BioC 3.3: CHECK report for ChIPpeakAnno on linux2.bioconductor.org

Package: ChIPpeakAnno

Version: 3.5.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.5.0.tar.gz

StartedAt: 2015-10-27 02:27:08 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:31:41 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 273.4 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPpeakAnno.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/ChIPpeakAnno.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘3.5.0’
* 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 ... [20s/20s] OK
* checking installed package size ... NOTE
  installed size is 18.4Mb
  sub-directories of 1Mb or more:
    data     12.7Mb
    extdata   4.7Mb
* 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 ... [25s/25s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [55s/55s]
 [55s/55s] 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-3.3-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	0.032	0.000	0.032
ChIPpeakAnno-package	0	0	0
ExonPlusUtr.human.GRCh37	3.885	0.040	3.925
GFF2RangedData	0.012	0.000	0.012
HOT.spots	0.130	0.004	0.134
Peaks.Ste12.Replicate1	0.023	0.000	0.023
Peaks.Ste12.Replicate2	0.02	0.00	0.02
Peaks.Ste12.Replicate3	0.019	0.000	0.020
TSS.human.GRCh37	0.124	0.000	0.124
TSS.human.GRCh38	0.427	0.008	0.435
TSS.human.NCBI36	0.177	0.008	0.184
TSS.mouse.GRCm38	0.543	0.004	0.547
TSS.mouse.NCBIM37	0.104	0.000	0.105
TSS.rat.RGSC3.4	0.087	0.000	0.087
TSS.rat.Rnor_5.0	0.076	0.004	0.080
TSS.zebrafish.Zv8	0.082	0.000	0.081
TSS.zebrafish.Zv9	0.1	0.0	0.1
addAncestors	1.281	0.068	1.350
addGeneIDs	1.846	0.068	1.917
annoGR	0.001	0.000	0.001
annotatePeakInBatch	0.750	0.064	0.814
annotatedPeak	0.088	0.000	0.088
assignChromosomeRegion	0.002	0.000	0.002
binOverFeature	0.328	0.004	0.333
condenseMatrixByColnames	0.023	0.000	0.024
convert2EntrezID	0.443	0.008	0.451
countPatternInSeqs	0.125	0.000	0.125
egOrgMap	0.001	0.000	0.001
enrichedGO	0.003	0.000	0.003
featureAlignedDistribution	1.290	0.004	1.294
featureAlignedHeatmap	1.055	0.020	1.081
featureAlignedSignal	1.043	0.020	1.064
findOverlappingPeaks	0.002	0.000	0.001
findOverlapsOfPeaks	0.439	0.000	0.439
getAllPeakSequence	0.643	0.008	0.651
getAnnotation	0.001	0.000	0.001
getEnrichedGO	0.018	0.000	0.018
getEnrichedPATH	0.001	0.000	0.001
getGeneSeq	0.004	0.000	0.003
getUniqueGOidCount	0.002	0.000	0.002
getVennCounts	0.003	0.000	0.003
hyperGtest	0.002	0.000	0.002
makeVennDiagram	0.005	0.000	0.005
mergePlusMinusPeaks	0.002	0.000	0.002
myPeakList	0.032	0.012	0.044
peakPermTest	0.003	0.000	0.003
peaksNearBDP	0.000	0.004	0.002
pie1	0.010	0.000	0.011
preparePool	0.001	0.000	0.001
summarizePatternInPeaks	0.680	0.004	0.689
toGRanges	0.032	0.000	0.033
translatePattern	0.002	0.000	0.001
wgEncodeTfbsV3	0.308	0.012	0.321
write2FASTA	0.014	0.000	0.014