BioC experimental data: CHECK report for DmelSGI on morelia

Package: DmelSGI

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DmelSGI_1.3.0.tar.gz

StartedAt: 2015-11-25 10:24:41 -0800 (Wed, 25 Nov 2015)

EndedAt: 2015-11-25 10:27:38 -0800 (Wed, 25 Nov 2015)

EllapsedTime: 177.6 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_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-data-experiment/meat/DmelSGI.Rcheck’
* using R Under development (unstable) (2015-11-08 r69614)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.3.0’
* 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/44s] OK
* checking installed package size ... NOTE
  installed size is 140.9Mb
  sub-directories of 1Mb or more:
    Rscripts    1.7Mb
    data      137.3Mb
    doc         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 ... [12s/30s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
ChromatinSet-package 3.838  0.113   5.039
* 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-3.3-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	3.838	0.113	5.039
DPiM	0.015	0.000	0.259
FBgn2anno	0.392	0.022	0.468
Features	0.006	0.000	0.945
Interactions	2.000	0.095	4.153
Intogen	0.017	0.000	0.017
RohnEtAl	0.003	0.001	0.004
SKDdata	0.420	0.029	1.021
SelectedClusters	0.003	0.001	0.209
SelectedClustersComplexes	0.002	0.001	0.232
TID2HUGO	0.007	0.001	0.300
applyDimensionReduction	0.002	0.000	0.003
callInteractions	0.001	0.000	0.002
datamatrix	3.524	0.045	3.576
estimatePairwiseInteractions	0.002	0.000	0.002
fitepistasis	0.137	0.017	1.943
getBaseDir	0.001	0.001	0.001
grid.spider	0.002	0.000	0.003
hrNames	0.002	0.000	0.001
learnCoComplexityFct	0.002	0.000	0.002
mainEffects	0.059	0.004	1.075
myHeatmap	0.002	0.000	0.002
mymedpolish	0.002	0.000	0.003
orderDim	0.000	0.000	0.001
orderSpiderAxis	0.001	0.000	0.001
pimatrix	0.460	0.033	3.569
plot2Phenotypes	0.004	0.001	0.004
plotHairballLabels	0.001	0.000	0.002
qualityControlFeature	0.005	0.000	0.101
qualityControlGene	0.019	0.019	0.891
selectByStability	0.002	0.001	0.002
stabilitySelection	0.123	0.006	0.664
subSampleForStabilitySelection	0.052	0.008	1.076
subSampleForStabilitySelectionFct	0.002	0.000	0.002
toMatrix	0.001	0.000	0.001
toRaster	0.000	0.000	0.001
trsf	0.001	0.000	0.001