BioC 3.2: CHECK report for ChIPpeakAnno on perceval

Package: ChIPpeakAnno

Version: 3.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPpeakAnno_3.4.0.tar.gz

StartedAt: 2015-10-27 06:16:09 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:23:01 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 412.5 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_3.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘3.4.0’
* 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 ... [29s/29s] 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 ... [39s/43s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
ExonPlusUtr.human.GRCh37 5.289  0.149   5.437
addGeneIDs               2.336  0.251   6.112
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [77s/77s]
 [77s/78s] 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-3.2-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	0.062	0.002	0.063
ChIPpeakAnno-package	0.002	0.000	0.001
ExonPlusUtr.human.GRCh37	5.289	0.149	5.437
GFF2RangedData	0.020	0.000	0.021
HOT.spots	0.173	0.041	0.214
Peaks.Ste12.Replicate1	0.035	0.003	0.037
Peaks.Ste12.Replicate2	0.032	0.002	0.034
Peaks.Ste12.Replicate3	0.030	0.002	0.031
TSS.human.GRCh37	0.173	0.037	0.210
TSS.human.GRCh38	0.701	0.013	0.714
TSS.human.NCBI36	0.248	0.040	0.287
TSS.mouse.GRCm38	0.727	0.051	0.777
TSS.mouse.NCBIM37	0.147	0.037	0.184
TSS.rat.RGSC3.4	0.118	0.036	0.153
TSS.rat.Rnor_5.0	0.109	0.037	0.146
TSS.zebrafish.Zv8	0.109	0.039	0.148
TSS.zebrafish.Zv9	0.140	0.039	0.179
addAncestors	2.667	0.152	2.819
addGeneIDs	2.336	0.251	6.112
annoGR	0.000	0.000	0.001
annotatePeakInBatch	1.210	0.068	1.278
annotatedPeak	0.126	0.008	0.135
assignChromosomeRegion	0.006	0.000	0.007
binOverFeature	0.510	0.032	0.542
condenseMatrixByColnames	0.026	0.001	0.027
convert2EntrezID	1.636	0.016	1.651
countPatternInSeqs	0.126	0.001	0.127
egOrgMap	0.002	0.000	0.001
enrichedGO	0.003	0.000	0.003
featureAlignedDistribution	1.341	0.001	1.343
featureAlignedHeatmap	1.516	0.003	1.565
featureAlignedSignal	1.362	0.033	1.395
findOverlappingPeaks	0.005	0.000	0.004
findOverlapsOfPeaks	0.682	0.003	0.686
getAllPeakSequence	0.863	0.025	0.947
getAnnotation	0.001	0.000	0.001
getEnrichedGO	0.028	0.002	0.029
getEnrichedPATH	0.002	0.000	0.002
getGeneSeq	0.007	0.001	0.007
getUniqueGOidCount	0.003	0.000	0.003
getVennCounts	0.005	0.001	0.005
hyperGtest	0.005	0.001	0.005
makeVennDiagram	0.009	0.000	0.009
mergePlusMinusPeaks	0.003	0.000	0.004
myPeakList	0.042	0.002	0.044
peakPermTest	0.003	0.000	0.004
peaksNearBDP	0.002	0.001	0.003
pie1	0.013	0.001	0.014
preparePool	0.002	0.000	0.003
summarizePatternInPeaks	0.877	0.024	0.900
toGRanges	0.033	0.001	0.034
translatePattern	0.001	0.000	0.001
wgEncodeTfbsV3	0.288	0.022	0.310
write2FASTA	0.016	0.001	0.017