BioC 3.5: CHECK report for ChIPpeakAnno on oaxaca

Package: ChIPpeakAnno

Version: 3.9.12

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.9.12.tar.gz

StartedAt: 2017-03-04 00:27:11 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 00:36:13 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 542.3 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_3.9.12.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 r72177)
* 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 ‘3.9.12’
* 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 20.1Mb
  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 ... NOTE
removeAncestor : <anonymous> : <anonymous>: no visible global function
  definition for 'fisher.test'
Undefined global functions or variables:
  fisher.test
Consider adding
  importFrom("stats", "fisher.test")
to your NAMESPACE file.
* 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 21.280  0.194  21.599
addGeneIDs     1.945  0.400  52.217
* 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: 3 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	0.209	0.001	0.210
ChIPpeakAnno-package	0.002	0.001	0.002
ExonPlusUtr.human.GRCh37	3.693	0.096	3.827
GFF2RangedData	0.195	0.002	0.198
HOT.spots	0.768	0.033	0.802
IDRfilter	0.003	0.001	0.002
Peaks.Ste12.Replicate1	0.033	0.002	0.041
Peaks.Ste12.Replicate2	0.029	0.002	0.031
Peaks.Ste12.Replicate3	0.034	0.003	0.036
TSS.human.GRCh37	0.138	0.023	0.161
TSS.human.GRCh38	0.623	0.010	0.633
TSS.human.NCBI36	0.166	0.028	0.214
TSS.mouse.GRCm38	0.139	0.026	0.175
TSS.mouse.NCBIM37	0.144	0.029	0.187
TSS.rat.RGSC3.4	0.116	0.028	0.162
TSS.rat.Rnor_5.0	0.112	0.027	0.201
TSS.zebrafish.Zv8	0.119	0.027	0.155
TSS.zebrafish.Zv9	0.130	0.027	0.158
addAncestors	2.427	0.179	3.129
addGeneIDs	1.945	0.400	52.217
addMetadata	2.082	0.051	2.134
annoGR	0.000	0.000	0.001
annoPeaks	3.826	0.289	4.966
annotatePeakInBatch	2.943	0.172	3.147
annotatedPeak	0.127	0.009	0.135
assignChromosomeRegion	0.003	0.000	0.004
bdp	0.001	0.000	0.000
binOverFeature	0.513	0.023	0.550
condenseMatrixByColnames	0.053	0.001	0.054
convert2EntrezID	0.414	0.006	0.420
countPatternInSeqs	0.384	0.002	0.413
egOrgMap	0.023	0.000	0.023
enrichedGO	0.003	0.002	0.020
estFragmentLength	0.002	0.000	0.002
estLibSize	0.001	0.001	0.002
featureAlignedDistribution	0.567	0.007	0.575
featureAlignedExtentSignal	0.004	0.000	0.004
featureAlignedHeatmap	0.902	0.003	0.914
featureAlignedSignal	0.471	0.029	0.501
findEnhancers	21.280	0.194	21.599
findOverlappingPeaks	0.004	0.001	0.004
findOverlapsOfPeaks	1.207	0.006	1.319
getAllPeakSequence	0.724	0.020	0.935
getAnnotation	0.001	0.000	0.001
getEnrichedGO	0.020	0.002	0.022
getEnrichedPATH	0.001	0.001	0.001
getGeneSeq	0.004	0.000	0.004
getUniqueGOidCount	0.001	0.000	0.001
getVennCounts	0.004	0.001	0.004
hyperGtest	0.022	0.000	0.023
makeVennDiagram	0.008	0.001	0.008
mergePlusMinusPeaks	0.003	0.000	0.003
myPeakList	0.025	0.004	0.029
oligoFrequency	0.033	0.003	0.054
oligoSummary	0.002	0.000	0.002
peakPermTest	0.004	0.000	0.004
peaksNearBDP	0.002	0.000	0.003
pie1	0.016	0.001	0.026
preparePool	0.003	0.000	0.002
reCenterPeaks	0.018	0.001	0.019
summarizeOverlapsByBins	0.368	0.133	4.368
summarizePatternInPeaks	0.919	0.087	1.007
tileCount	0.565	0.188	4.599
tileGRanges	0.053	0.029	0.082
toGRanges	0.088	0.013	0.839
translatePattern	0.001	0.000	0.001
wgEncodeTfbsV3	0.268	0.015	0.343
write2FASTA	0.046	0.005	0.051
xget	0.151	0.009	0.159

BioC 3.5: CHECK report for ChIPpeakAnno on oaxaca

Summary

Command output