BioC 3.3: CHECK report for ChIPpeakAnno on morelia

Package: ChIPpeakAnno

Version: 3.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.5.0.tar.gz

StartedAt: 2015-10-22 04:22:42 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 04:27:08 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 266.1 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPpeakAnno.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/ChIPpeakAnno.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘3.5.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘grid’ ‘IRanges’ ‘Biostrings’ ‘GenomicRanges’ ‘S4Vectors’
  ‘VennDiagram’
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 18.7Mb
  sub-directories of 1Mb or more:
    data     12.7Mb
    extdata   4.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [25s/32s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
addGeneIDs 1.654  0.094   8.929
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [50s/50s]
 [50s/51s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.

* installing *source* package ‘ChIPpeakAnno’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ChIPpeakAnno)

name	user	system	elapsed
BED2RangedData	0.033	0.000	0.033
ChIPpeakAnno-package	0.001	0.000	0.001
ExonPlusUtr.human.GRCh37	3.626	0.082	3.708
GFF2RangedData	0.019	0.000	0.020
HOT.spots	0.170	0.024	0.194
Peaks.Ste12.Replicate1	0.037	0.001	0.040
Peaks.Ste12.Replicate2	0.037	0.002	0.038
Peaks.Ste12.Replicate3	0.032	0.002	0.034
TSS.human.GRCh37	0.123	0.022	0.143
TSS.human.GRCh38	0.705	0.009	0.716
TSS.human.NCBI36	0.572	0.035	0.607
TSS.mouse.GRCm38	0.147	0.025	0.172
TSS.mouse.NCBIM37	0.149	0.026	0.175
TSS.rat.RGSC3.4	0.098	0.023	0.120
TSS.rat.Rnor_5.0	0.074	0.016	0.090
TSS.zebrafish.Zv8	0.075	0.018	0.093
TSS.zebrafish.Zv9	0.136	0.020	0.157
addAncestors	1.349	0.110	1.460
addGeneIDs	1.654	0.094	8.929
annoGR	0.001	0.000	0.001
annotatePeakInBatch	1.206	0.082	1.288
annotatedPeak	0.123	0.006	0.129
assignChromosomeRegion	0.003	0.001	0.003
binOverFeature	0.334	0.019	0.352
condenseMatrixByColnames	0.017	0.000	0.017
convert2EntrezID	0.368	0.010	0.377
countPatternInSeqs	0.092	0.001	0.093
egOrgMap	0.001	0.000	0.002
enrichedGO	0.003	0.001	0.004
featureAlignedDistribution	1.057	0.002	1.059
featureAlignedHeatmap	1.222	0.002	1.225
featureAlignedSignal	0.867	0.018	0.886
findOverlappingPeaks	0.003	0.000	0.003
findOverlapsOfPeaks	0.421	0.003	0.524
getAllPeakSequence	0.537	0.018	0.739
getAnnotation	0.002	0.000	0.001
getEnrichedGO	0.025	0.001	0.026
getEnrichedPATH	0.001	0.000	0.002
getGeneSeq	0.006	0.000	0.007
getUniqueGOidCount	0.002	0.001	0.002
getVennCounts	0.004	0.000	0.004
hyperGtest	0.002	0.001	0.003
makeVennDiagram	0.008	0.000	0.008
mergePlusMinusPeaks	0.003	0.000	0.003
myPeakList	0.028	0.002	0.030
peakPermTest	0.002	0.000	0.002
peaksNearBDP	0.002	0.000	0.002
pie1	0.008	0.001	0.009
preparePool	0.001	0.000	0.002
summarizePatternInPeaks	0.443	0.004	0.447
toGRanges	0.028	0.000	0.029
translatePattern	0.001	0.000	0.001
wgEncodeTfbsV3	0.283	0.013	0.296
write2FASTA	0.012	0.001	0.012