| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:36:55 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 | ||||
| Package 347/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| circRNAprofiler 1.14.0 (landing page) Simona Aufiero
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the circRNAprofiler package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: circRNAprofiler |
| Version: 1.14.0 |
| 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_1.14.0.tar.gz |
| StartedAt: 2023-10-15 23:49:00 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-16 00:23:02 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 2041.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: circRNAprofiler.Rcheck |
| Warnings: 0 |
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### Running 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_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/circRNAprofiler.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘circRNAprofiler/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘circRNAprofiler’ version ‘1.14.0’
* 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 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 ... NOTE
.getRBPmotifsAttract: no visible binding for global variable ‘Organism’
.getRBPmotifsAttract: no visible binding for global variable
‘Gene_name’
.getRBPmotifsAttract: no visible binding for global variable ‘Motif’
.getRBPmotifsMEME: no visible binding for global variable ‘path’
.matchWithKnowRBPs: no visible binding for global variable ‘motif’
.reshapeCounts: no visible binding for global variable ‘motif’
.splitRBPs: no visible binding for global variable ‘motif’
mergeMotifs: no visible binding for global variable ‘motif’
Undefined global functions or variables:
Gene_name Motif Organism motif path
* 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
plotMotifs 38.059 0.545 59.781
liftBSJcoords 34.522 3.687 56.528
getMotifs 24.095 0.322 46.320
mergeMotifs 23.777 0.216 38.563
mergeBSJunctions 11.536 0.612 18.669
getDeseqRes 7.785 0.308 11.977
volcanoPlot 7.739 0.114 10.865
plotLenBSEs 3.796 0.068 5.442
plotLenIntrons 3.642 0.054 5.173
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.17-bioc/meat/circRNAprofiler.Rcheck/00check.log’
for details.
circRNAprofiler.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL circRNAprofiler ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 31 | SKIP 1 | PASS 255 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_annotateRepeats.R:4:1'
[ FAIL 0 | WARN 31 | SKIP 1 | PASS 255 ]
>
> proc.time()
user system elapsed
700.382 10.161 959.768
circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings
| name | user | system | elapsed | |
| ahChainFiles | 0.406 | 0.014 | 0.639 | |
| ahRepeatMasker | 0.003 | 0.003 | 0.009 | |
| annotateBSJs | 1.038 | 0.030 | 1.559 | |
| annotateRepeats | 3.039 | 0.060 | 4.487 | |
| annotateSNPsGWAS | 1.532 | 0.082 | 2.329 | |
| attractSpecies | 0.002 | 0.002 | 0.005 | |
| backSplicedJunctions | 1.168 | 0.015 | 1.682 | |
| checkProjectFolder | 0.003 | 0.002 | 0.005 | |
| filterCirc | 0.896 | 0.037 | 1.405 | |
| formatGTF | 0.000 | 0.000 | 0.001 | |
| getBackSplicedJunctions | 0.002 | 0.001 | 0.003 | |
| getCircSeqs | 1.447 | 0.106 | 2.316 | |
| getDeseqRes | 7.785 | 0.308 | 11.977 | |
| getDetectionTools | 0.004 | 0.001 | 0.004 | |
| getEdgerRes | 1.377 | 0.029 | 2.184 | |
| getMiRsites | 1.383 | 0.054 | 2.166 | |
| getMotifs | 24.095 | 0.322 | 46.320 | |
| getRandomBSJunctions | 0.323 | 0.014 | 0.502 | |
| getRegexPattern | 0.003 | 0.002 | 0.006 | |
| getSeqsAcrossBSJs | 1.390 | 0.048 | 2.141 | |
| getSeqsFromGRs | 1.538 | 0.050 | 2.403 | |
| gtf | 0.035 | 0.004 | 0.055 | |
| gwasTraits | 0.007 | 0.003 | 0.011 | |
| importCircExplorer2 | 0.055 | 0.005 | 0.091 | |
| importCircMarker | 0.255 | 0.011 | 0.391 | |
| importKnife | 0.060 | 0.004 | 0.096 | |
| importMapSplice | 0.138 | 0.004 | 0.207 | |
| importNCLscan | 0.055 | 0.005 | 0.092 | |
| importOther | 0.049 | 0.004 | 0.082 | |
| importUroborus | 0.052 | 0.004 | 0.078 | |
| initCircRNAprofiler | 0.001 | 0.000 | 0.001 | |
| iupac | 0.001 | 0.003 | 0.008 | |
| liftBSJcoords | 34.522 | 3.687 | 56.528 | |
| memeDB | 0.002 | 0.002 | 0.004 | |
| mergeBSJunctions | 11.536 | 0.612 | 18.669 | |
| mergeMotifs | 23.777 | 0.216 | 38.563 | |
| mergedBSJunctions | 0.735 | 0.014 | 1.059 | |
| miRspeciesCodes | 0.003 | 0.006 | 0.012 | |
| plotExBetweenBSEs | 2.082 | 0.040 | 2.963 | |
| plotExPosition | 2.081 | 0.043 | 2.830 | |
| plotHostGenes | 1.954 | 0.037 | 2.784 | |
| plotLenBSEs | 3.796 | 0.068 | 5.442 | |
| plotLenIntrons | 3.642 | 0.054 | 5.173 | |
| plotMiR | 1.394 | 0.053 | 2.083 | |
| plotMotifs | 38.059 | 0.545 | 59.781 | |
| plotTotExons | 2.064 | 0.045 | 2.882 | |
| rearrangeMiRres | 1.482 | 0.050 | 2.028 | |
| volcanoPlot | 7.739 | 0.114 | 10.865 | |