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BioC experimental data: CHECK report for DmelSGI on malbec2

This page was generated on 2017-08-15 15:07:57 -0400 (Tue, 15 Aug 2017).

Package 76/316HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DmelSGI 1.8.0
Bernd Fischer
Snapshot Date: 2017-08-15 09:00:06 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_5/experiment/pkgs/DmelSGI
Last Changed Rev: 4155 / Revision: 4227
Last Changed Date: 2017-04-24 16:09:26 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

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

Command output

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### Running command:
###
###   /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.


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)

DmelSGI.Rcheck/DmelSGI-Ex.timings:

nameusersystemelapsed
ChromatinSet-package4.2680.2804.551
DPiM0.0160.0000.015
FBgn2anno0.3240.0360.358
Features0.0000.0040.005
Interactions1.9800.1282.108
Intogen0.0080.0000.009
RohnEtAl0.0000.0000.002
SKDdata0.3360.0280.366
SelectedClusters0.0040.0000.002
SelectedClustersComplexes0.0000.0000.001
TID2HUGO0.0040.0040.008
applyDimensionReduction0.0000.0000.002
callInteractions0.0040.0000.002
datamatrix3.7440.1323.878
estimatePairwiseInteractions0.0000.0000.002
fitepistasis0.2000.0080.211
getBaseDir0.0000.0000.001
grid.spider0.0000.0000.002
hrNames0.0000.0000.001
learnCoComplexityFct0.0000.0000.001
mainEffects0.0680.0080.075
myHeatmap0.0040.0000.001
mymedpolish0.0000.0000.001
orderDim0.0040.0000.001
orderSpiderAxis000
pimatrix0.5960.0280.622
plot2Phenotypes0.0000.0000.002
plotHairballLabels0.0040.0000.000
qualityControlFeature0.0040.0000.003
qualityControlGene0.0160.0000.016
selectByStability0.0000.0000.001
stabilitySelection0.1400.0000.139
subSampleForStabilitySelection0.0640.0040.069
subSampleForStabilitySelectionFct0.0000.0000.001
toMatrix0.0000.0000.001
toRaster0.0000.0000.001
trsf0.0000.0000.001