BioC 3.4: CHECK report for rcellminer on morelia

Package: rcellminer

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rcellminer_1.6.0.tar.gz

StartedAt: 2017-04-15 06:55:01 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 06:57:37 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 156.2 seconds

RetCode: 0

Status:  OK

CheckDir: rcellminer.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rcellminer_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/rcellminer.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.6.0’
* 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  8.0Mb
  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
Examples with CPU or elapsed time > 5s
                user system elapsed
plotStructures 2.328  0.954    9.96
* 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-3.4-bioc/meat/rcellminer.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
compareFingerprints	2.272	0.181	2.443
crossCors	0.01	0.00	0.01
crossCorsSpearman	0	0	0
getActivityRangeStats	0.036	0.003	0.039
getColumnQuantiles	0.004	0.001	0.004
getDrugActivityData	0.005	0.001	0.007
getDrugActivityRange	0.008	0.001	0.010
getDrugActivityRepeatData	0.005	0.000	0.005
getDrugMoaList	0.046	0.005	0.051
getDrugName	0.002	0.000	0.002
getFeatureDataFromMatList	2.058	0.256	2.455
getFingerprintList	0.148	0.007	0.058
getMedSenLineActivity	0.005	0.001	0.005
getMinDrugActivityRepeatCor	0.006	0.000	0.007
getMoaStr	0.171	0.043	0.214
getMoaToCompounds	0.033	0.000	0.034
getMolDataMatrices	0.319	0.121	0.438
getMolDataType	0.001	0.000	0.001
getNumDrugActivityRepeats	0.011	0.001	0.012
getNumMissingLines	0.001	0.000	0.001
getRsd	0.005	0.000	0.006
getSmiles	0.002	0.001	0.002
hasMoa	0.037	0.002	0.040
isPublic	0.001	0.000	0.001
loadCellminerPlotInfo	0.002	0.000	0.002
loadNciColorSet	0.003	0.000	0.003
passRuleOf5	0.109	0.010	0.606
passRuleOf5FromNsc	0.053	0.003	0.034
patternComparison	0.267	0.086	0.353
plotCellMiner	0.574	0.128	0.703
plotDrugActivityRepeats	0.439	0.148	0.588
plotDrugSets	0.070	0.027	0.097
plotStructures	2.328	0.954	9.960
plotStructuresFromNscs	0.262	0.025	0.184
rcdkplot	0.060	0.007	0.057
removeMolDataType	0.001	0.000	0.000
restrictFeatureMat	0.002	0.000	0.002
rowCors	0.001	0.000	0.002
runShinyApp	0.001	0.000	0.000
runShinyComparePlots	0	0	0
runShinyCompareStructures	0	0	0
runShinyCompoundBrowser	0	0	0
searchForNscs	0.008	0.001	0.009
selectCorrelatedRows	0.002	0.000	0.003
selectCorrelatedRowsFromMatrices	0.005	0.001	0.006