Simona Aufiero
| Snapshot Date: 2023-03-27 14:00:21 -0400 (Mon, 27 Mar 2023) |
| git_url: https://git.bioconductor.org/packages/circRNAprofiler |
| git_branch: devel |
| git_last_commit: a1cfa55 |
| git_last_commit_date: 2023-01-23 04:19:23 -0400 (Mon, 23 Jan 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-03-28 11:05:50 -0400 (Tue, 28 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" | 4547 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" | 4308 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" | 4301 |
| 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 342/2195 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| circRNAprofiler 1.13.7 (landing page) Simona Aufiero
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: circRNAprofiler |
| Version: 1.13.7 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:circRNAprofiler.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings circRNAprofiler_1.13.7.tar.gz |
| StartedAt: 2023-03-28 00:20:11 -0400 (Tue, 28 Mar 2023) |
| EndedAt: 2023-03-28 00:37:01 -0400 (Tue, 28 Mar 2023) |
| EllapsedTime: 1010.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: circRNAprofiler.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:circRNAprofiler.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings circRNAprofiler_1.13.7.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/circRNAprofiler.Rcheck'
* using R Under development (unstable) (2023-03-15 r83984 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'circRNAprofiler/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'circRNAprofiler' version '1.13.7'
* 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
* 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
liftBSJcoords 36.58 1.54 55.85
plotMotifs 18.84 0.44 20.61
mergeMotifs 11.12 0.36 12.13
getMotifs 11.01 0.33 12.64
mergeBSJunctions 5.14 0.20 5.34
* 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
'F:/biocbuild/bbs-3.17-bioc/meat/circRNAprofiler.Rcheck/00check.log'
for details.
circRNAprofiler.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL circRNAprofiler ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2023 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)
>
> 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 ═══════════════════════════════════════════════════════════════
• empty test (1)
[ FAIL 0 | WARN 31 | SKIP 1 | PASS 255 ]
>
> proc.time()
user system elapsed
527.45 9.56 541.61
circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings
| name | user | system | elapsed | |
| ahChainFiles | 0.13 | 0.07 | 0.18 | |
| ahRepeatMasker | 0 | 0 | 0 | |
| annotateBSJs | 1.74 | 0.23 | 1.97 | |
| annotateRepeats | 1.01 | 0.24 | 1.25 | |
| annotateSNPsGWAS | 0.89 | 0.12 | 1.02 | |
| attractSpecies | 0 | 0 | 0 | |
| backSplicedJunctions | 0.5 | 0.0 | 0.5 | |
| checkProjectFolder | 0 | 0 | 0 | |
| filterCirc | 0.50 | 0.14 | 0.64 | |
| formatGTF | 0 | 0 | 0 | |
| getBackSplicedJunctions | 0 | 0 | 0 | |
| getCircSeqs | 0.80 | 0.27 | 1.06 | |
| getDeseqRes | 3.91 | 0.28 | 4.20 | |
| getDetectionTools | 0 | 0 | 0 | |
| getEdgerRes | 2.05 | 0.14 | 2.19 | |
| getMiRsites | 0.78 | 0.20 | 0.98 | |
| getMotifs | 11.01 | 0.33 | 12.64 | |
| getRandomBSJunctions | 0.12 | 0.14 | 0.27 | |
| getRegexPattern | 0 | 0 | 0 | |
| getSeqsAcrossBSJs | 0.71 | 0.23 | 0.95 | |
| getSeqsFromGRs | 0.86 | 0.21 | 1.06 | |
| gtf | 0.04 | 0.11 | 0.16 | |
| gwasTraits | 0.02 | 0.00 | 0.01 | |
| importCircExplorer2 | 0.03 | 0.00 | 0.05 | |
| importCircMarker | 0.13 | 0.11 | 0.28 | |
| importKnife | 0.03 | 0.00 | 0.07 | |
| importMapSplice | 0.07 | 0.00 | 0.09 | |
| importNCLscan | 0.04 | 0.00 | 0.03 | |
| importOther | 0.03 | 0.00 | 0.06 | |
| importUroborus | 0.01 | 0.02 | 0.05 | |
| initCircRNAprofiler | 0 | 0 | 0 | |
| iupac | 0 | 0 | 0 | |
| liftBSJcoords | 36.58 | 1.54 | 55.85 | |
| memeDB | 0 | 0 | 0 | |
| mergeBSJunctions | 5.14 | 0.20 | 5.34 | |
| mergeMotifs | 11.12 | 0.36 | 12.13 | |
| mergedBSJunctions | 0.31 | 0.19 | 0.50 | |
| miRspeciesCodes | 0.02 | 0.00 | 0.01 | |
| plotExBetweenBSEs | 1.00 | 0.27 | 1.27 | |
| plotExPosition | 1.02 | 0.21 | 1.23 | |
| plotHostGenes | 0.98 | 0.17 | 1.16 | |
| plotLenBSEs | 1.97 | 0.28 | 2.25 | |
| plotLenIntrons | 1.98 | 0.28 | 2.28 | |
| plotMiR | 0.75 | 0.21 | 0.96 | |
| plotMotifs | 18.84 | 0.44 | 20.61 | |
| plotTotExons | 0.89 | 0.29 | 1.18 | |
| rearrangeMiRres | 0.77 | 0.16 | 0.93 | |
| volcanoPlot | 3.92 | 0.17 | 4.10 | |