Simona Aufiero
| Snapshot Date: 2023-03-17 14:27:35 -0400 (Fri, 17 Mar 2023) |
| git_url: https://git.bioconductor.org/packages/circRNAprofiler |
| git_branch: master |
| 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 2023-03-18 11:05:55 -0400 (Sat, 18 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" | 4282 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" | 4279 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" | 4145 |
| 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 342/2189 | 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: /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_1.13.7.tar.gz |
| StartedAt: 2023-03-17 23:20:03 -0400 (Fri, 17 Mar 2023) |
| EndedAt: 2023-03-17 23:57:48 -0400 (Fri, 17 Mar 2023) |
| EllapsedTime: 2265.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: circRNAprofiler.Rcheck |
| Warnings: NA |
##############################################################################
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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_1.13.7.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/circRNAprofiler.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
Apple clang version 12.0.0 (clang-1200.0.32.29)
GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* 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 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
liftBSJcoords 33.692 2.863 54.976
plotLenBSEs 19.947 0.139 27.145
plotLenIntrons 19.761 0.134 26.757
mergeBSJunctions 11.480 0.469 18.073
plotExPosition 10.278 0.066 14.990
plotTotExons 10.234 0.071 13.997
plotExBetweenBSEs 10.223 0.072 14.212
plotHostGenes 10.054 0.060 14.079
getDeseqRes 9.179 0.105 14.296
volcanoPlot 7.989 0.085 11.287
plotMotifs 4.151 0.070 8.199
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
── Error ('test_getMotifs.R:193:13'): getMotifs() and mergeMotifs() generates the correct data structure
with circRNA and BSJ seqs ──
Error in `.getUserDBmotifs(database, species, memeIndexFilePath, reverse,
pathToMotifs)`: object 'rbpMotifsFromDBnew' not found
Backtrace:
▆
1. └─circRNAprofiler::getMotifs(...) at test_getMotifs.R:193:12
2. └─circRNAprofiler:::.filterMotifs(...)
3. └─circRNAprofiler:::.getUserDBmotifs(...)
4. └─base::rbind(motifsFromFileNew[, c(1, 2)], rbpMotifsFromDBnew)
5. └─base::rbind(deparse.level, ...)
[ FAIL 3 | WARN 31 | SKIP 1 | PASS 216 ]
Error: Test failures
Execution halted
* 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 ERROR, 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/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.fail
R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences"
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 3730 bytes
URL can not be reached: https://attract.cnic.es/attract/static/ATtRACT.zip .
ATtRACT motif can not be analyzed.trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
downloaded 3730 bytes
URL can not be reached: https://attract.cnic.es/attract/static/ATtRACT.zip .
ATtRACT motif can not be analyzed.trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
downloaded 3730 bytes
URL can not be reached: https://attract.cnic.es/attract/static/ATtRACT.zip .
ATtRACT motif can not be analyzed.[ FAIL 3 | WARN 31 | SKIP 1 | PASS 216 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_getMotifs.R:34:19'): getMotifs() and mergeMotifs() generate the correct data structure
with GR seqs ──
Error in `.getUserDBmotifs(database, species, memeIndexFilePath, reverse,
pathToMotifs)`: object 'rbpMotifsFromDBnew' not found
Backtrace:
▆
1. └─circRNAprofiler::getMotifs(...) at test_getMotifs.R:34:18
2. └─circRNAprofiler:::.filterMotifs(...)
3. └─circRNAprofiler:::.getUserDBmotifs(...)
4. └─base::rbind(motifsFromFileNew[, c(1, 2)], rbpMotifsFromDBnew)
5. └─base::rbind(deparse.level, ...)
── Error ('test_getMotifs.R:118:19'): getMotifs() generates a list with the correct
content with GR seqs ──
Error in `.getUserDBmotifs(database, species, memeIndexFilePath, reverse,
pathToMotifs)`: object 'rbpMotifsFromDBnew' not found
Backtrace:
▆
1. └─circRNAprofiler::getMotifs(...) at test_getMotifs.R:118:18
2. └─circRNAprofiler:::.filterMotifs(...)
3. └─circRNAprofiler:::.getUserDBmotifs(...)
4. └─base::rbind(motifsFromFileNew[, c(1, 2)], rbpMotifsFromDBnew)
5. └─base::rbind(deparse.level, ...)
── Error ('test_getMotifs.R:193:13'): getMotifs() and mergeMotifs() generates the correct data structure
with circRNA and BSJ seqs ──
Error in `.getUserDBmotifs(database, species, memeIndexFilePath, reverse,
pathToMotifs)`: object 'rbpMotifsFromDBnew' not found
Backtrace:
▆
1. └─circRNAprofiler::getMotifs(...) at test_getMotifs.R:193:12
2. └─circRNAprofiler:::.filterMotifs(...)
3. └─circRNAprofiler:::.getUserDBmotifs(...)
4. └─base::rbind(motifsFromFileNew[, c(1, 2)], rbpMotifsFromDBnew)
5. └─base::rbind(deparse.level, ...)
[ FAIL 3 | WARN 31 | SKIP 1 | PASS 216 ]
Error: Test failures
Execution halted
circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings
| name | user | system | elapsed | |
| ahChainFiles | 0.252 | 0.011 | 0.369 | |
| ahRepeatMasker | 0.003 | 0.002 | 0.004 | |
| annotateBSJs | 3.067 | 0.074 | 4.447 | |
| annotateRepeats | 3.017 | 0.224 | 4.808 | |
| annotateSNPsGWAS | 2.410 | 0.041 | 3.879 | |
| attractSpecies | 0.002 | 0.002 | 0.009 | |
| backSplicedJunctions | 1.159 | 0.009 | 1.783 | |
| checkProjectFolder | 0.003 | 0.001 | 0.005 | |
| filterCirc | 0.990 | 0.013 | 1.471 | |
| formatGTF | 0.001 | 0.000 | 0.005 | |
| getBackSplicedJunctions | 0.001 | 0.001 | 0.002 | |
| getCircSeqs | 2.373 | 0.043 | 3.645 | |
| getDeseqRes | 9.179 | 0.105 | 14.296 | |
| getDetectionTools | 0.004 | 0.000 | 0.004 | |
| getEdgerRes | 1.392 | 0.017 | 2.106 | |
| getMiRsites | 2.353 | 0.042 | 3.676 | |
| getMotifs | 2.452 | 0.052 | 4.822 | |
| getRandomBSJunctions | 0.577 | 0.011 | 0.788 | |
| getRegexPattern | 0.003 | 0.001 | 0.004 | |
| getSeqsAcrossBSJs | 2.291 | 0.041 | 3.336 | |
| getSeqsFromGRs | 2.381 | 0.039 | 3.556 | |
| gtf | 0.034 | 0.004 | 0.054 | |
| gwasTraits | 0.008 | 0.002 | 0.013 | |
| importCircExplorer2 | 0.074 | 0.003 | 0.109 | |
| importCircMarker | 0.258 | 0.007 | 0.370 | |
| importKnife | 0.060 | 0.002 | 0.084 | |
| importMapSplice | 0.144 | 0.002 | 0.193 | |
| importNCLscan | 0.073 | 0.003 | 0.100 | |
| importOther | 0.051 | 0.002 | 0.068 | |
| importUroborus | 0.053 | 0.002 | 0.079 | |
| initCircRNAprofiler | 0 | 0 | 0 | |
| iupac | 0.002 | 0.002 | 0.004 | |
| liftBSJcoords | 33.692 | 2.863 | 54.976 | |
| memeDB | 0.002 | 0.002 | 0.005 | |
| mergeBSJunctions | 11.480 | 0.469 | 18.073 | |
| mergeMotifs | 2.371 | 0.050 | 4.868 | |
| mergedBSJunctions | 0.760 | 0.008 | 0.974 | |
| miRspeciesCodes | 0.004 | 0.005 | 0.008 | |
| plotExBetweenBSEs | 10.223 | 0.072 | 14.212 | |
| plotExPosition | 10.278 | 0.066 | 14.990 | |
| plotHostGenes | 10.054 | 0.060 | 14.079 | |
| plotLenBSEs | 19.947 | 0.139 | 27.145 | |
| plotLenIntrons | 19.761 | 0.134 | 26.757 | |
| plotMiR | 2.360 | 0.048 | 3.214 | |
| plotMotifs | 4.151 | 0.070 | 8.199 | |
| plotTotExons | 10.234 | 0.071 | 13.997 | |
| rearrangeMiRres | 2.369 | 0.040 | 3.294 | |
| volcanoPlot | 7.989 | 0.085 | 11.287 | |