BioC 3.5: CHECK report for ChIPpeakAnno on toluca2

Package: ChIPpeakAnno

Version: 3.9.19

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.9.19.tar.gz

StartedAt: 2017-04-23 01:40:04 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 01:47:58 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 473.4 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_3.9.19.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ChIPpeakAnno.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘3.9.19’
* 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       1.6Mb
    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           23.389  0.207  23.815
summarizeOverlapsByBins  6.352  2.064   4.581
* 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	0.213	0.001	0.215
ChIPpeakAnno-package	0.001	0.001	0.002
ExonPlusUtr.human.GRCh37	4.650	0.114	4.802
GFF2RangedData	0.173	0.002	0.179
HOT.spots	0.157	0.029	0.193
IDRfilter	0.002	0.000	0.002
Peaks.Ste12.Replicate1	0.037	0.003	0.050
Peaks.Ste12.Replicate2	0.031	0.002	0.035
Peaks.Ste12.Replicate3	0.030	0.002	0.032
TSS.human.GRCh37	0.165	0.026	0.191
TSS.human.GRCh38	0.722	0.013	0.740
TSS.human.NCBI36	0.165	0.024	0.190
TSS.mouse.GRCm38	0.162	0.030	0.195
TSS.mouse.NCBIM37	0.245	0.029	0.276
TSS.rat.RGSC3.4	0.121	0.025	0.151
TSS.rat.Rnor_5.0	0.111	0.029	0.143
TSS.zebrafish.Zv8	0.108	0.027	0.138
TSS.zebrafish.Zv9	0.133	0.008	0.143
addAncestors	2.870	0.206	3.102
addGeneIDs	1.793	0.174	1.990
addMetadata	2.145	0.009	2.161
annoGR	0.001	0.000	0.001
annoPeaks	3.591	0.287	3.990
annotatePeakInBatch	4.105	0.174	4.336
annotatedPeak	0.138	0.007	0.147
assignChromosomeRegion	0.004	0.000	0.005
bdp	0.001	0.001	0.002
binOverFeature	0.662	0.038	0.707
condenseMatrixByColnames	0.074	0.001	0.076
convert2EntrezID	0.451	0.008	0.463
countPatternInSeqs	0.409	0.006	0.419
cumulativePercentage	0.001	0.001	0.001
egOrgMap	0.024	0.000	0.024
enrichedGO	0.003	0.001	0.004
estFragmentLength	0.001	0.000	0.002
estLibSize	0.002	0.000	0.001
featureAlignedDistribution	0.555	0.001	0.558
featureAlignedExtentSignal	0.006	0.000	0.006
featureAlignedHeatmap	0.911	0.002	0.920
featureAlignedSignal	0.505	0.027	0.537
findEnhancers	23.389	0.207	23.815
findOverlappingPeaks	0.004	0.000	0.004
findOverlapsOfPeaks	1.496	0.006	1.532
getAllPeakSequence	0.756	0.018	0.784
getAnnotation	0.001	0.000	0.001
getEnrichedGO	0.021	0.002	0.023
getEnrichedPATH	0.002	0.000	0.001
getGeneSeq	0.006	0.001	0.006
getUniqueGOidCount	0.001	0.000	0.002
getVennCounts	0.004	0.000	0.004
hyperGtest	0.020	0.001	0.021
makeVennDiagram	0.008	0.000	0.008
mergePlusMinusPeaks	0.003	0.001	0.003
myPeakList	0.024	0.003	0.030
oligoFrequency	0.031	0.001	0.034
oligoSummary	0.002	0.000	0.002
peakPermTest	0.003	0.000	0.004
peaksNearBDP	0.002	0.001	0.002
pie1	0.013	0.000	0.014
preparePool	0.002	0.000	0.002
reCenterPeaks	0.019	0.000	0.020
summarizeOverlapsByBins	6.352	2.064	4.581
summarizePatternInPeaks	0.967	0.089	1.058
tileCount	0.618	0.129	4.999
tileGRanges	0.050	0.059	0.109
toGRanges	0.110	0.035	0.146
translatePattern	0.001	0.001	0.001
wgEncodeTfbsV3	0.252	0.018	0.270
write2FASTA	0.083	0.018	0.102
xget	0.152	0.010	0.162