BioC 3.2: CHECK report for ChIPpeakAnno on oaxaca

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 22:06:04 -0700 (Wed, 12 Aug 2015)

EndedAt: 2015-08-12 22:11:53 -0700 (Wed, 12 Aug 2015)

EllapsedTime: 348.7 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 beta (2015-08-05 r68859)
* 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 ‘3.3.3’
* 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 ... [23s/25s] 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 ... [29s/38s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
addGeneIDs 2.424  0.125  10.754
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [59s/69s]
 [60s/69s] 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	0.054	0.006	0.060
ChIPpeakAnno-package	1.035	0.034	1.069
ExonPlusUtr.human.GRCh37	4.424	0.132	4.563
GFF2RangedData	0.018	0.000	0.020
Peaks.Ste12.Replicate1	0.040	0.002	0.043
Peaks.Ste12.Replicate2	0.030	0.002	0.033
Peaks.Ste12.Replicate3	0.028	0.002	0.031
TSS.human.GRCh37	0.170	0.030	0.199
TSS.human.GRCh38	1.203	0.014	1.218
TSS.human.NCBI36	0.157	0.026	0.183
TSS.mouse.GRCm38	0.149	0.025	0.174
TSS.mouse.NCBIM37	0.140	0.025	0.164
TSS.rat.RGSC3.4	0.108	0.026	0.134
TSS.rat.Rnor_5.0	0.107	0.029	0.136
TSS.zebrafish.Zv8	0.109	0.033	0.143
TSS.zebrafish.Zv9	0.137	0.030	0.168
addAncestors	1.721	0.140	1.863
addGeneIDs	2.424	0.125	10.754
annotatePeakInBatch	1.198	0.075	1.273
annotatedPeak	0.137	0.011	0.148
assignChromosomeRegion	0.005	0.001	0.006
binOverFeature	0.500	0.028	0.529
condenseMatrixByColnames	0.024	0.000	0.025
convert2EntrezID	0.491	0.011	0.502
countPatternInSeqs	0.115	0.001	0.116
egOrgMap	0.001	0.000	0.001
enrichedGO	0.002	0.000	0.003
findOverlappingPeaks	0.003	0.000	0.004
findOverlapsOfPeaks	0.698	0.004	0.704
getAllPeakSequence	0.636	0.019	0.752
getAnnotation	0.001	0.000	0.001
getEnrichedGO	0.026	0.002	0.027
getEnrichedPATH	0.002	0.000	0.002
getGeneSeq	0.006	0.000	0.007
getUniqueGOidCount	0.002	0.000	0.003
getVennCounts	0.003	0.000	0.003
hyperGtest	0.002	0.000	0.003
makeVennDiagram	0.007	0.001	0.008
mergePlusMinusPeaks	0.001	0.000	0.002
myPeakList	0.044	0.002	0.047
peaksNearBDP	0.002	0.000	0.002
summarizePatternInPeaks	1.082	0.026	1.109
toGRanges	0.055	0.001	0.055
translatePattern	0.001	0.000	0.001
write2FASTA	0.049	0.001	0.050