| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:15 -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: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings circRNAprofiler_1.14.0.tar.gz |
| StartedAt: 2023-10-15 20:06:10 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 20:19:34 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 803.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: circRNAprofiler.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings circRNAprofiler_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/circRNAprofiler.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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
liftBSJcoords 22.543 2.265 25.951
plotMotifs 15.819 0.213 25.385
getMotifs 10.537 0.673 16.564
mergeMotifs 10.087 0.196 15.275
* 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 ...
‘circRNAprofiler.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/circRNAprofiler.Rcheck/00check.log’
for details.
circRNAprofiler.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL circRNAprofiler ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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-pc-linux-gnu (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
304.987 10.204 338.905
circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings
| name | user | system | elapsed | |
| ahChainFiles | 0.246 | 0.008 | 0.253 | |
| ahRepeatMasker | 0.002 | 0.000 | 0.002 | |
| annotateBSJs | 0.467 | 0.008 | 0.474 | |
| annotateRepeats | 1.897 | 0.208 | 2.105 | |
| annotateSNPsGWAS | 0.672 | 0.044 | 0.716 | |
| attractSpecies | 0.002 | 0.000 | 0.002 | |
| backSplicedJunctions | 0.536 | 0.000 | 0.536 | |
| checkProjectFolder | 0.002 | 0.000 | 0.002 | |
| filterCirc | 0.421 | 0.023 | 0.444 | |
| formatGTF | 0 | 0 | 0 | |
| getBackSplicedJunctions | 0.001 | 0.000 | 0.001 | |
| getCircSeqs | 0.640 | 0.040 | 0.679 | |
| getDeseqRes | 3.224 | 0.108 | 3.333 | |
| getDetectionTools | 0.002 | 0.000 | 0.002 | |
| getEdgerRes | 0.607 | 0.024 | 0.630 | |
| getMiRsites | 0.602 | 0.012 | 0.615 | |
| getMotifs | 10.537 | 0.673 | 16.564 | |
| getRandomBSJunctions | 0.175 | 0.009 | 0.184 | |
| getRegexPattern | 0.003 | 0.000 | 0.003 | |
| getSeqsAcrossBSJs | 0.597 | 0.024 | 0.621 | |
| getSeqsFromGRs | 0.665 | 0.045 | 0.710 | |
| gtf | 0.012 | 0.004 | 0.016 | |
| gwasTraits | 0.005 | 0.000 | 0.006 | |
| importCircExplorer2 | 0.027 | 0.004 | 0.031 | |
| importCircMarker | 0.099 | 0.024 | 0.123 | |
| importKnife | 0.027 | 0.000 | 0.028 | |
| importMapSplice | 0.060 | 0.004 | 0.065 | |
| importNCLscan | 0.027 | 0.000 | 0.027 | |
| importOther | 0.022 | 0.004 | 0.026 | |
| importUroborus | 0.026 | 0.000 | 0.026 | |
| initCircRNAprofiler | 0.000 | 0.000 | 0.001 | |
| iupac | 0.000 | 0.001 | 0.001 | |
| liftBSJcoords | 22.543 | 2.265 | 25.951 | |
| memeDB | 0.001 | 0.000 | 0.002 | |
| mergeBSJunctions | 4.810 | 0.096 | 4.908 | |
| mergeMotifs | 10.087 | 0.196 | 15.275 | |
| mergedBSJunctions | 0.326 | 0.004 | 0.330 | |
| miRspeciesCodes | 0.002 | 0.000 | 0.002 | |
| plotExBetweenBSEs | 0.927 | 0.004 | 0.930 | |
| plotExPosition | 0.998 | 0.036 | 1.033 | |
| plotHostGenes | 0.864 | 0.008 | 0.872 | |
| plotLenBSEs | 1.680 | 0.024 | 1.704 | |
| plotLenIntrons | 1.682 | 0.004 | 1.686 | |
| plotMiR | 0.612 | 0.004 | 0.617 | |
| plotMotifs | 15.819 | 0.213 | 25.385 | |
| plotTotExons | 0.853 | 0.004 | 0.857 | |
| rearrangeMiRres | 0.589 | 0.008 | 0.597 | |
| volcanoPlot | 3.022 | 0.024 | 3.046 | |