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CHECK report for rcellminer on malbec1

This page was generated on 2018-04-12 13:13:25 -0400 (Thu, 12 Apr 2018).

Package 1133/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rcellminer 2.0.0
Augustin Luna , Vinodh Rajapakse
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/rcellminer
Branch: RELEASE_3_6
Last Commit: 80f5ba3
Last Changed Date: 2017-11-21 10:30:04 -0400 (Tue, 21 Nov 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: rcellminer
Version: 2.0.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings rcellminer_2.0.0.tar.gz
StartedAt: 2018-04-12 02:12:25 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:19:45 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 440.1 seconds
RetCode: 0
Status:  OK 
CheckDir: rcellminer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings rcellminer_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/rcellminer.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 ‘2.0.0’
* 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 ... NOTE
  installed size is 10.4Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    6.5Mb
* 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 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 installed files from ‘inst/doc’ ... 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/rcellminer.Rcheck/00check.log’
for details.



Installation output

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)

Tests output

rcellminer.Rcheck/tests/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, cbind, colMeans, colSums, colnames, 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 
371.036   1.236 368.536 

Example timings

rcellminer.Rcheck/rcellminer-Ex.timings

nameusersystemelapsed
compareFingerprints2.2040.1001.802
crossCors0.0720.0000.074
crossCorsSpearman000
getActivityRangeStats0.0840.0000.084
getColumnQuantiles0.0000.0040.002
getDrugActivityData0.0040.0000.003
getDrugActivityRange0.0160.0000.015
getDrugActivityRepeatData0.0080.0000.009
getDrugMoaList0.0560.0040.060
getDrugName0.0440.0000.045
getFeatureDataFromMatList2.8480.2843.198
getFingerprintList0.0920.0000.043
getMedSenLineActivity0.0040.0000.004
getMinDrugActivityRepeatCor0.0040.0000.005
getMoaStr0.1280.0000.127
getMoaToCompounds0.0760.0040.082
getMolDataMatrices0.4320.0600.488
getNumDrugActivityRepeats0.0000.0000.002
getNumMissingLines0.0000.0000.001
getRsd0.0040.0000.005
getSmiles0.0440.0040.049
hasMoa0.0360.0000.035
isPublic0.0000.0000.001
loadCellminerPlotInfo0.0000.0000.001
loadNciColorSet0.0040.0000.002
parCorPatternComparison0.4480.0040.453
passRuleOf50.1600.0080.210
passRuleOf5FromNsc0.1280.0040.094
patternComparison0.3480.0400.389
plotCellMiner0.9120.0640.976
plotCellMiner2D0.0000.0000.001
plotDrugActivityRepeats0.7880.1040.892
plotDrugSets0.0320.0000.029
plotStructures1.9920.0721.118
plotStructuresFromNscs0.4680.0080.245
rcdkplot0.0840.0120.071
removeMolDataType0.0000.0000.001
rowCors0.0040.0000.001
runShinyApp000
runShinyComparePlots000
runShinyCompareStructures0.0040.0000.000
runShinyCompoundBrowser0.0000.0000.001
searchForNscs0.0080.0040.014
selectCorrelatedRows0.0000.0000.001
selectCorrelatedRowsFromMatrices0.0040.0000.004