Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-10-16 11:36:00 -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: 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_1.14.0.tar.gz |
StartedAt: 2023-10-16 00:37:19 -0400 (Mon, 16 Oct 2023) |
EndedAt: 2023-10-16 00:54:33 -0400 (Mon, 16 Oct 2023) |
EllapsedTime: 1034.1 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_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/circRNAprofiler.Rcheck' * using R version 4.3.1 (2023-06-16 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 '1.14.0' * 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 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 37.31 1.69 54.89 plotMotifs 18.96 0.44 27.32 getMotifs 12.04 0.39 16.97 mergeMotifs 12.06 0.31 16.25 * 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 version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 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 (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test_annotateRepeats.R:4:1' [ FAIL 0 | WARN 31 | SKIP 1 | PASS 255 ] > > proc.time() user system elapsed 538.23 9.79 569.17
circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings
name | user | system | elapsed | |
ahChainFiles | 0.14 | 0.07 | 0.20 | |
ahRepeatMasker | 0 | 0 | 0 | |
annotateBSJs | 0.64 | 0.32 | 0.97 | |
annotateRepeats | 2.00 | 0.31 | 2.31 | |
annotateSNPsGWAS | 0.77 | 0.35 | 1.11 | |
attractSpecies | 0 | 0 | 0 | |
backSplicedJunctions | 0.5 | 0.0 | 0.5 | |
checkProjectFolder | 0 | 0 | 0 | |
filterCirc | 0.45 | 0.21 | 0.67 | |
formatGTF | 0 | 0 | 0 | |
getBackSplicedJunctions | 0 | 0 | 0 | |
getCircSeqs | 0.70 | 0.33 | 1.04 | |
getDeseqRes | 3.71 | 0.39 | 4.09 | |
getDetectionTools | 0 | 0 | 0 | |
getEdgerRes | 0.79 | 0.24 | 1.03 | |
getMiRsites | 0.69 | 0.37 | 1.06 | |
getMotifs | 12.04 | 0.39 | 16.97 | |
getRandomBSJunctions | 0.17 | 0.11 | 0.28 | |
getRegexPattern | 0 | 0 | 0 | |
getSeqsAcrossBSJs | 0.67 | 0.42 | 1.10 | |
getSeqsFromGRs | 0.99 | 0.32 | 1.29 | |
gtf | 0.01 | 0.17 | 0.19 | |
gwasTraits | 0.02 | 0.00 | 0.02 | |
importCircExplorer2 | 0.03 | 0.00 | 0.04 | |
importCircMarker | 0.19 | 0.08 | 0.30 | |
importKnife | 0.01 | 0.03 | 0.06 | |
importMapSplice | 0.08 | 0.01 | 0.10 | |
importNCLscan | 0.03 | 0.00 | 0.04 | |
importOther | 0.03 | 0.00 | 0.04 | |
importUroborus | 0.05 | 0.02 | 0.06 | |
initCircRNAprofiler | 0 | 0 | 0 | |
iupac | 0 | 0 | 0 | |
liftBSJcoords | 37.31 | 1.69 | 54.89 | |
memeDB | 0.02 | 0.00 | 0.01 | |
mergeBSJunctions | 4.39 | 0.28 | 4.68 | |
mergeMotifs | 12.06 | 0.31 | 16.25 | |
mergedBSJunctions | 0.33 | 0.25 | 0.57 | |
miRspeciesCodes | 0.00 | 0.02 | 0.02 | |
plotExBetweenBSEs | 1.19 | 0.36 | 1.55 | |
plotExPosition | 1.18 | 0.41 | 1.61 | |
plotHostGenes | 0.99 | 0.34 | 1.33 | |
plotLenBSEs | 2.06 | 0.35 | 2.41 | |
plotLenIntrons | 2.14 | 0.28 | 2.42 | |
plotMiR | 0.77 | 0.40 | 1.17 | |
plotMotifs | 18.96 | 0.44 | 27.32 | |
plotTotExons | 0.89 | 0.30 | 1.19 | |
rearrangeMiRres | 0.67 | 0.27 | 0.93 | |
volcanoPlot | 3.69 | 0.25 | 3.94 | |