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CHECK report for DmelSGI on malbec1

This page was generated on 2020-04-14 17:46:23 -0400 (Tue, 14 Apr 2020).

Package 95/384HostnameOS / ArchINSTALLBUILDCHECK
DmelSGI 1.18.0
Bernd Fischer
Snapshot Date: 2020-04-14 09:30:11 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/DmelSGI
Branch: RELEASE_3_10
Last Commit: f7ead31
Last Changed Date: 2019-10-29 13:29:43 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: DmelSGI
Version: 1.18.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:DmelSGI.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings DmelSGI_1.18.0.tar.gz
StartedAt: 2020-04-14 13:24:02 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 13:24:58 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 56.2 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-3.10-bioc/R/bin/R CMD check --install=check:DmelSGI.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings DmelSGI_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-data-experiment/meat/DmelSGI.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.18.0’
* 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 139.3Mb
  sub-directories of 1Mb or more:
    Rscripts    1.7Mb
    data      137.3Mb
* 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 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 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-3.10-data-experiment/meat/DmelSGI.Rcheck/00check.log’
for details.



Installation output

DmelSGI.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL DmelSGI
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘DmelSGI’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DmelSGI)

Tests output


Example timings

DmelSGI.Rcheck/DmelSGI-Ex.timings

nameusersystemelapsed
ChromatinSet-package3.7760.0563.833
DPiM0.0160.0000.016
FBgn2anno0.3240.0080.332
Features0.0000.0040.007
Interactions1.8480.0241.874
Intogen0.0080.0000.010
RohnEtAl0.0000.0000.002
SKDdata0.3520.0080.362
SelectedClusters0.0000.0000.001
SelectedClustersComplexes0.0040.0000.001
TID2HUGO0.0040.0040.010
applyDimensionReduction0.0040.0000.001
callInteractions0.0000.0000.001
datamatrix3.6840.0763.761
estimatePairwiseInteractions0.0000.0040.001
fitepistasis0.1360.0120.147
getBaseDir000
grid.spider0.0040.0000.001
hrNames000
learnCoComplexityFct0.0000.0000.001
mainEffects0.0760.0000.077
myHeatmap0.0000.0000.001
mymedpolish0.0000.0000.001
orderDim000
orderSpiderAxis0.0000.0000.001
pimatrix0.6000.0440.645
plot2Phenotypes0.0000.0000.002
plotHairballLabels0.0040.0000.001
qualityControlFeature0.0000.0000.003
qualityControlGene0.0120.0000.015
selectByStability0.0000.0000.001
stabilitySelection0.1520.0040.157
subSampleForStabilitySelection0.0680.0040.070
subSampleForStabilitySelectionFct0.0000.0000.001
toMatrix0.0000.0000.001
toRaster000
trsf000