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BioC experimental data: CHECK report for DmelSGI on moscato1

This page was generated on 2016-05-28 20:31:23 -0700 (Sat, 28 May 2016).

Package 68/292HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DmelSGI 1.5.2
Bernd Fischer
Snapshot Date: 2016-05-28 09:20:19 -0700 (Sat, 28 May 2016)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/DmelSGI
Last Changed Rev: 3773 / Revision: 3781
Last Changed Date: 2016-05-15 13:21:08 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK 

Summary

Package: DmelSGI
Version: 1.5.2
Command: rm -rf DmelSGI.buildbin-libdir DmelSGI.Rcheck && mkdir DmelSGI.buildbin-libdir DmelSGI.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DmelSGI.buildbin-libdir DmelSGI_1.5.2.tar.gz >DmelSGI.Rcheck\00install.out 2>&1 && cp DmelSGI.Rcheck\00install.out DmelSGI-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=DmelSGI.buildbin-libdir --install="check:DmelSGI-install.out" --force-multiarch --no-vignettes --timings DmelSGI_1.5.2.tar.gz
StartedAt: 2016-05-28 14:11:22 -0700 (Sat, 28 May 2016)
EndedAt: 2016-05-28 14:16:21 -0700 (Sat, 28 May 2016)
EllapsedTime: 298.8 seconds
RetCode: 0
Status:  OK  
CheckDir: DmelSGI.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf DmelSGI.buildbin-libdir DmelSGI.Rcheck && mkdir DmelSGI.buildbin-libdir DmelSGI.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DmelSGI.buildbin-libdir DmelSGI_1.5.2.tar.gz >DmelSGI.Rcheck\00install.out 2>&1 && cp DmelSGI.Rcheck\00install.out DmelSGI-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=DmelSGI.buildbin-libdir --install="check:DmelSGI-install.out" --force-multiarch --no-vignettes --timings DmelSGI_1.5.2.tar.gz
###
##############################################################################
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* using log directory 'D:/biocbld/bbs-3.4-data-experiment/meat/DmelSGI.Rcheck'
* using R version 3.3.0 (2016-05-03)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DmelSGI/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DmelSGI' version '1.5.2'
* 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 whether package 'DmelSGI' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 140.4Mb
  sub-directories of 1Mb or more:
    Rscripts    1.7Mb
    data      137.3Mb
    doc         1.2Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'D:/biocbld/bbs-3.4-data-experiment/meat/DmelSGI.Rcheck/00check.log'
for details.


DmelSGI.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'DmelSGI' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DmelSGI' as DmelSGI_1.5.2.zip
* DONE (DmelSGI)

DmelSGI.Rcheck/examples_i386/DmelSGI-Ex.timings:

nameusersystemelapsed
ChromatinSet-package4.610.094.73
DPiM0.020.000.01
FBgn2anno0.640.030.68
Features0.010.000.01
Interactions2.420.032.45
Intogen0.020.020.59
RohnEtAl000
SKDdata0.680.030.72
SelectedClusters000
SelectedClustersComplexes0.020.000.02
TID2HUGO0.000.010.01
applyDimensionReduction000
callInteractions000
datamatrix4.470.104.57
estimatePairwiseInteractions000
fitepistasis0.210.000.20
getBaseDir000
grid.spider000
hrNames000
learnCoComplexityFct0.010.000.02
mainEffects0.060.010.42
myHeatmap0.020.000.01
mymedpolish000
orderDim000
orderSpiderAxis000
pimatrix0.950.040.99
plot2Phenotypes000
plotHairballLabels000
qualityControlFeature000
qualityControlGene0.020.000.01
selectByStability0.010.000.02
stabilitySelection0.080.000.08
subSampleForStabilitySelection0.080.000.07
subSampleForStabilitySelectionFct000
toMatrix000
toRaster000
trsf000

DmelSGI.Rcheck/examples_x64/DmelSGI-Ex.timings:

nameusersystemelapsed
ChromatinSet-package3.980.034.00
DPiM0.010.000.02
FBgn2anno0.390.000.39
Features0.000.010.01
Interactions2.170.052.22
Intogen000
RohnEtAl000
SKDdata0.360.010.38
SelectedClusters0.000.020.01
SelectedClustersComplexes000
TID2HUGO0.000.020.02
applyDimensionReduction000
callInteractions000
datamatrix4.550.014.60
estimatePairwiseInteractions000
fitepistasis0.150.050.20
getBaseDir000
grid.spider0.000.000.01
hrNames000
learnCoComplexityFct000
mainEffects0.080.000.08
myHeatmap000
mymedpolish000
orderDim0.010.000.02
orderSpiderAxis000
pimatrix0.610.030.64
plot2Phenotypes000
plotHairballLabels000
qualityControlFeature000
qualityControlGene0.010.000.02
selectByStability000
stabilitySelection0.100.000.09
subSampleForStabilitySelection0.070.000.08
subSampleForStabilitySelectionFct000
toMatrix000
toRaster000
trsf000