BioC experimental data: CHECK report for DmelSGI on perceval

Package: DmelSGI

Version: 1.1.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DmelSGI_1.1.2.tar.gz

StartedAt: 2015-08-22 09:07:04 -0700 (Sat, 22 Aug 2015)

EndedAt: 2015-08-22 09:09:07 -0700 (Sat, 22 Aug 2015)

EllapsedTime: 122.5 seconds

RetCode: 0

Status:  OK

CheckDir: DmelSGI.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 DmelSGI_1.1.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-data-experiment/meat/DmelSGI.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DmelSGI/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DmelSGI’ version ‘1.1.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘DmelSGI’ can be installed ... [4s/17s] OK
* checking installed package size ... NOTE
  installed size is 141.2Mb
  sub-directories of 1Mb or more:
    data      137.3Mb
    doc         2.0Mb
    Rscripts    1.7Mb
* 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 loading without being on the library search path ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [14s/17s] 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-data-experiment/meat/DmelSGI.Rcheck/00check.log’
for details.

* installing *source* package ‘DmelSGI’ ...
** 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 (DmelSGI)

name	user	system	elapsed
ChromatinSet-package	3.703	0.262	4.016
DPiM	0.021	0.001	0.022
FBgn2anno	0.540	0.066	0.609
Features	0.005	0.001	0.006
Interactions	1.995	0.131	2.158
Intogen	0.013	0.000	0.013
RohnEtAl	0.003	0.000	0.005
SKDdata	0.350	0.054	0.405
SelectedClusters	0.003	0.000	0.003
SelectedClustersComplexes	0.002	0.001	0.002
TID2HUGO	0.007	0.001	0.008
applyDimensionReduction	0.004	0.001	0.005
callInteractions	0.003	0.000	0.003
datamatrix	3.688	0.115	3.972
estimatePairwiseInteractions	0.003	0.001	0.004
fitepistasis	0.252	0.040	0.296
getBaseDir	0.001	0.000	0.001
grid.spider	0.004	0.001	0.004
hrNames	0.001	0.000	0.001
learnCoComplexityFct	0.002	0.000	0.002
mainEffects	0.091	0.008	0.381
myHeatmap	0.002	0.001	0.002
mymedpolish	0.003	0.000	0.003
orderDim	0.001	0.000	0.001
orderSpiderAxis	0.000	0.000	0.001
pimatrix	0.756	0.065	0.834
plot2Phenotypes	0.004	0.001	0.004
plotHairballLabels	0.002	0.001	0.003
qualityControlFeature	0.005	0.001	0.007
qualityControlGene	0.020	0.046	0.067
selectByStability	0.002	0.001	0.002
stabilitySelection	0.152	0.016	0.398
subSampleForStabilitySelection	0.076	0.018	0.110
subSampleForStabilitySelectionFct	0.002	0.001	0.002
toMatrix	0.000	0.000	0.001
toRaster	0.001	0.000	0.001
trsf	0.001	0.000	0.001