Multiple platform build/check report for BioC 3.11 - CHECK report for circRNAprofiler on tokay2

Package: circRNAprofiler

Version: 1.2.1

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:circRNAprofiler.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings circRNAprofiler_1.2.1.tar.gz

StartedAt: 2020-10-17 02:37:09 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 03:01:30 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 1460.6 seconds

RetCode: 0

Status: OK

CheckDir: circRNAprofiler.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:circRNAprofiler.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings circRNAprofiler_1.2.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/circRNAprofiler.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 'circRNAprofiler/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'circRNAprofiler' version '1.2.1'
* 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 'circRNAprofiler' 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
liftBSJcoords    31.37   1.97   41.29
plotMotifs       28.71   0.11   29.27
getMotifs        22.27   0.25   23.72
mergeMotifs      18.86   0.14   19.98
annotateRepeats  17.45   0.95   22.44
mergeBSJunctions  8.10   0.39    8.49
getDeseqRes       5.58   1.44    7.02
getMiRsites       5.84   0.27    8.79
volcanoPlot       5.75   0.34    6.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
plotMotifs       30.81   0.22   31.50
liftBSJcoords    24.76   1.72   27.00
annotateRepeats  15.50   0.86   16.85
mergeMotifs      16.05   0.11   16.47
getMotifs        13.99   0.21   14.97
mergeBSJunctions  5.79   0.28    6.08
getMiRsites       4.48   0.19    7.14
* 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/circRNAprofiler_1.2.1.tar.gz && rm -rf circRNAprofiler.buildbin-libdir && mkdir circRNAprofiler.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=circRNAprofiler.buildbin-libdir circRNAprofiler_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL circRNAprofiler_1.2.1.zip && rm circRNAprofiler_1.2.1.tar.gz circRNAprofiler_1.2.1.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3596k  100 3596k    0     0  42.6M      0 --:--:-- --:--:-- --:--:-- 45.6M

install for i386

* installing *source* package 'circRNAprofiler' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'circRNAprofiler'
    finding HTML links ... done
    ahChainFiles                            html  
    ahRepeatMasker                          html  
    annotateBSJs                            html  
    annotateRepeats                         html  
    finding level-2 HTML links ... done

    annotateSNPsGWAS                        html  
    attractSpecies                          html  
    backSplicedJunctions                    html  
    checkProjectFolder                      html  
    filterCirc                              html  
    formatGTF                               html  
    getBackSplicedJunctions                 html  
    getCircSeqs                             html  
    getDeseqRes                             html  
    getDetectionTools                       html  
    getEdgerRes                             html  
    getMiRsites                             html  
    getMotifs                               html  
    getRandomBSJunctions                    html  
    getRegexPattern                         html  
    getSeqsAcrossBSJs                       html  
    getSeqsFromGRs                          html  
    gtf                                     html  
    gwasTraits                              html  
    importCircExplorer2                     html  
    importCircMarker                        html  
    importKnife                             html  
    importMapSplice                         html  
    importNCLscan                           html  
    importOther                             html  
    importUroborus                          html  
    initCircRNAprofiler                     html  
    iupac                                   html  
    liftBSJcoords                           html  
    memeDB                                  html  
    mergeBSJunctions                        html  
    mergeMotifs                             html  
    mergedBSJunctions                       html  
    miRspeciesCodes                         html  
    plotExBetweenBSEs                       html  
    plotExPosition                          html  
    plotHostGenes                           html  
    plotLenBSEs                             html  
    plotLenIntrons                          html  
    plotMiR                                 html  
    plotMotifs                              html  
    plotTotExons                            html  
    rearrangeMiRres                         html  
    volcanoPlot                             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 'circRNAprofiler' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'circRNAprofiler' as circRNAprofiler_1.2.1.zip
* DONE (circRNAprofiler)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'circRNAprofiler' successfully unpacked and MD5 sums checked


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(circRNAprofiler)
Loading required package: gwascat
gwascat loaded.  Use makeCurrentGwascat() to extract current image.
 from EBI.  The data folder of this package has some legacy extracts.
> 
> test_check("circRNAprofiler")
trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
Content type 'application/zip' length unknown
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... ...
downloaded 113 KB

trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
Content type 'application/zip' length unknown
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... ...
downloaded 113 KB

trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
Content type 'application/zip' length unknown
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... ...
downloaded 113 KB

trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
Content type 'application/zip' length unknown
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... ...
downloaded 113 KB

trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
Content type 'application/zip' length unknown
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... ...
downloaded 113 KB

== testthat results  ===========================================================
[ OK: 257 | SKIPPED: 0 | WARNINGS: 5 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 258.57    8.26  277.00


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(circRNAprofiler)
Loading required package: gwascat
gwascat loaded.  Use makeCurrentGwascat() to extract current image.
 from EBI.  The data folder of this package has some legacy extracts.
> 
> test_check("circRNAprofiler")
trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
Content type 'application/zip' length unknown
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... ...
downloaded 113 KB

trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
Content type 'application/zip' length unknown
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... ...
downloaded 113 KB

trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
Content type 'application/zip' length unknown
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... ...
downloaded 113 KB

trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
Content type 'application/zip' length unknown
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... ...
downloaded 113 KB

trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
Content type 'application/zip' length unknown
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... ...
downloaded 113 KB

== testthat results  ===========================================================
[ OK: 257 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 290.12    7.84  303.40

name	user	system	elapsed
ahChainFiles	0.2	0.0	0.2
ahRepeatMasker	0.02	0.00	0.02
annotateBSJs	0.72	0.11	0.82
annotateRepeats	17.45	0.95	22.44
annotateSNPsGWAS	1.75	0.22	2.30
attractSpecies	0.02	0.00	0.01
backSplicedJunctions	0.87	0.00	0.88
checkProjectFolder	0	0	0
filterCirc	0.58	0.07	0.64
formatGTF	0	0	0
getBackSplicedJunctions	0	0	0
getCircSeqs	0.87	0.15	1.03
getDeseqRes	5.58	1.44	7.02
getDetectionTools	0	0	0
getEdgerRes	1.25	0.12	1.37
getMiRsites	5.84	0.27	8.79
getMotifs	22.27	0.25	23.72
getRandomBSJunctions	0.28	0.05	0.33
getRegexPattern	0	0	0
getSeqsAcrossBSJs	1.56	0.14	1.71
getSeqsFromGRs	1.55	0.23	1.78
gtf	0.03	0.11	0.14
gwasTraits	0.02	0.00	0.01
importCircExplorer2	0.03	0.00	0.03
importCircMarker	0.29	0.06	0.36
importKnife	0.04	0.00	0.03
importMapSplice	0.09	0.00	0.10
importNCLscan	0.03	0.00	0.03
importOther	0.02	0.00	0.02
importUroborus	0.03	0.00	0.03
initCircRNAprofiler	0	0	0
iupac	0	0	0
liftBSJcoords	31.37	1.97	41.29
memeDB	0	0	0
mergeBSJunctions	8.10	0.39	8.49
mergeMotifs	18.86	0.14	19.98
mergedBSJunctions	0.50	0.03	0.53
miRspeciesCodes	0	0	0
plotExBetweenBSEs	1.20	0.16	1.36
plotExPosition	1.41	0.17	1.58
plotHostGenes	1.39	0.12	1.51
plotLenBSEs	1.81	0.14	1.96
plotLenIntrons	1.92	0.11	2.03
plotMiR	0.97	0.10	1.06
plotMotifs	28.71	0.11	29.27
plotTotExons	1.68	0.12	1.79
rearrangeMiRres	1.07	0.13	1.21
volcanoPlot	5.75	0.34	6.11

name	user	system	elapsed
ahChainFiles	0.20	0.06	0.27
ahRepeatMasker	0	0	0
annotateBSJs	0.79	0.14	0.93
annotateRepeats	15.50	0.86	16.85
annotateSNPsGWAS	1.28	0.24	1.51
attractSpecies	0	0	0
backSplicedJunctions	0.63	0.00	0.63
checkProjectFolder	0	0	0
filterCirc	0.48	0.11	0.59
formatGTF	0	0	0
getBackSplicedJunctions	0	0	0
getCircSeqs	0.87	0.12	1.00
getDeseqRes	4.08	0.31	4.39
getDetectionTools	0	0	0
getEdgerRes	0.72	0.03	0.75
getMiRsites	4.48	0.19	7.14
getMotifs	13.99	0.21	14.97
getRandomBSJunctions	0.14	0.04	0.18
getRegexPattern	0	0	0
getSeqsAcrossBSJs	0.73	0.11	0.85
getSeqsFromGRs	0.91	0.14	1.04
gtf	0.02	0.06	0.08
gwasTraits	0.01	0.00	0.01
importCircExplorer2	0.05	0.00	0.05
importCircMarker	0.20	0.07	0.27
importKnife	0.02	0.00	0.01
importMapSplice	0.08	0.00	0.08
importNCLscan	0.03	0.00	0.03
importOther	0.02	0.00	0.02
importUroborus	0.01	0.00	0.01
initCircRNAprofiler	0	0	0
iupac	0	0	0
liftBSJcoords	24.76	1.72	27.00
memeDB	0	0	0
mergeBSJunctions	5.79	0.28	6.08
mergeMotifs	16.05	0.11	16.47
mergedBSJunctions	0.72	0.06	0.78
miRspeciesCodes	0	0	0
plotExBetweenBSEs	1.80	0.14	1.94
plotExPosition	1.44	0.17	1.61
plotHostGenes	1.23	0.08	1.31
plotLenBSEs	1.86	0.12	1.99
plotLenIntrons	2.33	0.10	2.42
plotMiR	1.09	0.09	1.19
plotMotifs	30.81	0.22	31.50
plotTotExons	1.29	0.11	1.39
rearrangeMiRres	0.92	0.14	1.06
volcanoPlot	4.26	0.14	4.40

CHECK report for circRNAprofiler on tokay2

Summary

Command output

Installation output

Tests output

Example timings