BioC 3.2: CHECK report for ChIPpeakAnno on oaxaca

Package: ChIPpeakAnno

Version: 3.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.4.0.tar.gz

StartedAt: 2015-10-27 02:09:11 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:15:37 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 385.1 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_3.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘3.4.0’
* 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 ... [26s/27s] OK
* checking installed package size ... NOTE
  installed size is 18.7Mb
  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 ... [35s/45s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
addGeneIDs 2.069  0.147  11.865
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [69s/71s]
 [70s/71s] 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-3.2-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	0.081	0.001	0.082
ChIPpeakAnno-package	0.001	0.000	0.002
ExonPlusUtr.human.GRCh37	4.607	0.108	4.720
GFF2RangedData	0.022	0.000	0.023
HOT.spots	0.169	0.029	0.198
Peaks.Ste12.Replicate1	0.033	0.002	0.035
Peaks.Ste12.Replicate2	0.023	0.002	0.024
Peaks.Ste12.Replicate3	0.027	0.002	0.027
TSS.human.GRCh37	0.164	0.021	0.185
TSS.human.GRCh38	0.826	0.014	0.841
TSS.human.NCBI36	0.254	0.027	0.281
TSS.mouse.GRCm38	0.602	0.041	0.648
TSS.mouse.NCBIM37	0.136	0.025	0.162
TSS.rat.RGSC3.4	0.117	0.022	0.139
TSS.rat.Rnor_5.0	0.109	0.027	0.136
TSS.zebrafish.Zv8	0.104	0.027	0.131
TSS.zebrafish.Zv9	0.132	0.025	0.159
addAncestors	1.990	0.145	2.208
addGeneIDs	2.069	0.147	11.865
annoGR	0.001	0.000	0.001
annotatePeakInBatch	1.283	0.067	1.353
annotatedPeak	0.128	0.008	0.136
assignChromosomeRegion	0.003	0.000	0.003
binOverFeature	0.512	0.027	0.540
condenseMatrixByColnames	0.029	0.000	0.029
convert2EntrezID	0.559	0.012	0.574
countPatternInSeqs	0.148	0.001	0.149
egOrgMap	0.001	0.000	0.001
enrichedGO	0.003	0.000	0.004
featureAlignedDistribution	1.484	0.005	1.489
featureAlignedHeatmap	1.828	0.005	1.835
featureAlignedSignal	1.734	0.046	1.782
findOverlappingPeaks	0.004	0.000	0.004
findOverlapsOfPeaks	0.730	0.006	0.782
getAllPeakSequence	0.735	0.022	0.829
getAnnotation	0.001	0.000	0.001
getEnrichedGO	0.024	0.002	0.027
getEnrichedPATH	0.002	0.000	0.002
getGeneSeq	0.005	0.001	0.005
getUniqueGOidCount	0.002	0.000	0.003
getVennCounts	0.004	0.000	0.004
hyperGtest	0.003	0.000	0.002
makeVennDiagram	0.007	0.000	0.007
mergePlusMinusPeaks	0.003	0.000	0.002
myPeakList	0.043	0.002	0.045
peakPermTest	0.003	0.000	0.003
peaksNearBDP	0.002	0.000	0.003
pie1	0.012	0.000	0.013
preparePool	0.002	0.001	0.002
summarizePatternInPeaks	0.693	0.023	0.716
toGRanges	0.038	0.001	0.039
translatePattern	0.001	0.000	0.001
wgEncodeTfbsV3	0.263	0.010	0.273
write2FASTA	0.014	0.000	0.015