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This page was generated on 2021-10-15 15:06:18 -0400 (Fri, 15 Oct 2021).

CHECK results for rcellminer on tokay2

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
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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: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rcellminer.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings rcellminer_2.14.0.tar.gz
StartedAt: 2021-10-15 04:10:18 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 04:15:11 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 292.9 seconds
RetCode: 0
Status:   OK  
CheckDir: rcellminer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rcellminer.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings rcellminer_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/rcellminer.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '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 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
* 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 ... OK
** checking whether the namespace can be unloaded cleanly ... 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
getFeatureDataFromMatList 3.41   0.46   14.36
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
getFeatureDataFromMatList 3.98   0.59    8.22
plotDrugActivityRepeats   1.27   0.09   10.50
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/rcellminer.Rcheck/00check.log'
for details.



Installation output

rcellminer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/rcellminer_2.14.0.tar.gz && rm -rf rcellminer.buildbin-libdir && mkdir rcellminer.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rcellminer.buildbin-libdir rcellminer_2.14.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL rcellminer_2.14.0.zip && rm rcellminer_2.14.0.tar.gz rcellminer_2.14.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 81884  100 81884    0     0   522k      0 --:--:-- --:--:-- --:--:--  526k

install for i386

* 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
  converting help for package 'rcellminer'
    finding HTML links ... done
    DrugData-class                          html  
    DrugData-eSet-eSet-MIAxE-method         html  
    DrugData                                html  
    Drug_MOA_Key                            html  
    MolData-class                           html  
    MolData-list-MIAxE-method               html  
    MolData                                 html  
    cmVersion                               html  
    crossCors                               html  
    crossCorsSpearman                       html  
    dot-onAttach                            html  
    dot-onLoad                              html  
    drugDB                                  html  
    elNetMolDataNCI60                       html  
    fingerprintList                         html  
    getAct-DrugData-method                  html  
    getAct                                  html  
    getActivityRangeStats                   html  
    getAllFeatureData-MolData-method        html  
    getAllFeatureData                       html  
    getBinaryMutationData                   html  
    getColumnQuantiles                      html  
    getDrugActivityData                     html  
    getDrugActivityRange                    html  
    getDrugActivityRepeatData               html  
    getDrugMoaList                          html  
    getDrugName                             html  
    getESetList-MolData-method              html  
    getESetList                             html  
    getFeatureAnnot-DrugData-method         html  
    getFeatureAnnot-MolData-method          html  
    getFeatureAnnot                         html  
    getFeatureDataFromMatList               html  
    getMedSenLineActivity                   html  
    getMinDrugActivityRepeatCor             html  
    getMoaStr                               html  
    getMoaToCompounds                       html  
    getMolDataMatrices                      html  
    getMolDataType                          html  
    getNumDrugActivityRepeats               html  
    getNumMissingLines                      html  
    getRepeatAct-DrugData-method            html  
    getRepeatAct                            html  
    getRsd                                  html  
    getSampleData-DrugData-method           html  
    getSampleData-MolData-method            html  
    getSampleData                           html  
    getSmiles                               html  
    hasMoa                                  html  
    initialize-DrugData-method              html  
    initialize-MolData-method               html  
    isPublic                                html  
    loadCellminerPlotInfo                   html  
    loadNciColorSet                         html  
    parCorPatternComparison                 html  
    patternComparison                       html  
    plotCellMiner                           html  
    plotCellMiner2D                         html  
    plotDrugActivityRepeats                 html  
    plotDrugSets                            html  
    removeMolDataType                       html  
    restrictFeatureMat                      html  
    rowCors                                 html  
    searchForNscs                           html  
    selectCorrelatedRows                    html  
    selectCorrelatedRowsFromMatrices        html  
    sub-sub-MolData-method                  html  
    sub-subset-MolData-method               html  
** 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

install for x64

* installing *source* package 'rcellminer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rcellminer' as rcellminer_2.14.0.zip
* DONE (rcellminer)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'rcellminer' successfully unpacked and MD5 sums checked

Tests output

rcellminer.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  68.62    6.32   77.78 

rcellminer.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  62.20    4.60   67.09 

Example timings

rcellminer.Rcheck/examples_i386/rcellminer-Ex.timings

nameusersystemelapsed
crossCors0.820.112.07
crossCorsSpearman000
getActivityRangeStats0.250.020.27
getColumnQuantiles0.020.000.01
getDrugActivityData0.070.000.08
getDrugActivityRange0.140.000.14
getDrugActivityRepeatData0.070.000.06
getDrugMoaList0.150.000.16
getDrugName0.030.000.03
getFeatureDataFromMatList 3.41 0.4614.36
getMedSenLineActivity0.050.000.05
getMinDrugActivityRepeatCor0.040.000.04
getMoaStr0.290.000.28
getMoaToCompounds0.090.000.10
getMolDataMatrices0.520.050.56
getNumDrugActivityRepeats0.070.000.08
getNumMissingLines000
getRsd000
getSmiles0.010.000.02
hasMoa0.080.000.08
isPublic000
loadCellminerPlotInfo0.020.000.01
loadNciColorSet000
parCorPatternComparison0.370.020.39
patternComparison0.270.090.40
plotCellMiner0.470.130.60
plotCellMiner2D000
plotDrugActivityRepeats0.650.150.85
plotDrugSets0.020.030.05
removeMolDataType000
rowCors000
searchForNscs0.210.000.22
selectCorrelatedRows000
selectCorrelatedRowsFromMatrices000

rcellminer.Rcheck/examples_x64/rcellminer-Ex.timings

nameusersystemelapsed
crossCors0.800.030.83
crossCorsSpearman000
getActivityRangeStats0.250.000.26
getColumnQuantiles000
getDrugActivityData0.060.000.06
getDrugActivityRange0.140.020.16
getDrugActivityRepeatData0.060.000.06
getDrugMoaList0.160.000.16
getDrugName0.030.000.03
getFeatureDataFromMatList3.980.598.22
getMedSenLineActivity0.050.000.05
getMinDrugActivityRepeatCor0.050.000.04
getMoaStr0.260.030.30
getMoaToCompounds0.100.020.11
getMolDataMatrices0.670.080.75
getNumDrugActivityRepeats0.110.000.11
getNumMissingLines000
getRsd0.010.000.01
getSmiles0.020.000.02
hasMoa0.120.000.12
isPublic000
loadCellminerPlotInfo000
loadNciColorSet000
parCorPatternComparison0.490.030.52
patternComparison0.620.200.83
plotCellMiner0.920.161.08
plotCellMiner2D000
plotDrugActivityRepeats 1.27 0.0910.50
plotDrugSets0.560.050.61
removeMolDataType000
rowCors000
searchForNscs0.330.000.33
selectCorrelatedRows000
selectCorrelatedRowsFromMatrices000