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This page was generated on 2021-10-15 15:05:50 -0400 (Fri, 15 Oct 2021).

CHECK results for rcellminer on nebbiolo1

To the developers/maintainers of the rcellminer package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rcellminer.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 1517/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rcellminer 2.14.0  (landing page)
Augustin Luna , Vinodh Rajapakse
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/rcellminer
git_branch: RELEASE_3_13
git_last_commit: 65b993c
git_last_commit_date: 2021-05-19 12:12:16 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: rcellminer
Version: 2.14.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:rcellminer.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings rcellminer_2.14.0.tar.gz
StartedAt: 2021-10-14 11:14:57 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:16:42 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 104.4 seconds
RetCode: 0
Status:   OK  
CheckDir: rcellminer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:rcellminer.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings rcellminer_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/rcellminer.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘2.14.0’
* package encoding: UTF-8
* 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 ... 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 ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 LazyData ... 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/rcellminer.Rcheck/00check.log’
for details.



Installation output

rcellminer.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL rcellminer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘rcellminer’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rcellminer)

Tests output

rcellminer.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, 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: 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")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 2 | SKIP 1 | PASS 226 ]
> 
> proc.time()
   user  system elapsed 
 52.275   4.371  56.632 

Example timings

rcellminer.Rcheck/rcellminer-Ex.timings

nameusersystemelapsed
crossCors0.4730.1090.590
crossCorsSpearman0.0000.0000.001
getActivityRangeStats0.1270.0040.132
getColumnQuantiles0.0030.0000.002
getDrugActivityData0.0330.0000.032
getDrugActivityRange0.0740.0070.082
getDrugActivityRepeatData0.0310.0000.030
getDrugMoaList0.0880.0000.089
getDrugName0.0160.0000.016
getFeatureDataFromMatList2.5760.2992.882
getMedSenLineActivity0.0340.0000.034
getMinDrugActivityRepeatCor0.0330.0000.033
getMoaStr0.2430.0120.254
getMoaToCompounds0.0830.0000.083
getMolDataMatrices0.2400.0520.293
getNumDrugActivityRepeats0.0620.0000.061
getNumMissingLines0.0010.0000.001
getRsd0.0030.0000.004
getSmiles0.0170.0000.016
hasMoa0.0850.0000.084
isPublic0.0020.0000.002
loadCellminerPlotInfo0.0020.0000.001
loadNciColorSet0.0010.0020.002
parCorPatternComparison0.2960.0130.309
patternComparison0.3300.0520.381
plotCellMiner0.4640.0520.516
plotCellMiner2D000
plotDrugActivityRepeats0.7440.0840.827
plotDrugSets0.0360.0000.036
removeMolDataType0.0000.0010.001
rowCors0.0000.0000.001
searchForNscs0.0520.0010.052
selectCorrelatedRows0.0020.0000.002
selectCorrelatedRowsFromMatrices0.0040.0000.004