Simona Aufiero
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/circRNAprofiler |
| Branch: RELEASE_3_10 |
| Last Commit: 9167757 |
| Last Changed Date: 2019-10-29 13:11:46 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:32:48 -0400 (Wed, 15 Apr 2020).
| Package 293/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| circRNAprofiler 1.0.0 Simona Aufiero
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: circRNAprofiler |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:circRNAprofiler.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings circRNAprofiler_1.0.0.tar.gz |
| StartedAt: 2020-04-15 02:04:36 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 02:21:55 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 1039.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: circRNAprofiler.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:circRNAprofiler.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings circRNAprofiler_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/circRNAprofiler.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.0.0'
* 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 '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 or elapsed time > 5s
user system elapsed
plotMotifs 19.64 0.07 20.18
mergeMotifs 17.07 0.41 17.72
getMotifs 15.98 0.52 17.64
getDeseqRes 4.98 0.55 5.53
getMiRsites 3.44 0.25 5.69
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotMotifs 18.12 0.12 18.92
mergeMotifs 12.29 0.16 12.90
getMotifs 12.14 0.17 13.55
getMiRsites 3.40 0.14 5.57
* 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
circRNAprofiler.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/circRNAprofiler_1.0.0.tar.gz && rm -rf circRNAprofiler.buildbin-libdir && mkdir circRNAprofiler.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=circRNAprofiler.buildbin-libdir circRNAprofiler_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL circRNAprofiler_1.0.0.zip && rm circRNAprofiler_1.0.0.tar.gz circRNAprofiler_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 3103k 100 3103k 0 0 24.6M 0 --:--:-- --:--:-- --:--:-- 25.4M
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
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_1.0.0.zip
* DONE (circRNAprofiler)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'circRNAprofiler' successfully unpacked and MD5 sums checked
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circRNAprofiler.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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
Loading required package: Homo.sapiens
Loading required package: AnnotationDbi
Loading required package: stats4
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, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db
Loading required package: org.Hs.eg.db
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
gwascat loaded. Use data(ebicat38) for hg38 coordinates;
data(ebicat37) for hg19 coordinates.
>
> 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
210.25 8.18 225.85
|
circRNAprofiler.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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
Loading required package: Homo.sapiens
Loading required package: AnnotationDbi
Loading required package: stats4
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, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db
Loading required package: org.Hs.eg.db
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
gwascat loaded. Use data(ebicat38) for hg38 coordinates;
data(ebicat37) for hg19 coordinates.
>
> 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
225.23 8.06 241.46
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circRNAprofiler.Rcheck/examples_i386/circRNAprofiler-Ex.timings
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circRNAprofiler.Rcheck/examples_x64/circRNAprofiler-Ex.timings
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