BioC experimental data: CHECK report for DmelSGI on linux2.bioconductor.org

Package: DmelSGI

Version: 1.3.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings DmelSGI_1.3.0.tar.gz

StartedAt: 2015-10-24 12:04:14 -0400 (Sat, 24 Oct 2015)

EndedAt: 2015-10-24 12:05:04 -0400 (Sat, 24 Oct 2015)

EllapsedTime: 49.9 seconds

RetCode: 0

Status:  OK

CheckDir: DmelSGI.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings DmelSGI_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-data-experiment/meat/DmelSGI.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (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 ... [2s/2s] OK
* checking installed package size ... NOTE
  installed size is 141.3Mb
  sub-directories of 1Mb or more:
    Rscripts    1.7Mb
    data      137.3Mb
    doc         2.0Mb
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/13s] 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
  ‘/home/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	3.852	0.063	3.935
DPiM	0.029	0.000	0.029
FBgn2anno	0.615	0.013	0.631
Features	0.004	0.000	0.004
Interactions	1.789	0.024	1.813
Intogen	0.009	0.000	0.008
RohnEtAl	0.002	0.000	0.002
SKDdata	0.437	0.000	0.438
SelectedClusters	0.002	0.000	0.003
SelectedClustersComplexes	0.001	0.000	0.002
TID2HUGO	0.005	0.003	0.010
applyDimensionReduction	0.002	0.000	0.003
callInteractions	0.002	0.000	0.002
datamatrix	4.401	0.043	4.447
estimatePairwiseInteractions	0.001	0.004	0.002
fitepistasis	0.177	0.008	0.186
getBaseDir	0.000	0.000	0.001
grid.spider	0.002	0.000	0.001
hrNames	0.000	0.004	0.001
learnCoComplexityFct	0.000	0.000	0.001
mainEffects	0.058	0.004	0.063
myHeatmap	0.001	0.000	0.001
mymedpolish	0.000	0.004	0.001
orderDim	0	0	0
orderSpiderAxis	0.000	0.000	0.001
pimatrix	0.503	0.036	0.540
plot2Phenotypes	0.002	0.000	0.001
plotHairballLabels	0.001	0.000	0.001
qualityControlFeature	0.003	0.000	0.003
qualityControlGene	0.009	0.004	0.012
selectByStability	0.001	0.000	0.001
stabilitySelection	0.074	0.000	0.074
subSampleForStabilitySelection	0.055	0.004	0.060
subSampleForStabilitySelectionFct	0.001	0.000	0.000
toMatrix	0.001	0.000	0.000
toRaster	0.001	0.000	0.001
trsf	0.000	0.000	0.001