BioC 3.2: CHECK report for ChIPpeakAnno on perceval

Package: ChIPpeakAnno

Version: 3.3.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.3.3.tar.gz

StartedAt: 2015-08-12 23:07:26 -0700 (Wed, 12 Aug 2015)

EndedAt: 2015-08-12 23:14:05 -0700 (Wed, 12 Aug 2015)

EllapsedTime: 399.0 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_3.3.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.2.2 RC (2015-08-07 r68909)
* 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 ‘3.3.3’
* 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 ... [27s/27s] OK
* checking installed package size ... NOTE
  installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data      9.7Mb
    extdata   2.0Mb
* 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 : 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’
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’
mergePlusMinusPeaks: no visible global function definition for
  ‘rowMins’
mergePlusMinusPeaks: no visible global function definition for
  ‘rowMaxs’
* 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 ... [38s/39s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
ExonPlusUtr.human.GRCh37 6.015  0.211   6.227
addGeneIDs               4.659  0.265   5.205
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [72s/81s]
 [72s/82s] 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-3.2-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.

* installing *source* package ‘ChIPpeakAnno’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "matrixStats" for requests: makeGRangesFromDataFrame
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "matrixStats" for requests: makeGRangesFromDataFrame
* DONE (ChIPpeakAnno)

name	user	system	elapsed
BED2RangedData	0.055	0.014	0.070
ChIPpeakAnno-package	1.297	0.060	1.357
ExonPlusUtr.human.GRCh37	6.015	0.211	6.227
GFF2RangedData	0.019	0.000	0.019
Peaks.Ste12.Replicate1	0.030	0.003	0.032
Peaks.Ste12.Replicate2	0.025	0.002	0.027
Peaks.Ste12.Replicate3	0.025	0.002	0.027
TSS.human.GRCh37	0.165	0.043	0.208
TSS.human.GRCh38	1.302	0.022	1.324
TSS.human.NCBI36	0.157	0.046	0.204
TSS.mouse.GRCm38	0.150	0.043	0.192
TSS.mouse.NCBIM37	0.137	0.042	0.180
TSS.rat.RGSC3.4	0.111	0.045	0.156
TSS.rat.Rnor_5.0	0.111	0.050	0.161
TSS.zebrafish.Zv8	0.114	0.052	0.166
TSS.zebrafish.Zv9	0.148	0.070	0.218
addAncestors	2.115	0.262	2.420
addGeneIDs	4.659	0.265	5.205
annotatePeakInBatch	1.311	0.164	1.475
annotatedPeak	0.118	0.008	0.127
assignChromosomeRegion	0.007	0.000	0.006
binOverFeature	0.480	0.045	0.525
condenseMatrixByColnames	0.022	0.001	0.022
convert2EntrezID	1.479	0.017	1.497
countPatternInSeqs	0.129	0.001	0.131
egOrgMap	0.001	0.000	0.002
enrichedGO	0.003	0.000	0.004
findOverlappingPeaks	0.004	0.000	0.005
findOverlapsOfPeaks	0.803	0.005	0.809
getAllPeakSequence	0.900	0.040	1.006
getAnnotation	0.002	0.000	0.001
getEnrichedGO	0.026	0.002	0.027
getEnrichedPATH	0.002	0.001	0.002
getGeneSeq	0.007	0.000	0.007
getUniqueGOidCount	0.003	0.001	0.004
getVennCounts	0.005	0.000	0.005
hyperGtest	0.003	0.000	0.004
makeVennDiagram	0.009	0.001	0.010
mergePlusMinusPeaks	0.003	0.000	0.003
myPeakList	0.036	0.002	0.038
peaksNearBDP	0.002	0.001	0.003
summarizePatternInPeaks	0.779	0.020	0.800
toGRanges	0.06	0.00	0.06
translatePattern	0.001	0.000	0.001
write2FASTA	0.046	0.001	0.047