BioC 3.5: CHECK report for ChIPpeakAnno on veracruz2

Package: ChIPpeakAnno

Version: 3.10.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.10.1.tar.gz

StartedAt: 2017-08-16 00:52:03 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:59:06 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 423.1 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_3.10.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-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 ‘3.10.1’
* 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 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 20.676  0.149  21.475
* 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-3.5-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	0.160	0.001	0.168
ChIPpeakAnno-package	0.001	0.000	0.002
ExonPlusUtr.human.GRCh37	4.364	0.096	4.611
GFF2RangedData	0.130	0.002	0.136
HOT.spots	0.150	0.030	0.191
IDRfilter	0.003	0.000	0.003
Peaks.Ste12.Replicate1	0.031	0.002	0.034
Peaks.Ste12.Replicate2	0.030	0.002	0.034
Peaks.Ste12.Replicate3	0.023	0.002	0.030
TSS.human.GRCh37	0.152	0.026	0.185
TSS.human.GRCh38	0.684	0.011	0.720
TSS.human.NCBI36	0.150	0.032	0.186
TSS.mouse.GRCm38	0.148	0.031	0.182
TSS.mouse.NCBIM37	0.253	0.030	0.288
TSS.rat.RGSC3.4	0.104	0.026	0.136
TSS.rat.Rnor_5.0	0.087	0.030	0.119
TSS.zebrafish.Zv8	0.104	0.032	0.152
TSS.zebrafish.Zv9	0.706	0.035	0.763
addAncestors	1.832	0.098	2.011
addGeneIDs	1.438	0.107	1.604
addMetadata	2.569	0.078	2.725
annoGR	0.001	0.000	0.000
annoPeaks	2.512	0.181	2.797
annotatePeakInBatch	2.862	0.130	3.077
annotatedPeak	0.141	0.008	0.149
assignChromosomeRegion	0.005	0.001	0.005
bdp	0.001	0.000	0.002
binOverFeature	0.526	0.019	0.559
condenseMatrixByColnames	0.070	0.000	0.071
convert2EntrezID	0.532	0.010	0.560
countPatternInSeqs	0.325	0.002	0.349
cumulativePercentage	0.000	0.000	0.001
egOrgMap	0.021	0.001	0.021
enrichedGO	0.002	0.001	0.003
estFragmentLength	0.001	0.000	0.002
estLibSize	0.002	0.000	0.002
featureAlignedDistribution	0.519	0.001	0.545
featureAlignedExtentSignal	0.006	0.001	0.006
featureAlignedHeatmap	0.726	0.002	0.739
featureAlignedSignal	0.434	0.025	0.482
findEnhancers	20.676	0.149	21.475
findOverlappingPeaks	0.004	0.000	0.004
findOverlapsOfPeaks	1.300	0.005	1.345
getAllPeakSequence	0.697	0.018	0.742
getAnnotation	0.001	0.000	0.001
getEnrichedGO	0.016	0.002	0.021
getEnrichedPATH	0.001	0.000	0.001
getGeneSeq	0.005	0.000	0.006
getUniqueGOidCount	0.001	0.000	0.002
getVennCounts	0.003	0.001	0.004
hyperGtest	0.054	0.000	0.057
makeVennDiagram	0.006	0.001	0.007
mergePlusMinusPeaks	0.003	0.000	0.003
myPeakList	0.016	0.003	0.019
oligoFrequency	0.028	0.002	0.031
oligoSummary	0.002	0.000	0.002
peakPermTest	0.003	0.001	0.004
peaksNearBDP	0.002	0.000	0.002
pie1	0.010	0.001	0.010
preparePool	0.002	0.000	0.002
reCenterPeaks	0.012	0.000	0.013
summarizeOverlapsByBins	0.406	0.155	4.316
summarizePatternInPeaks	0.766	0.072	0.852
tileCount	0.448	0.207	4.460
tileGRanges	0.038	0.010	0.048
toGRanges	0.087	0.012	0.101
translatePattern	0.002	0.000	0.001
wgEncodeTfbsV3	0.230	0.012	0.243
write2FASTA	0.039	0.004	0.051
xget	0.166	0.007	0.174