.002	0.718
featureAlignedSignal	0.537	0.024	0.563
findEnhancers	22.890	0.167	23.091
findOverlappingPeaks	0.004	0.001	0.005
findOverlapsOfPeaks	0.458	0.003	0.508
getAllPeakSequence	0.612	0.023	0.780
getAnnotation	0.001	0.000	0.001
getEnrichedGO	0.026	0.003	0.029
getEnrichedPATH	0.002	0.000	0.002
getGeneSeq	0.006	0.001	0.007
getUniqueGOidCount	0.002	0.000	0.002
getVennCounts	0.005	0.000	0.004
hyperGtest	0.003	0.000	0.003
makeVennDiagram	0.008	0.000	0.009
mergePlusMinusPeaks	0.003	0.000	0.003
myPeakList	0.020	0.004	0.023
oligoFrequency	0.011	0.002	0.013
oligoSummary	0.002	0.000	0.002
peakPermTest	0.003	0.001	0.004
peaksNearBDP	0.002	0.000	0.003
pie1	0.014	0.001	0.015
preparePool	0.002	0.000	0.002
reCenterPeaks	0.023	0.000	0.023
summarizeOverlapsByBins	0.213	0.109	3.540
summarizePatternInPeaks	0.585	0.053	0.639
tileCount	0.123	0.068	3.436
tileGRanges	0.048	0.012	0.060
toGRanges	0.056	0.020	0.090
translatePattern	0.002	0.001	0.003
wgEncodeTfbsV3	0.247	0.014	0.274
write2FASTA	0.015	0.002	0.018
xget	0.160	0.006	0.166