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BioC 3.5: CHECK report for rcellminer on tokay2

This page was generated on 2017-07-22 13:24:51 -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: rm -rf rcellminer.buildbin-libdir rcellminer.Rcheck && mkdir rcellminer.buildbin-libdir rcellminer.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rcellminer.buildbin-libdir rcellminer_1.8.0.tar.gz >rcellminer.Rcheck\00install.out 2>&1 && cp rcellminer.Rcheck\00install.out rcellminer-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=rcellminer.buildbin-libdir --install="check:rcellminer-install.out" --force-multiarch --no-vignettes --timings rcellminer_1.8.0.tar.gz
StartedAt: 2017-07-22 02:24:23 -0400 (Sat, 22 Jul 2017)
EndedAt: 2017-07-22 02:28:21 -0400 (Sat, 22 Jul 2017)
EllapsedTime: 238.1 seconds
RetCode: 0
Status:  OK  
CheckDir: rcellminer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf rcellminer.buildbin-libdir rcellminer.Rcheck && mkdir rcellminer.buildbin-libdir rcellminer.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rcellminer.buildbin-libdir rcellminer_1.8.0.tar.gz >rcellminer.Rcheck\00install.out 2>&1 && cp rcellminer.Rcheck\00install.out rcellminer-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=rcellminer.buildbin-libdir --install="check:rcellminer-install.out" --force-multiarch --no-vignettes --timings rcellminer_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/rcellminer.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'rcellminer' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    3.0Mb
* 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 ... 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
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
compareFingerprints 2.63   0.15   14.86
plotStructures      0.91   0.08    7.41
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plotStructures 1.85   0.19    7.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/rcellminer.Rcheck/00check.log'
for details.


rcellminer.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'rcellminer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rcellminer' as rcellminer_1.8.0.zip
* DONE (rcellminer)

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

nameusersystemelapsed
compareFingerprints 2.63 0.1514.86
crossCors0.070.000.08
crossCorsSpearman000
getActivityRangeStats0.110.000.10
getColumnQuantiles000
getDrugActivityData0.010.000.02
getDrugActivityRange0.020.000.02
getDrugActivityRepeatData0.020.000.01
getDrugMoaList0.040.000.05
getDrugName000
getFeatureDataFromMatList3.200.364.36
getFingerprintList0.030.000.03
getMedSenLineActivity0.020.000.02
getMinDrugActivityRepeatCor000
getMoaStr0.120.020.14
getMoaToCompounds0.100.000.09
getMolDataMatrices0.480.120.61
getMolDataType000
getNumDrugActivityRepeats000
getNumMissingLines000
getRsd0.020.000.02
getSmiles000
hasMoa0.030.000.03
isPublic000
loadCellminerPlotInfo0.010.000.02
loadNciColorSet000
passRuleOf50.110.000.95
passRuleOf5FromNsc0.060.000.06
patternComparison0.330.100.42
plotCellMiner1.160.171.33
plotDrugActivityRepeats0.400.190.59
plotDrugSets0.060.000.06
plotStructures0.910.087.41
plotStructuresFromNscs0.290.000.21
rcdkplot0.140.040.18
removeMolDataType000
restrictFeatureMat0.020.000.01
rowCors000
runShinyApp000
runShinyComparePlots000
runShinyCompareStructures000
runShinyCompoundBrowser000
searchForNscs0.010.000.02
selectCorrelatedRows000
selectCorrelatedRowsFromMatrices0.020.000.01

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

nameusersystemelapsed
compareFingerprints3.050.182.52
crossCors0.110.000.11
crossCorsSpearman000
getActivityRangeStats0.120.000.12
getColumnQuantiles000
getDrugActivityData000
getDrugActivityRange0.020.000.02
getDrugActivityRepeatData0.010.000.01
getDrugMoaList0.070.000.06
getDrugName000
getFeatureDataFromMatList2.250.242.49
getFingerprintList0.150.000.05
getMedSenLineActivity000
getMinDrugActivityRepeatCor0.020.000.01
getMoaStr0.110.000.11
getMoaToCompounds0.090.000.09
getMolDataMatrices0.200.060.27
getMolDataType000
getNumDrugActivityRepeats000
getNumMissingLines000
getRsd0.020.000.02
getSmiles000
hasMoa0.030.000.03
isPublic000
loadCellminerPlotInfo000
loadNciColorSet000
passRuleOf50.160.010.09
passRuleOf5FromNsc0.360.050.34
patternComparison0.300.080.37
plotCellMiner1.360.161.52
plotDrugActivityRepeats0.830.231.06
plotDrugSets0.010.030.05
plotStructures1.850.197.03
plotStructuresFromNscs0.210.030.19
rcdkplot0.180.000.30
removeMolDataType000
restrictFeatureMat000
rowCors000
runShinyApp000
runShinyComparePlots000
runShinyCompareStructures000
runShinyCompoundBrowser000
searchForNscs0.020.000.02
selectCorrelatedRows000
selectCorrelatedRowsFromMatrices000