BioC experimental data: CHECK report for DmelSGI on malbec2

Package: DmelSGI

Version: 1.8.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings DmelSGI_1.8.0.tar.gz

StartedAt: 2017-08-15 10:39:36 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 10:40:28 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 52.1 seconds

RetCode: 0

Status:  OK

CheckDir: DmelSGI.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings DmelSGI_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-data-experiment/meat/DmelSGI.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.8.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 141.1Mb
  sub-directories of 1Mb or more:
    Rscripts    1.7Mb
    data      137.3Mb
    doc         1.8Mb
* 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 ... NOTE
callInteractions: no visible global function definition for ‘p.adjust’
fitMatrices: no visible global function definition for ‘png’
fitMatrices: no visible global function definition for ‘dev.off’
makeDall: no visible global function definition for ‘mad’
mymedpolish: no visible binding for global variable ‘median’
mymedpolish : <anonymous>: no visible binding for global variable
  ‘median’
mymedpolish: no visible global function definition for ‘median’
orderDim: no visible global function definition for ‘cor’
orderDim: no visible global function definition for ‘hclust’
orderDim: no visible global function definition for ‘as.dist’
orderSpiderAxis: no visible global function definition for ‘dist’
plot2Phenotypes: no visible global function definition for ‘layout’
plot2Phenotypes: no visible global function definition for ‘par’
plot2Phenotypes: no visible global function definition for ‘plot’
plot2Phenotypes: no visible global function definition for ‘points’
plot2Phenotypes: no visible global function definition for ‘arrows’
plot2Phenotypes: no visible global function definition for ‘segments’
plot2Phenotypes: no visible global function definition for ‘abline’
plot2Phenotypes: no visible global function definition for ‘text’
plotHairballLabels: no visible global function definition for ‘text’
plotHairballLabels: no visible global function definition for ‘lines’
plotPIdata: no visible global function definition for ‘par’
plotPIdata: no visible global function definition for ‘plot’
plotPIdata: no visible global function definition for ‘abline’
saveHeatmapFile: no visible global function definition for ‘png’
saveHeatmapFile: no visible global function definition for ‘dev.off’
saveHeatmapFile: no visible global function definition for ‘cairo_pdf’
selectByStability: no visible global function definition for ‘lm’
selectByStability : <anonymous>: no visible global function definition
  for ‘cor’
subSampleForStabilitySelectionFct : <anonymous>: no visible global
  function definition for ‘median’
subSampleForStabilitySelectionFct : <anonymous>: no visible global
  function definition for ‘mad’
Undefined global functions or variables:
  abline arrows as.dist cairo_pdf cor dev.off dist hclust layout lines
  lm mad median p.adjust par plot png points segments text
Consider adding
  importFrom("grDevices", "cairo_pdf", "dev.off", "png")
  importFrom("graphics", "abline", "arrows", "layout", "lines", "par",
             "plot", "points", "segments", "text")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "lm", "mad",
             "median", "p.adjust")
to your NAMESPACE file.
* 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 ... 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
  ‘/home/biocbuild/bbs-3.5-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	4.268	0.280	4.551
DPiM	0.016	0.000	0.015
FBgn2anno	0.324	0.036	0.358
Features	0.000	0.004	0.005
Interactions	1.980	0.128	2.108
Intogen	0.008	0.000	0.009
RohnEtAl	0.000	0.000	0.002
SKDdata	0.336	0.028	0.366
SelectedClusters	0.004	0.000	0.002
SelectedClustersComplexes	0.000	0.000	0.001
TID2HUGO	0.004	0.004	0.008
applyDimensionReduction	0.000	0.000	0.002
callInteractions	0.004	0.000	0.002
datamatrix	3.744	0.132	3.878
estimatePairwiseInteractions	0.000	0.000	0.002
fitepistasis	0.200	0.008	0.211
getBaseDir	0.000	0.000	0.001
grid.spider	0.000	0.000	0.002
hrNames	0.000	0.000	0.001
learnCoComplexityFct	0.000	0.000	0.001
mainEffects	0.068	0.008	0.075
myHeatmap	0.004	0.000	0.001
mymedpolish	0.000	0.000	0.001
orderDim	0.004	0.000	0.001
orderSpiderAxis	0	0	0
pimatrix	0.596	0.028	0.622
plot2Phenotypes	0.000	0.000	0.002
plotHairballLabels	0.004	0.000	0.000
qualityControlFeature	0.004	0.000	0.003
qualityControlGene	0.016	0.000	0.016
selectByStability	0.000	0.000	0.001
stabilitySelection	0.140	0.000	0.139
subSampleForStabilitySelection	0.064	0.004	0.069
subSampleForStabilitySelectionFct	0.000	0.000	0.001
toMatrix	0.000	0.000	0.001
toRaster	0.000	0.000	0.001
trsf	0.000	0.000	0.001