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BioC 3.5: CHECK report for rcellminer on veracruz2

This page was generated on 2017-07-22 13:33:27 -0400 (Sat, 22 Jul 2017).

Package 1074/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rcellminer 1.8.0
Augustin Luna , Vinodh Rajapakse
Snapshot Date: 2017-07-21 17:18:02 -0400 (Fri, 21 Jul 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/rcellminer
Last Changed Rev: 129126 / Revision: 131496
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: rcellminer
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rcellminer_1.8.0.tar.gz
StartedAt: 2017-07-22 07:02:49 -0400 (Sat, 22 Jul 2017)
EndedAt: 2017-07-22 07:04:58 -0400 (Sat, 22 Jul 2017)
EllapsedTime: 128.7 seconds
RetCode: 0
Status:  OK 
CheckDir: rcellminer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rcellminer_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/rcellminer.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rcellminer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rcellminer’ 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 ‘rcellminer’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    4.5Mb
* 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘rcellminer’ for: ‘initialize’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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
.DrugData: no visible global function definition for ‘new’
.MolData: no visible global function definition for ‘new’
compareFingerprints: no visible global function definition for
  ‘txtProgressBar’
compareFingerprints: no visible global function definition for
  ‘setTxtProgressBar’
crossCors: no visible global function definition for ‘cor.test’
crossCors: no visible global function definition for ‘pt’
crossCorsSpearman: no visible global function definition for ‘cor.test’
getActivityRangeStats: no visible global function definition for
  ‘median’
getColumnQuantiles: no visible global function definition for
  ‘quantile’
getDrugActivityRange: no visible global function definition for ‘as’
getDrugActivityRange: no visible global function definition for ‘IQR’
getDrugActivityRepeatData: no visible global function definition for
  ‘as’
getDrugName: no visible global function definition for ‘as’
getFingerprintList: no visible global function definition for
  ‘txtProgressBar’
getFingerprintList: no visible global function definition for
  ‘setTxtProgressBar’
getMedSenLineActivity: no visible global function definition for
  ‘median’
getMinDrugActivityRepeatCor: no visible global function definition for
  ‘as’
getMoaToCompounds: no visible global function definition for ‘as’
getNumDrugActivityRepeats: no visible global function definition for
  ‘as’
getRsd: no visible binding for global variable ‘sd’
getRsd: no visible global function definition for ‘median’
getSmiles: no visible global function definition for ‘as’
passRuleOf5FromNsc: no visible global function definition for ‘as’
plotCellMiner: no visible global function definition for ‘par’
plotCellMiner: no visible global function definition for ‘layout’
plotCellMiner: no visible global function definition for ‘lcm’
plotCellMiner: no visible global function definition for ‘str’
plotCellMiner: no visible global function definition for ‘axis’
plotDrugActivityRepeats: no visible global function definition for ‘as’
plotDrugActivityRepeats: no visible global function definition for
  ‘pdf’
plotDrugActivityRepeats: no visible global function definition for
  ‘dev.off’
plotDrugSets: no visible binding for global variable ‘median’
plotDrugSets: no visible binding for global variable ‘sd’
plotDrugSets: no visible global function definition for ‘pdf’
plotDrugSets: no visible global function definition for ‘par’
plotDrugSets: no visible global function definition for ‘axis’
plotDrugSets: no visible global function definition for ‘segments’
plotDrugSets: no visible global function definition for ‘dev.off’
plotStructures: no visible global function definition for ‘par’
plotStructuresFromNscs: no visible global function definition for ‘as’
rcdkplot: no visible global function definition for ‘par’
rcdkplot: no visible global function definition for ‘plot’
rcdkplot: no visible global function definition for ‘rasterImage’
rowCors: no visible global function definition for ‘pt’
searchForNscs: no visible global function definition for ‘as’
[[<-,MolData: no visible global function definition for ‘validObject’
getFeatureAnnot,DrugData: no visible global function definition for
  ‘as’
getFeatureAnnot,MolData : <anonymous>: no visible global function
  definition for ‘as’
initialize,DrugData: no visible global function definition for
  ‘validObject’
initialize,MolData: no visible global function definition for
  ‘validObject’
Undefined global functions or variables:
  IQR as axis cor.test dev.off layout lcm median new par pdf plot pt
  quantile rasterImage sd segments setTxtProgressBar str txtProgressBar
  validObject
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "axis", "layout", "lcm", "par", "plot",
             "rasterImage", "segments")
  importFrom("methods", "as", "new", "validObject")
  importFrom("stats", "IQR", "cor.test", "median", "pt", "quantile",
             "sd")
  importFrom("utils", "setTxtProgressBar", "str", "txtProgressBar")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/rcellminer.Rcheck/00check.log’
for details.


rcellminer.Rcheck/00install.out:

* installing *source* package ‘rcellminer’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rcellminer)

rcellminer.Rcheck/rcellminer-Ex.timings:

nameusersystemelapsed
compareFingerprints2.4020.1692.065
crossCors0.0850.0000.089
crossCorsSpearman0.0010.0010.000
getActivityRangeStats0.1310.0040.149
getColumnQuantiles0.0030.0000.004
getDrugActivityData0.0070.0010.009
getDrugActivityRange0.0240.0010.026
getDrugActivityRepeatData0.0040.0010.005
getDrugMoaList0.0670.0030.077
getDrugName0.0020.0000.002
getFeatureDataFromMatList2.1330.2342.451
getFingerprintList0.0970.0030.059
getMedSenLineActivity0.0130.0010.007
getMinDrugActivityRepeatCor0.0090.0000.009
getMoaStr0.1180.0120.137
getMoaToCompounds0.0770.0350.117
getMolDataMatrices0.4300.1090.553
getMolDataType0.0010.0000.001
getNumDrugActivityRepeats0.0100.0000.011
getNumMissingLines0.0010.0000.002
getRsd0.0090.0010.009
getSmiles0.0020.0000.002
hasMoa0.0370.0030.039
isPublic0.0020.0000.003
loadCellminerPlotInfo0.0010.0010.002
loadNciColorSet0.0020.0000.003
passRuleOf50.1650.0090.100
passRuleOf5FromNsc0.0860.0050.055
patternComparison0.3250.0580.395
plotCellMiner1.2610.1481.447
plotDrugActivityRepeats0.8220.1160.964
plotDrugSets0.0460.0170.063
plotStructures2.2050.4702.440
plotStructuresFromNscs0.2230.0180.157
rcdkplot0.0520.0050.054
removeMolDataType0.0000.0000.001
restrictFeatureMat0.0010.0000.002
rowCors0.0010.0010.001
runShinyApp0.0010.0000.001
runShinyComparePlots000
runShinyCompareStructures0.0000.0010.000
runShinyCompoundBrowser0.0000.0000.001
searchForNscs0.0070.0000.007
selectCorrelatedRows0.0010.0000.002
selectCorrelatedRowsFromMatrices0.0030.0010.005