BioC experimental data: CHECK report for DmelSGI on petty

Package: DmelSGI

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DmelSGI_1.0.0.tar.gz

StartedAt: 2015-10-07 09:14:30 -0700 (Wed, 07 Oct 2015)

EndedAt: 2015-10-07 09:15:53 -0700 (Wed, 07 Oct 2015)

EllapsedTime: 82.6 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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-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 ‘1.0.0’
* 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 ... [3s/7s] 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 ... [16s/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-3.1-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	4.642	0.194	4.861
DPiM	0.022	0.001	0.023
FBgn2anno	0.484	0.047	0.530
Features	0.005	0.001	0.005
Interactions	2.387	0.101	2.492
Intogen	0.013	0.000	0.014
RohnEtAl	0.003	0.000	0.004
SKDdata	0.448	0.041	0.498
SelectedClusters	0.002	0.000	0.002
SelectedClustersComplexes	0.002	0.001	0.003
TID2HUGO	0.008	0.000	0.009
applyDimensionReduction	0.003	0.000	0.004
callInteractions	0.003	0.000	0.002
datamatrix	4.730	0.095	4.843
estimatePairwiseInteractions	0.004	0.000	0.004
fitepistasis	0.236	0.030	0.267
getBaseDir	0.001	0.001	0.002
grid.spider	0.003	0.000	0.004
hrNames	0.001	0.001	0.001
learnCoComplexityFct	0.003	0.000	0.003
mainEffects	0.090	0.004	0.095
myHeatmap	0.002	0.000	0.003
mymedpolish	0.002	0.000	0.003
orderDim	0.001	0.001	0.001
orderSpiderAxis	0.001	0.000	0.001
pimatrix	0.706	0.043	0.750
plot2Phenotypes	0.004	0.001	0.004
plotHairballLabels	0.002	0.000	0.001
qualityControlFeature	0.004	0.000	0.005
qualityControlGene	0.022	0.036	0.058
selectByStability	0.002	0.000	0.003
stabilitySelection	0.149	0.012	0.161
subSampleForStabilitySelection	0.077	0.010	0.086
subSampleForStabilitySelectionFct	0.001	0.000	0.002
toMatrix	0.001	0.000	0.001
toRaster	0.001	0.000	0.001
trsf	0.000	0.000	0.001