BioC 3.2: CHECK report for ChIPpeakAnno on zin1

Package: ChIPpeakAnno

Version: 3.3.3

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.3.3.tar.gz

StartedAt: 2015-08-12 22:28:52 -0700 (Wed, 12 Aug 2015)

EndedAt: 2015-08-12 22:33:06 -0700 (Wed, 12 Aug 2015)

EllapsedTime: 254.2 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPpeakAnno.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.3.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.2.2 beta (2015-08-05 r68859)
* using platform: x86_64-pc-linux-gnu (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 ... [18s/18s] OK
* checking installed package size ... NOTE
  installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data      9.7Mb
    extdata   2.1Mb
* 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 ... [23s/23s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [45s/54s]
 [46s/54s] 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
  ‘/home/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	0.039	0.000	0.042
ChIPpeakAnno-package	0.565	0.012	0.577
ExonPlusUtr.human.GRCh37	4.145	0.020	4.162
GFF2RangedData	0.014	0.000	0.014
Peaks.Ste12.Replicate1	0.026	0.000	0.025
Peaks.Ste12.Replicate2	0.022	0.000	0.022
Peaks.Ste12.Replicate3	0.017	0.004	0.021
TSS.human.GRCh37	0.131	0.004	0.142
TSS.human.GRCh38	0.505	0.012	0.516
TSS.human.NCBI36	0.201	0.004	0.206
TSS.mouse.GRCm38	0.491	0.008	0.498
TSS.mouse.NCBIM37	0.112	0.000	0.112
TSS.rat.RGSC3.4	0.09	0.00	0.09
TSS.rat.Rnor_5.0	0.084	0.000	0.084
TSS.zebrafish.Zv8	0.085	0.000	0.085
TSS.zebrafish.Zv9	0.108	0.000	0.109
addAncestors	1.240	0.032	1.278
addGeneIDs	2.355	0.056	2.410
annotatePeakInBatch	0.851	0.036	0.886
annotatedPeak	0.096	0.000	0.096
assignChromosomeRegion	0.002	0.000	0.003
binOverFeature	0.393	0.004	0.396
condenseMatrixByColnames	0.019	0.000	0.020
convert2EntrezID	0.382	0.000	0.381
countPatternInSeqs	0.127	0.000	0.127
egOrgMap	0.001	0.000	0.001
enrichedGO	0.003	0.000	0.003
findOverlappingPeaks	0.002	0.000	0.002
findOverlapsOfPeaks	0.497	0.008	0.504
getAllPeakSequence	0.591	0.004	0.613
getAnnotation	0.001	0.000	0.001
getEnrichedGO	0.016	0.000	0.016
getEnrichedPATH	0.001	0.000	0.001
getGeneSeq	0.003	0.000	0.003
getUniqueGOidCount	0.001	0.000	0.002
getVennCounts	0.002	0.000	0.002
hyperGtest	0.002	0.000	0.002
makeVennDiagram	0.004	0.000	0.004
mergePlusMinusPeaks	0.002	0.000	0.001
myPeakList	0.033	0.004	0.040
peaksNearBDP	0.001	0.000	0.001
summarizePatternInPeaks	0.616	0.004	0.620
toGRanges	0.041	0.000	0.041
translatePattern	0.001	0.000	0.001
write2FASTA	0.036	0.000	0.036