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CHECK report for DmelSGI on malbec1

This page was generated on 2018-04-12 12:49:54 -0400 (Thu, 12 Apr 2018).

Package 77/326HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DmelSGI 1.10.0
Bernd Fischer
Snapshot Date: 2018-04-12 07:35:06 -0400 (Thu, 12 Apr 2018)
URL: https://git.bioconductor.org/packages/DmelSGI
Branch: RELEASE_3_6
Last Commit: 4161b88
Last Changed Date: 2017-10-30 11:58:30 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: DmelSGI
Version: 1.10.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DmelSGI_1.10.0.tar.gz
StartedAt: 2018-04-12 09:54:43 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 09:55:37 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 53.8 seconds
RetCode: 0
Status:  OK 
CheckDir: DmelSGI.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DmelSGI_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-data-experiment/meat/DmelSGI.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.10.0’
* 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 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 ... 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-3.6-data-experiment/meat/DmelSGI.Rcheck/00check.log’
for details.



Installation output

DmelSGI.Rcheck/00install.out

* 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)

Tests output


Example timings

DmelSGI.Rcheck/DmelSGI-Ex.timings

nameusersystemelapsed
ChromatinSet-package3.6120.0483.660
DPiM0.0120.0000.014
FBgn2anno0.3160.0040.322
Features0.0080.0000.007
Interactions1.8640.0241.889
Intogen0.0120.0000.009
RohnEtAl0.0000.0000.002
SKDdata0.3480.0000.345
SelectedClusters0.0000.0000.002
SelectedClustersComplexes0.0000.0000.001
TID2HUGO0.0040.0080.011
applyDimensionReduction0.0000.0000.002
callInteractions0.0040.0000.001
datamatrix3.5640.0403.606
estimatePairwiseInteractions0.0000.0000.002
fitepistasis0.1880.0080.196
getBaseDir0.0000.0000.001
grid.spider0.0000.0000.002
hrNames0.0000.0000.001
learnCoComplexityFct0.0000.0000.001
mainEffects0.0720.0040.074
myHeatmap0.0000.0000.001
mymedpolish0.0040.0000.001
orderDim000
orderSpiderAxis000
pimatrix0.5160.0520.568
plot2Phenotypes0.0040.0000.001
plotHairballLabels0.0000.0000.001
qualityControlFeature0.0040.0000.003
qualityControlGene0.0080.0040.013
selectByStability0.0000.0000.001
stabilitySelection0.1160.0040.119
subSampleForStabilitySelection0.0600.0040.064
subSampleForStabilitySelectionFct0.0000.0000.001
toMatrix000
toRaster000
trsf000