| Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:02 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
To the developers/maintainers of the circRNAprofiler package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/circRNAprofiler.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 332/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| circRNAprofiler 1.12.2 (landing page) Simona Aufiero
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: circRNAprofiler |
| Version: 1.12.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings circRNAprofiler_1.12.2.tar.gz |
| StartedAt: 2023-04-10 19:23:50 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 19:36:13 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 742.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: circRNAprofiler.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings circRNAprofiler_1.12.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/circRNAprofiler.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘circRNAprofiler/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘circRNAprofiler’ version ‘1.12.2’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
liftBSJcoords 22.607 1.975 25.949
plotMotifs 20.151 0.334 23.810
mergeMotifs 12.675 0.239 22.383
mergeBSJunctions 4.897 0.580 5.548
* 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
circRNAprofiler.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL circRNAprofiler ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘circRNAprofiler’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (circRNAprofiler)
circRNAprofiler.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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)
>
> test_check("circRNAprofiler")
Analysing: Ncoa6:-:chr2:155440785:155437860
Analysing: Arhgap5:+:chr12:52516079:52542636
Analysing: Arhgap5:+:chr12:52516079:52542636
Analysing: Pwwp2a:+:chr11:43704534:43705477trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
downloaded 113 KB
trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
downloaded 113 KB
trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
downloaded 113 KB
trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
downloaded 113 KB
trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
downloaded 113 KB
[ FAIL 0 | WARN 34 | SKIP 1 | PASS 255 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)
[ FAIL 0 | WARN 34 | SKIP 1 | PASS 255 ]
>
> proc.time()
user system elapsed
319.902 6.434 337.382
circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings
| name | user | system | elapsed | |
| ahChainFiles | 0.146 | 0.007 | 0.153 | |
| ahRepeatMasker | 0.001 | 0.001 | 0.003 | |
| annotateBSJs | 0.648 | 0.020 | 0.679 | |
| annotateRepeats | 1.907 | 0.039 | 1.955 | |
| annotateSNPsGWAS | 0.911 | 0.059 | 0.978 | |
| attractSpecies | 0.000 | 0.001 | 0.002 | |
| backSplicedJunctions | 0.751 | 0.009 | 0.778 | |
| checkProjectFolder | 0.002 | 0.001 | 0.003 | |
| filterCirc | 0.481 | 0.017 | 0.500 | |
| formatGTF | 0.000 | 0.000 | 0.001 | |
| getBackSplicedJunctions | 0.001 | 0.000 | 0.001 | |
| getCircSeqs | 0.872 | 0.030 | 0.908 | |
| getDeseqRes | 4.475 | 0.188 | 4.699 | |
| getDetectionTools | 0.002 | 0.001 | 0.002 | |
| getEdgerRes | 0.728 | 0.014 | 0.748 | |
| getMiRsites | 0.760 | 0.028 | 0.795 | |
| getMotifs | 0.903 | 0.032 | 0.962 | |
| getRandomBSJunctions | 0.160 | 0.009 | 0.170 | |
| getRegexPattern | 0.002 | 0.001 | 0.003 | |
| getSeqsAcrossBSJs | 0.812 | 0.032 | 0.848 | |
| getSeqsFromGRs | 0.871 | 0.029 | 0.906 | |
| gtf | 0.020 | 0.004 | 0.026 | |
| gwasTraits | 0.005 | 0.002 | 0.008 | |
| importCircExplorer2 | 0.029 | 0.003 | 0.033 | |
| importCircMarker | 0.108 | 0.006 | 0.115 | |
| importKnife | 0.025 | 0.002 | 0.028 | |
| importMapSplice | 0.059 | 0.002 | 0.063 | |
| importNCLscan | 0.031 | 0.002 | 0.034 | |
| importOther | 0.026 | 0.002 | 0.029 | |
| importUroborus | 0.023 | 0.002 | 0.025 | |
| initCircRNAprofiler | 0.000 | 0.000 | 0.001 | |
| iupac | 0.001 | 0.002 | 0.002 | |
| liftBSJcoords | 22.607 | 1.975 | 25.949 | |
| memeDB | 0.001 | 0.002 | 0.003 | |
| mergeBSJunctions | 4.897 | 0.580 | 5.548 | |
| mergeMotifs | 12.675 | 0.239 | 22.383 | |
| mergedBSJunctions | 0.437 | 0.006 | 0.448 | |
| miRspeciesCodes | 0.002 | 0.005 | 0.007 | |
| plotExBetweenBSEs | 1.109 | 0.023 | 1.142 | |
| plotExPosition | 1.035 | 0.021 | 1.063 | |
| plotHostGenes | 0.966 | 0.016 | 0.991 | |
| plotLenBSEs | 1.920 | 0.067 | 2.000 | |
| plotLenIntrons | 1.686 | 0.037 | 1.737 | |
| plotMiR | 0.866 | 0.028 | 0.904 | |
| plotMotifs | 20.151 | 0.334 | 23.810 | |
| plotTotExons | 1.107 | 0.019 | 1.138 | |
| rearrangeMiRres | 0.888 | 0.033 | 0.933 | |
| volcanoPlot | 3.331 | 0.079 | 3.423 | |