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CHECK report for NoRCE on tokay2

This page was generated on 2020-10-17 11:57:17 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE NoRCE PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1199/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NoRCE 1.0.0
Gulden Olgun
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/NoRCE
Branch: RELEASE_3_11
Last Commit: bda1f3d
Last Changed Date: 2020-04-27 15:34:50 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: NoRCE
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NoRCE.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings NoRCE_1.0.0.tar.gz
StartedAt: 2020-10-17 06:30:00 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:43:02 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 782.6 seconds
RetCode: 0
Status:  OK  
CheckDir: NoRCE.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NoRCE.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings NoRCE_1.0.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/NoRCE.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'NoRCE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'NoRCE' version '1.0.0'
* 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 'NoRCE' 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
predictmiTargets    22.67   0.16   23.39
genePathwayEnricher 14.73   0.12   17.12
KeggEnrichment      11.27   0.60   29.43
assembly             8.72   0.70   25.94
geneGOEnricher       8.15   0.25    8.82
calculateCorr        8.28   0.01    8.29
mirnaGOEnricher      6.95   0.19   14.89
writeEnrichment      6.34   0.22    7.03
reactomeEnrichment   4.55   0.04    5.39
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
predictmiTargets      16.10   0.23   16.46
genePathwayEnricher   12.13   0.07   13.67
KeggEnrichment        10.84   0.25   26.69
calculateCorr          8.47   0.00    9.06
assembly               7.25   0.26   23.95
writeEnrichment        7.07   0.20    7.26
geneGOEnricher         6.72   0.34    7.06
mirnaRegionGOEnricher  5.25   0.23    5.49
mirnaGOEnricher        5.10   0.07    5.17
* 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

NoRCE.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/NoRCE_1.0.0.tar.gz && rm -rf NoRCE.buildbin-libdir && mkdir NoRCE.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NoRCE.buildbin-libdir NoRCE_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL NoRCE_1.0.0.zip && rm NoRCE_1.0.0.tar.gz NoRCE_1.0.0.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 1646k  100 1646k    0     0  20.4M      0 --:--:-- --:--:-- --:--:-- 22.3M

install for i386

* installing *source* package 'NoRCE' ...
** 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 'NoRCE'
    finding HTML links ... done
    KeggEnrichment                          html  
    NoRCE-class                             html  
    WikiEnrichment                          html  
    annGO                                   html  
    assembly                                html  
    brain_disorder_ncRNA                    html  
    brain_mirna                             html  
    breastmRNA                              html  
    calculateCorr                           html  
    convertGMT                              html  
    convertGeneID                           html  
    corrbased                               html  
    corrbasedMrna                           html  
    createNetwork                           html  
    drawDotPlot                             html  
    extractBiotype                          html  
    filterBiotype                           html  
    geneGOEnricher                          html  
    genePathwayEnricher                     html  
    geneRegionGOEnricher                    html  
    geneRegionPathwayEnricher               html  
    getGoDag                                html  
    getKeggDiagram                          html  
    getNearToExon                           html  
    getNearToIntron                         html  
    getReactomeDiagram                      html  
    getTADOverlap                           html  
    getUCSC                                 html  
    getmiRNACount                           html  
    goEnrichment                            html  
    listTAD                                 html  
    mirna                                   html  
    mirnaGOEnricher                         html  
    mirnaPathwayEnricher                    html  
    mirnaRegionGOEnricher                   html  
    mirnaRegionPathwayEnricher              html  
    mrna                                    html  
    ncRegion                                html  
    packageCheck                            html  
    pathwayEnrichment                       html  
    predictmiTargets                        html  
    reactomeEnrichment                      html  
    setParameters                           html  
    tad_dmel                                html  
    tad_hg19                                html  
    tad_hg38                                html  
    tad_mm10                                html  
    topEnrichment                           html  
    writeEnrichment                         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 'NoRCE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NoRCE' as NoRCE_1.0.0.zip
* DONE (NoRCE)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'NoRCE' successfully unpacked and MD5 sums checked

Tests output

NoRCE.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(NoRCE)

> 
> test_check("NoRCE")
== testthat results  ===========================================================
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  11.09    1.28   15.81 

NoRCE.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(NoRCE)

> 
> test_check("NoRCE")
== testthat results  ===========================================================
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  13.15    0.64   17.04 

Example timings

NoRCE.Rcheck/examples_i386/NoRCE-Ex.timings

nameusersystemelapsed
KeggEnrichment11.27 0.6029.43
WikiEnrichment2.720.193.92
assembly 8.72 0.7025.94
brain_disorder_ncRNA0.020.000.02
brain_mirna000
breastmRNA000
calculateCorr8.280.018.29
convertGeneID0.450.043.63
extractBiotype0.190.030.22
filterBiotype0.040.000.04
geneGOEnricher8.150.258.82
genePathwayEnricher14.73 0.1217.12
geneRegionGOEnricher4.030.174.21
geneRegionPathwayEnricher1.560.021.78
getGoDag2.880.063.96
getKeggDiagram2.650.042.90
getNearToExon1.600.041.63
getNearToIntron1.190.031.22
getReactomeDiagram4.760.124.89
getTADOverlap0.070.030.09
getUCSC0.120.020.14
goEnrichment2.700.112.81
listTAD000
mirna000
mirnaGOEnricher 6.95 0.1914.89
mirnaPathwayEnricher2.970.073.23
mirnaRegionGOEnricher4.670.114.81
mirnaRegionPathwayEnricher1.550.031.76
mrna0.000.020.02
ncRegion000
predictmiTargets22.67 0.1623.39
reactomeEnrichment4.550.045.39
setParameters000
tad_dmel000
tad_hg19000
tad_hg380.000.020.02
tad_mm10000
writeEnrichment6.340.227.03

NoRCE.Rcheck/examples_x64/NoRCE-Ex.timings

nameusersystemelapsed
KeggEnrichment10.84 0.2526.69
WikiEnrichment2.900.134.09
assembly 7.25 0.2623.95
brain_disorder_ncRNA000
brain_mirna000
breastmRNA000
calculateCorr8.470.009.06
convertGeneID0.420.000.42
extractBiotype0.130.000.13
filterBiotype0.010.020.03
geneGOEnricher6.720.347.06
genePathwayEnricher12.13 0.0713.67
geneRegionGOEnricher3.590.123.72
geneRegionPathwayEnricher0.630.000.83
getGoDag2.590.062.85
getKeggDiagram2.830.043.06
getNearToExon1.420.041.47
getNearToIntron1.110.021.12
getReactomeDiagram4.830.094.92
getTADOverlap0.110.000.11
getUCSC0.140.000.14
goEnrichment2.060.032.10
listTAD000
mirna000
mirnaGOEnricher5.100.075.17
mirnaPathwayEnricher2.320.122.69
mirnaRegionGOEnricher5.250.235.49
mirnaRegionPathwayEnricher0.480.000.67
mrna0.000.020.01
ncRegion000
predictmiTargets16.10 0.2316.46
reactomeEnrichment4.450.024.47
setParameters000
tad_dmel000
tad_hg19000
tad_hg38000
tad_mm100.010.000.02
writeEnrichment7.070.207.26