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CHECK report for RCAS on tokay1

This page was generated on 2020-08-07 12:09:51 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE RCAS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1404/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCAS 1.15.0
Bora Uyar
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/RCAS
Branch: master
Last Commit: ec2d4f7
Last Changed Date: 2020-04-27 14:59:40 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 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
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RCAS
Version: 1.15.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RCAS_1.15.0.tar.gz
StartedAt: 2020-08-07 03:08:33 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 03:31:37 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 1384.7 seconds
RetCode: 0
Status:  OK  
CheckDir: RCAS.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RCAS_1.15.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/RCAS.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RCAS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RCAS' version '1.15.0'
* 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 whether package 'RCAS' 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 ... OK
* 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 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
getFeatureBoundaryCoverageMulti 21.64   0.48   22.13
getMotifSummaryTable            17.96   0.54   88.68
runMotifDiscovery               17.77   0.45   71.77
calculateCoverageProfileList    13.77   1.66   15.42
calculateCoverageProfile         9.89   0.70   10.60
summarizeQueryRegions            9.72   0.12    9.84
findDifferentialMotifs           9.37   0.37   36.80
getTargetedGenesTable            8.30   0.16    8.45
summarizeQueryRegionsMulti       7.86   0.52   21.50
getTxdbFeaturesFromGRanges       7.34   0.17    7.52
getFeatureBoundaryCoverage       4.98   0.11    5.10
createDB                         2.86   0.07   56.98
getIntervalOverlapMatrix         1.17   0.08   12.98
findEnrichedFunctions            1.02   0.11    5.01
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
getMotifSummaryTable            20.48   0.53   90.19
runMotifDiscovery               18.97   0.47   63.29
calculateCoverageProfileList    15.48   0.40   15.89
getFeatureBoundaryCoverageMulti 13.74   0.64   14.39
calculateCoverageProfile        11.89   0.60   12.48
getTargetedGenesTable            8.72   0.25    8.97
getTxdbFeaturesFromGRanges       8.56   0.20    8.78
summarizeQueryRegionsMulti       8.30   0.22   30.92
findDifferentialMotifs           8.02   0.33   48.09
summarizeQueryRegions            7.25   0.16    7.40
plotFeatureBoundaryCoverage      6.09   0.20    6.30
getFeatureBoundaryCoverageBin    5.23   0.09    5.32
createDB                         4.49   0.05   34.69
getIntervalOverlapMatrix         1.00   0.05   14.02
* 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: OK


Installation output

RCAS.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/RCAS_1.15.0.tar.gz && rm -rf RCAS.buildbin-libdir && mkdir RCAS.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RCAS.buildbin-libdir RCAS_1.15.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL RCAS_1.15.0.zip && rm RCAS_1.15.0.tar.gz RCAS_1.15.0.zip
###
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  % 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 1644k  100 1644k    0     0  29.8M      0 --:--:-- --:--:-- --:--:-- 32.1M

install for i386

* installing *source* package 'RCAS' ...
** 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 'RCAS'
    finding HTML links ... done
    calculateCoverageProfile                html  
    calculateCoverageProfileFromTxdb        html  
    calculateCoverageProfileList            html  
    calculateCoverageProfileListFromTxdb    html  
    checkSeqDb                              html  
    createControlRegions                    html  
    createDB                                html  
    createOrthologousGeneSetList            html  
    deleteSampleDataFromDB                  html  
    discoverFeatureSpecificMotifs           html  
    extractSequences                        html  
    findDifferentialMotifs                  html  
    findEnrichedFunctions                   html  
    generateKmers                           html  
    getFeatureBoundaryCoverage              html  
    getFeatureBoundaryCoverageBin           html  
    getFeatureBoundaryCoverageMulti         html  
    getIntervalOverlapMatrix                html  
    getMotifSummaryTable                    html  
    getTargetedGenesTable                   html  
    getTxdbFeatures                         html  
    getTxdbFeaturesFromGRanges              html  
    gff                                     html  
    importBed                               html  
    importBedFiles                          html  
    importGtf                               html  
    parseMsigdb                             html  
    plotFeatureBoundaryCoverage             html  
    printMsigdbDataset                      html  
    queryGff                                html  
    queryRegions                            html  
    retrieveOrthologs                       html  
    runGSEA                                 html  
    runMotifDiscovery                       html  
    runMotifRG                              html  
    runReport                               html  
    runReportMetaAnalysis                   html  
    runTopGO                                html  
    summarizeDatabaseContent                html  
    summarizeQueryRegions                   html  
    summarizeQueryRegionsMulti              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 'RCAS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RCAS' as RCAS_1.15.0.zip
* DONE (RCAS)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'RCAS' successfully unpacked and MD5 sums checked

Tests output

RCAS.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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(RCAS)
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

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

    filter

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

    layout

Loading required package: DT
Loading required package: data.table
> 
> test_check("RCAS")
== testthat results  ===========================================================
[ OK: 48 | SKIPPED: 0 | WARNINGS: 11 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  55.64    4.84   88.32 

RCAS.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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(RCAS)
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

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

    filter

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

    layout

Loading required package: DT
Loading required package: data.table
> 
> test_check("RCAS")
== testthat results  ===========================================================
[ OK: 48 | SKIPPED: 0 | WARNINGS: 11 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  48.01    2.00   79.53 

Example timings

RCAS.Rcheck/examples_i386/RCAS-Ex.timings

nameusersystemelapsed
calculateCoverageProfile 9.89 0.7010.60
calculateCoverageProfileList13.77 1.6615.42
checkSeqDb0.500.060.64
createControlRegions0.300.060.36
createDB 2.86 0.0756.98
discoverFeatureSpecificMotifs000
extractSequences1.540.201.75
findDifferentialMotifs 9.37 0.3736.80
findEnrichedFunctions1.020.115.01
generateKmers000
getFeatureBoundaryCoverage4.980.115.10
getFeatureBoundaryCoverageBin4.660.184.82
getFeatureBoundaryCoverageMulti21.64 0.4822.13
getIntervalOverlapMatrix 1.17 0.0812.98
getMotifSummaryTable17.96 0.5488.68
getTargetedGenesTable8.300.168.45
getTxdbFeaturesFromGRanges7.340.177.52
importBed0.220.030.25
importBedFiles1.000.051.05
importGtf000
plotFeatureBoundaryCoverage4.440.114.59
queryGff0.640.000.64
runMotifDiscovery17.77 0.4571.77
runReport000
runReportMetaAnalysis0.920.414.35
summarizeQueryRegions9.720.129.84
summarizeQueryRegionsMulti 7.86 0.5221.50

RCAS.Rcheck/examples_x64/RCAS-Ex.timings

nameusersystemelapsed
calculateCoverageProfile11.89 0.6012.48
calculateCoverageProfileList15.48 0.4015.89
checkSeqDb0.690.050.84
createControlRegions0.360.000.36
createDB 4.49 0.0534.69
discoverFeatureSpecificMotifs000
extractSequences1.870.262.14
findDifferentialMotifs 8.02 0.3348.09
findEnrichedFunctions0.730.084.17
generateKmers000
getFeatureBoundaryCoverage4.270.194.46
getFeatureBoundaryCoverageBin5.230.095.32
getFeatureBoundaryCoverageMulti13.74 0.6414.39
getIntervalOverlapMatrix 1.00 0.0514.02
getMotifSummaryTable20.48 0.5390.19
getTargetedGenesTable8.720.258.97
getTxdbFeaturesFromGRanges8.560.208.78
importBed0.470.000.47
importBedFiles1.690.061.75
importGtf000
plotFeatureBoundaryCoverage6.090.206.30
queryGff1.500.051.55
runMotifDiscovery18.97 0.4763.29
runReport000
runReportMetaAnalysis0.830.282.07
summarizeQueryRegions7.250.167.40
summarizeQueryRegionsMulti 8.30 0.2230.92