BioC 3.2: CHECK report for ChIPpeakAnno on oaxaca

Package: ChIPpeakAnno

Version: 3.4.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.4.6.tar.gz

StartedAt: 2016-04-22 22:36:09 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 22:42:42 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 393.0 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_3.4.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘3.4.6’
* 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 ... [28s/28s] OK
* checking installed package size ... NOTE
  installed size is 18.6Mb
  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 ... [39s/40s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [70s/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	0.068	0.001	0.069
ChIPpeakAnno-package	0.001	0.000	0.001
ExonPlusUtr.human.GRCh37	4.509	0.114	4.629
GFF2RangedData	0.021	0.001	0.022
HOT.spots	0.721	0.038	0.759
Peaks.Ste12.Replicate1	0.034	0.003	0.037
Peaks.Ste12.Replicate2	0.031	0.003	0.034
Peaks.Ste12.Replicate3	0.033	0.003	0.036
TSS.human.GRCh37	0.182	0.027	0.210
TSS.human.GRCh38	0.701	0.011	0.712
TSS.human.NCBI36	0.149	0.028	0.178
TSS.mouse.GRCm38	0.148	0.030	0.178
TSS.mouse.NCBIM37	0.140	0.029	0.168
TSS.rat.RGSC3.4	0.115	0.030	0.144
TSS.rat.Rnor_5.0	0.115	0.028	0.143
TSS.zebrafish.Zv8	0.121	0.031	0.152
TSS.zebrafish.Zv9	0.147	0.033	0.179
addAncestors	2.216	0.156	2.374
addGeneIDs	2.465	0.099	2.599
annoGR	0.001	0.000	0.001
annotatePeakInBatch	2.771	0.230	3.436
annotatedPeak	0.117	0.010	0.127
assignChromosomeRegion	0.005	0.000	0.006
binOverFeature	0.521	0.030	0.551
condenseMatrixByColnames	0.028	0.001	0.029
convert2EntrezID	0.59	0.01	0.60
countPatternInSeqs	0.170	0.002	0.172
egOrgMap	0.001	0.000	0.002
enrichedGO	0.002	0.001	0.004
featureAlignedDistribution	1.560	0.008	1.569
featureAlignedHeatmap	1.721	0.005	1.730
featureAlignedSignal	1.384	0.029	1.415
findOverlappingPeaks	0.004	0.000	0.004
findOverlapsOfPeaks	0.747	0.005	0.752
getAllPeakSequence	0.783	0.016	0.861
getAnnotation	0.001	0.001	0.001
getEnrichedGO	0.027	0.002	0.030
getEnrichedPATH	0.002	0.000	0.002
getGeneSeq	0.006	0.000	0.005
getUniqueGOidCount	0.003	0.000	0.003
getVennCounts	0.004	0.000	0.004
hyperGtest	0.002	0.001	0.002
makeVennDiagram	0.008	0.000	0.009
mergePlusMinusPeaks	0.002	0.000	0.003
myPeakList	0.026	0.009	0.035
peakPermTest	0.004	0.001	0.004
peaksNearBDP	0.003	0.000	0.002
pie1	0.015	0.001	0.016
preparePool	0.003	0.000	0.003
summarizePatternInPeaks	0.751	0.016	0.768
toGRanges	0.036	0.000	0.036
translatePattern	0.001	0.000	0.001
wgEncodeTfbsV3	0.277	0.019	0.297
write2FASTA	0.016	0.000	0.016