BioC 3.1: CHECK report for ChIPpeakAnno on morelia

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: 2015-10-09 00:05:16 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:10:57 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 340.9 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 (2015-08-14)
* 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 ‘3.2.2’
* 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 ... [20s/21s] 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 ... [27s/63s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
addGeneIDs 2.523  0.386  35.916
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [54s/67s]
 [55s/67s] 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	0.034	0.000	0.034
ChIPpeakAnno-package	0.834	0.022	0.895
ExonPlusUtr.human.GRCh37	3.851	0.205	4.059
GFF2RangedData	0.023	0.000	0.023
Peaks.Ste12.Replicate1	0.030	0.003	0.033
Peaks.Ste12.Replicate2	0.021	0.008	0.029
Peaks.Ste12.Replicate3	0.023	0.009	0.032
TSS.human.GRCh37	0.142	0.069	0.213
TSS.human.GRCh38	0.792	0.097	0.889
TSS.human.NCBI36	0.485	0.027	0.513
TSS.mouse.GRCm38	0.149	0.025	0.174
TSS.mouse.NCBIM37	0.115	0.018	0.134
TSS.rat.RGSC3.4	0.098	0.022	0.120
TSS.rat.Rnor_5.0	0.097	0.020	0.118
TSS.zebrafish.Zv8	0.108	0.025	0.134
TSS.zebrafish.Zv9	0.10	0.02	0.12
addAncestors	2.110	0.133	2.280
addGeneIDs	2.523	0.386	35.916
annotatePeakInBatch	1.339	0.182	1.550
annotatedPeak	0.110	0.017	0.128
assignChromosomeRegion	0.003	0.000	0.003
binOverFeature	0.573	0.057	0.642
condenseMatrixByColnames	0.027	0.001	0.028
convert2EntrezID	0.414	0.015	0.429
countPatternInSeqs	0.161	0.001	0.162
egOrgMap	0.001	0.001	0.001
enrichedGO	0.003	0.000	0.005
findOverlappingPeaks	0.004	0.000	0.004
findOverlapsOfPeaks	0.736	0.175	1.114
getAllPeakSequence	0.557	0.089	0.844
getAnnotation	0.001	0.001	0.002
getEnrichedGO	0.017	0.007	0.025
getEnrichedPATH	0.001	0.001	0.002
getGeneSeq	0.006	0.003	0.009
getUniqueGOidCount	0.003	0.001	0.003
getVennCounts	0.004	0.001	0.004
hyperGtest	0.002	0.000	0.002
makeVennDiagram	0.004	0.000	0.005
myPeakList	0.037	0.002	0.038
peaksNearBDP	0.002	0.000	0.002
summarizePatternInPeaks	0.637	0.008	0.646
toGRanges	0.048	0.013	0.061
translatePattern	0.000	0.000	0.001
write2FASTA	0.050	0.013	0.064