BioC 3.2: CHECK report for ChIPpeakAnno on linux1.bioconductor.org

Package: ChIPpeakAnno

Version: 3.4.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.4.0.tar.gz

StartedAt: 2015-10-27 01:57:58 -0400 (Tue, 27 Oct 2015)

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

EllapsedTime: 273.0 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPpeakAnno.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘3.4.0’
* 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 ... [17s/17s] 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’ [51s/51s]
 [51s/51s] 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-3.2-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	0.044	0.000	0.045
ChIPpeakAnno-package	0.001	0.000	0.001
ExonPlusUtr.human.GRCh37	3.799	0.024	3.823
GFF2RangedData	0.014	0.000	0.013
HOT.spots	0.120	0.012	0.132
Peaks.Ste12.Replicate1	0.023	0.000	0.023
Peaks.Ste12.Replicate2	0.019	0.000	0.019
Peaks.Ste12.Replicate3	0.015	0.004	0.019
TSS.human.GRCh37	0.119	0.004	0.123
TSS.human.GRCh38	0.408	0.008	0.416
TSS.human.NCBI36	0.18	0.00	0.18
TSS.mouse.GRCm38	0.544	0.000	0.544
TSS.mouse.NCBIM37	0.105	0.000	0.106
TSS.rat.RGSC3.4	0.085	0.000	0.085
TSS.rat.Rnor_5.0	0.078	0.000	0.078
TSS.zebrafish.Zv8	0.079	0.000	0.079
TSS.zebrafish.Zv9	0.098	0.000	0.098
addAncestors	1.391	0.048	1.442
addGeneIDs	1.53	0.06	1.59
annoGR	0	0	0
annotatePeakInBatch	0.804	0.028	0.833
annotatedPeak	0.086	0.000	0.086
assignChromosomeRegion	0.002	0.000	0.002
binOverFeature	0.339	0.008	0.347
condenseMatrixByColnames	0.016	0.000	0.016
convert2EntrezID	0.346	0.004	0.350
countPatternInSeqs	0.084	0.004	0.088
egOrgMap	0.001	0.000	0.001
enrichedGO	0.002	0.000	0.002
featureAlignedDistribution	0.922	0.000	0.922
featureAlignedHeatmap	1.013	0.000	1.012
featureAlignedSignal	0.977	0.016	0.993
findOverlappingPeaks	0.002	0.000	0.002
findOverlapsOfPeaks	0.418	0.000	0.418
getAllPeakSequence	0.484	0.004	0.488
getAnnotation	0.001	0.000	0.001
getEnrichedGO	0.013	0.000	0.012
getEnrichedPATH	0.000	0.000	0.001
getGeneSeq	0.003	0.000	0.003
getUniqueGOidCount	0.001	0.000	0.001
getVennCounts	0.000	0.004	0.002
hyperGtest	0.000	0.000	0.001
makeVennDiagram	0.003	0.000	0.003
mergePlusMinusPeaks	0.001	0.000	0.001
myPeakList	0.032	0.000	0.033
peakPermTest	0.000	0.000	0.002
peaksNearBDP	0.001	0.000	0.001
pie1	0.009	0.000	0.008
preparePool	0.001	0.000	0.001
summarizePatternInPeaks	0.509	0.004	0.513
toGRanges	0.02	0.00	0.02
translatePattern	0.001	0.000	0.000
wgEncodeTfbsV3	0.212	0.004	0.217
write2FASTA	0.009	0.000	0.009