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This page was generated on 2022-01-27 11:07:39 -0500 (Thu, 27 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4167
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4062
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4004
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4121
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for NoRCE on riesling1


To the developers/maintainers of the NoRCE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NoRCE.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1296/2077HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NoRCE 1.7.1  (landing page)
Gulden Olgun
Snapshot Date: 2022-01-26 13:55:18 -0500 (Wed, 26 Jan 2022)
git_url: https://git.bioconductor.org/packages/NoRCE
git_branch: master
git_last_commit: 59b0d7d
git_last_commit_date: 2021-11-21 00:38:54 -0500 (Sun, 21 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'KEGGREST' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: NoRCE
Version: 1.7.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NoRCE.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings NoRCE_1.7.1.tar.gz
StartedAt: 2022-01-26 19:35:32 -0500 (Wed, 26 Jan 2022)
EndedAt: 2022-01-26 19:41:48 -0500 (Wed, 26 Jan 2022)
EllapsedTime: 376.5 seconds
RetCode: 0
Status:   OK  
CheckDir: NoRCE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NoRCE.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings NoRCE_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/NoRCE.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.7.1'
* 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
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
KeggEnrichment      16.61   0.69   40.40
genePathwayEnricher 12.33   0.08   14.11
assembly            11.79   0.59   36.31
writeEnrichment      5.47   0.41    8.46
calculateCorr        5.66   0.19    5.85
* 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: OK


Installation output

NoRCE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL NoRCE
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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
* DONE (NoRCE)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'Basic4Cseq' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'MethylSeekR' is missing or broken
 done

Tests output

NoRCE.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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(NoRCE)

> 
> test_check("NoRCE")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  12.96    1.84   18.68 

Example timings

NoRCE.Rcheck/NoRCE-Ex.timings

nameusersystemelapsed
KeggEnrichment16.61 0.6940.40
assembly11.79 0.5936.31
brain_disorder_ncRNA0.020.000.01
brain_mirna000
breastmRNA000
calculateCorr5.660.195.85
convertGeneID0.290.100.40
extractBiotype0.130.010.14
filterBiotype0.080.000.08
geneGOEnricher4.260.274.58
genePathwayEnricher12.33 0.0814.11
geneRegionGOEnricher2.450.152.60
geneRegionPathwayEnricher1.260.021.49
getGoDag1.600.061.91
getKeggDiagram1.720.112.04
getNearToExon0.780.060.85
getNearToIntron0.730.100.82
getReactomeDiagram2.870.153.03
getTADOverlap0.070.000.06
getUCSC0.090.000.10
goEnrichment1.480.111.59
listTAD0.020.000.02
mirna000
mirnaGOEnricher4.420.334.87
mirnaPathwayEnricher2.280.192.78
mirnaRegionGOEnricher4.470.254.91
mirnaRegionPathwayEnricher0.490.000.70
mrna0.010.000.01
ncRegion000
predictmiTargets0.950.091.57
reactomeEnrichment3.690.334.45
setParameters000
tad_dmel0.020.000.02
tad_hg19000
tad_hg38000
tad_mm10000
writeEnrichment5.470.418.46