BioC 3.6: CHECK report for ChIPpeakAnno on veracruz1

Package: ChIPpeakAnno

Version: 3.11.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.11.4.tar.gz

StartedAt: 2017-08-16 01:03:10 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:09:57 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 407.3 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPpeakAnno.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.11.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘3.11.4’
* 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 20.2Mb
  sub-directories of 1Mb or more:
    data     12.7Mb
    doc       1.7Mb
    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 20.039  0.133  20.774
* 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-3.6-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	0.174	0.001	0.181
ChIPpeakAnno-package	0.001	0.000	0.003
ExonPlusUtr.human.GRCh37	4.263	0.096	4.461
GFF2RangedData	0.130	0.002	0.148
HOT.spots	0.131	0.029	0.166
IDRfilter	0.003	0.000	0.003
Peaks.Ste12.Replicate1	0.032	0.003	0.034
Peaks.Ste12.Replicate2	0.026	0.003	0.029
Peaks.Ste12.Replicate3	0.030	0.003	0.032
TSS.human.GRCh37	0.113	0.026	0.139
TSS.human.GRCh38	0.630	0.011	0.676
TSS.human.NCBI36	0.138	0.031	0.168
TSS.mouse.GRCm38	0.132	0.030	0.168
TSS.mouse.NCBIM37	0.223	0.026	0.259
TSS.rat.RGSC3.4	0.088	0.027	0.116
TSS.rat.Rnor_5.0	0.091	0.027	0.124
TSS.zebrafish.Zv8	0.089	0.028	0.118
TSS.zebrafish.Zv9	0.698	0.034	0.752
addAncestors	1.568	0.093	1.710
addGeneIDs	1.438	0.114	1.602
addMetadata	2.405	0.076	2.544
annoGR	0.001	0.000	0.001
annoPeaks	2.578	0.220	2.953
annotatePeakInBatch	2.813	0.122	3.053
annotatedPeak	0.107	0.007	0.119
assignChromosomeRegion	0.003	0.001	0.003
bdp	0	0	0
binOverFeature	0.538	0.022	0.576
binOverGene	0.002	0.000	0.002
binOverRegions	0.003	0.000	0.003
condenseMatrixByColnames	0.073	0.000	0.075
convert2EntrezID	0.407	0.007	0.429
countPatternInSeqs	0.296	0.001	0.314
cumulativePercentage	0.000	0.000	0.001
egOrgMap	0.016	0.000	0.017
enrichedGO	0.002	0.001	0.004
estFragmentLength	0.001	0.000	0.002
estLibSize	0.002	0.000	0.002
featureAlignedDistribution	0.352	0.001	0.369
featureAlignedExtentSignal	0.004	0.000	0.004
featureAlignedHeatmap	0.786	0.004	0.807
featureAlignedSignal	0.175	0.029	0.220
findEnhancers	20.039	0.133	20.774
findOverlappingPeaks	0.004	0.000	0.004
findOverlapsOfPeaks	1.279	0.006	1.316
getAllPeakSequence	0.627	0.016	0.661
getAnnotation	0.001	0.000	0.001
getEnrichedGO	0.020	0.003	0.023
getEnrichedPATH	0.002	0.000	0.002
getGeneSeq	0.006	0.001	0.006
getUniqueGOidCount	0.002	0.000	0.002
getVennCounts	0.004	0.001	0.005
hyperGtest	0.019	0.000	0.020
makeVennDiagram	0.007	0.001	0.008
mergePlusMinusPeaks	0.003	0.000	0.004
myPeakList	0.022	0.003	0.026
oligoFrequency	0.021	0.001	0.026
oligoSummary	0.002	0.000	0.001
peakPermTest	0.003	0.001	0.004
peaksNearBDP	0.002	0.000	0.002
pie1	0.010	0.001	0.010
plotBinOverRegions	0.002	0.000	0.002
preparePool	0.001	0.000	0.001
reCenterPeaks	0.016	0.000	0.021
summarizeOverlapsByBins	0.483	0.145	0.924
summarizePatternInPeaks	0.822	0.067	0.924
tileCount	0.540	0.210	1.219
tileGRanges	0.030	0.016	0.045
toGRanges	0.066	0.012	0.078
translatePattern	0.001	0.000	0.000
wgEncodeTfbsV3	0.182	0.010	0.191
write2FASTA	0.036	0.004	0.041
xget	0.142	0.006	0.148