BioC 3.1: CHECK report for ChIPpeakAnno on petty

Package: ChIPpeakAnno

Version: 3.2.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.2.2.tar.gz

StartedAt: 2015-10-08 22:00:21 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:08:05 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 463.6 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_3.2.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘3.2.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘grid’ ‘VennDiagram’ ‘biomaRt’ ‘IRanges’ ‘Biostrings’ ‘GenomicRanges’
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 ... [30s/31s] OK
* checking installed package size ... NOTE
  installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data      9.7Mb
    extdata   1.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
* 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
annotatePeakInBatch: no visible global function definition for
  ‘seqlevels’
assignChromosomeRegion : formatSeqnames: no visible global function
  definition for ‘seqlevels’
assignChromosomeRegion: no visible global function definition for
  ‘seqlengths’
assignChromosomeRegion: no visible global function definition for
  ‘seqlevels’
assignChromosomeRegion: no visible global function definition for
  ‘keepSeqlevels’
findOverlappingPeaks: no visible global function definition for
  ‘DataFrame’
formatSeqnames: no visible global function definition for ‘seqlevels’
getAllPeakSequence: no visible global function definition for
  ‘seqlevels’
getAllPeakSequence: no visible global function definition for
  ‘seqlengths’
getAllPeakSequence: no visible global function definition for
  ‘seqlengths<-’
getEnrichedGO: no visible global function definition for ‘mappedkeys’
getEnrichedGO : <anonymous>: no visible global function definition for
  ‘GOID’
getEnrichedGO : <anonymous>: no visible global function definition for
  ‘Term’
getEnrichedGO : <anonymous>: no visible global function definition for
  ‘Definition’
getEnrichedGO : <anonymous>: no visible global function definition for
  ‘Ontology’
getEnrichedPATH: no visible global function definition for ‘mappedkeys’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [45s/45s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
ExonPlusUtr.human.GRCh37 6.646  0.214   6.863
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [86s/102s]
 [87s/103s] 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.

* installing *source* package ‘ChIPpeakAnno’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (ChIPpeakAnno)

name	user	system	elapsed
BED2RangedData	0.089	0.003	0.092
ChIPpeakAnno-package	1.402	0.042	1.443
ExonPlusUtr.human.GRCh37	6.646	0.214	6.863
GFF2RangedData	0.032	0.000	0.032
Peaks.Ste12.Replicate1	0.052	0.004	0.055
Peaks.Ste12.Replicate2	0.044	0.003	0.047
Peaks.Ste12.Replicate3	0.038	0.003	0.041
TSS.human.GRCh37	0.230	0.049	0.279
TSS.human.GRCh38	1.041	0.023	1.066
TSS.human.NCBI36	0.374	0.051	0.425
TSS.mouse.GRCm38	0.897	0.065	0.966
TSS.mouse.NCBIM37	0.212	0.048	0.260
TSS.rat.RGSC3.4	0.171	0.052	0.224
TSS.rat.Rnor_5.0	0.114	0.046	0.160
TSS.zebrafish.Zv8	0.152	0.053	0.205
TSS.zebrafish.Zv9	0.181	0.052	0.233
addAncestors	3.627	0.248	3.879
addGeneIDs	3.987	0.154	4.145
annotatePeakInBatch	1.757	0.084	1.843
annotatedPeak	0.189	0.018	0.207
assignChromosomeRegion	0.009	0.000	0.010
binOverFeature	0.793	0.061	0.854
condenseMatrixByColnames	0.035	0.001	0.036
convert2EntrezID	1.958	0.010	1.968
countPatternInSeqs	0.203	0.001	0.206
egOrgMap	0.002	0.000	0.001
enrichedGO	0.005	0.001	0.006
findOverlappingPeaks	0.006	0.000	0.007
findOverlapsOfPeaks	1.109	0.006	1.143
getAllPeakSequence	1.051	0.033	1.145
getAnnotation	0.001	0.000	0.002
getEnrichedGO	0.043	0.002	0.045
getEnrichedPATH	0.003	0.000	0.003
getGeneSeq	0.011	0.001	0.011
getUniqueGOidCount	0.004	0.000	0.003
getVennCounts	0.005	0.001	0.005
hyperGtest	0.003	0.000	0.002
makeVennDiagram	0.015	0.001	0.015
myPeakList	0.057	0.003	0.060
peaksNearBDP	0.004	0.000	0.003
summarizePatternInPeaks	1.202	0.018	1.222
toGRanges	0.091	0.001	0.092
translatePattern	0.002	0.000	0.003
write2FASTA	0.075	0.001	0.075