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CHECK report for rcellminer on merida1

This page was generated on 2019-04-16 11:58:28 -0400 (Tue, 16 Apr 2019).

Package 1263/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rcellminer 2.4.0
Augustin Luna , Vinodh Rajapakse
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/rcellminer
Branch: RELEASE_3_8
Last Commit: e4c66ad
Last Changed Date: 2018-10-30 11:41:57 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: rcellminer
Version: 2.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rcellminer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rcellminer_2.4.0.tar.gz
StartedAt: 2019-04-16 02:13:16 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:23:28 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 611.7 seconds
RetCode: 0
Status:  OK 
CheckDir: rcellminer.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rcellminer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rcellminer_2.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/rcellminer.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.4.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 ... OK
* 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 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
getColumnQuantiles: no visible global function definition for
  ‘quantile’
getDrugActivityRange: no visible global function definition for ‘IQR’
getRsd: no visible binding for global variable ‘sd’
parCorPatternComparison: no visible global function definition for
  ‘residuals’
parCorPatternComparison: no visible global function definition for ‘lm’
parCorPatternComparison: no visible global function definition for
  ‘na.exclude’
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 ‘axis’
plotCellMiner2D: no visible global function definition for
  ‘element_text’
plotCellMiner2D: no visible global function definition for ‘xlim’
plotCellMiner2D: no visible global function definition for ‘ylim’
plotDrugActivityRepeats: no visible global function definition for
  ‘pdf’
plotDrugActivityRepeats: no visible global function definition for
  ‘dev.off’
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’
rcdkplot: no visible global function definition for ‘par’
rcdkplot: no visible global function definition for ‘get.depictor’
rcdkplot: no visible global function definition for ‘plot’
rcdkplot: no visible global function definition for ‘rasterImage’
Undefined global functions or variables:
  IQR axis dev.off element_text get.depictor layout lcm lm na.exclude
  par pdf plot quantile rasterImage residuals sd segments xlim ylim
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "axis", "layout", "lcm", "par", "plot",
             "rasterImage", "segments")
  importFrom("stats", "IQR", "lm", "na.exclude", "quantile", "residuals",
             "sd")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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-3.8-bioc/meat/rcellminer.Rcheck/00check.log’
for details.



Installation output

rcellminer.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rcellminer
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘rcellminer’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rcellminer)

Tests output

rcellminer.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(rcellminer)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: rcdk
Loading required package: rcdklibs
Loading required package: rJava

Attaching package: 'rcdk'

The following object is masked from 'package:testthat':

    matches

Loading required package: fingerprint
Loading required package: rcellminerData
Consider citing this package: Luna A, et al. rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R. PMID: 26635141; citation("rcellminer")
> 
> #test_package("rcellminer")
> test_check("rcellminer")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 239 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
500.890  17.931 521.453 

Example timings

rcellminer.Rcheck/rcellminer-Ex.timings

nameusersystemelapsed
compareFingerprints1.7480.1981.312
crossCors0.0100.0010.012
crossCorsSpearman000
getActivityRangeStats0.0440.0120.054
getColumnQuantiles0.0040.0000.005
getDrugActivityData0.0030.0000.005
getDrugActivityRange0.0050.0000.006
getDrugActivityRepeatData0.0020.0000.003
getDrugMoaList0.0730.0040.077
getDrugName0.0570.0010.059
getFeatureDataFromMatList3.1190.3463.483
getFingerprintList0.0760.0030.042
getMedSenLineActivity0.0110.0010.006
getMinDrugActivityRepeatCor0.0090.0010.007
getMoaStr0.1430.0130.156
getMoaToCompounds0.0450.0030.049
getMolDataMatrices0.5300.0900.623
getNumDrugActivityRepeats0.0040.0000.004
getNumMissingLines0.0010.0000.001
getRsd0.0180.0000.018
getSmiles0.0680.0020.070
hasMoa0.0550.0030.058
isPublic0.0020.0010.003
loadCellminerPlotInfo0.0020.0000.003
loadNciColorSet0.0020.0010.003
parCorPatternComparison0.5800.0630.648
passRuleOf50.1480.0160.068
passRuleOf5FromNsc0.1120.0090.050
patternComparison0.6310.1210.754
plotCellMiner0.3630.0910.456
plotCellMiner2D000
plotDrugActivityRepeats0.6810.1930.879
plotDrugSets0.1130.0830.198
plotStructures3.6710.8093.771
plotStructuresFromNscs0.6280.0510.329
rcdkplot0.1270.0120.094
removeMolDataType0.0010.0000.000
rowCors0.0010.0000.001
runShinyApp000
runShinyComparePlots0.0000.0000.001
runShinyCompareStructures000
runShinyCompoundBrowser0.0000.0000.001
searchForNscs0.0110.0000.011
selectCorrelatedRows0.0010.0000.002
selectCorrelatedRowsFromMatrices0.0040.0010.004