Simona Aufiero
| Snapshot Date: 2023-09-27 14:05:07 -0400 (Wed, 27 Sep 2023) |
| git_url: https://git.bioconductor.org/packages/circRNAprofiler |
| git_branch: devel |
| git_last_commit: 517f613 |
| git_last_commit_date: 2023-08-27 04:40:48 -0400 (Sun, 27 Aug 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-09-28 11:39:01 -0400 (Thu, 28 Sep 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4660 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4395 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4409 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4400 |
| 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 348/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| circRNAprofiler 1.15.1 (landing page) Simona Aufiero
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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: 1.15.1 |
| 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_1.15.1.tar.gz |
| StartedAt: 2023-09-27 19:41:07 -0400 (Wed, 27 Sep 2023) |
| EndedAt: 2023-09-27 19:56:18 -0400 (Wed, 27 Sep 2023) |
| EllapsedTime: 910.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: circRNAprofiler.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.15.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/circRNAprofiler.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* 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 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘circRNAprofiler/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘circRNAprofiler’ version ‘1.15.1’
* 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 24.459 2.387 32.262
plotMotifs 20.069 0.202 29.753
getMotifs 13.286 0.157 19.336
mergeMotifs 12.837 0.219 19.534
getDeseqRes 5.146 0.186 5.391
mergeBSJunctions 4.601 0.644 5.610
* 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-3.18-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 Patched (2023-06-17 r84564) -- "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 257 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_annotateRepeats.R:4:1'
[ FAIL 0 | WARN 31 | SKIP 1 | PASS 257 ]
>
> proc.time()
user system elapsed
350.419 9.022 394.086
circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings
| name | user | system | elapsed | |
| ahChainFiles | 0.194 | 0.013 | 0.211 | |
| ahRepeatMasker | 0.002 | 0.003 | 0.005 | |
| annotateBSJs | 0.824 | 0.025 | 0.868 | |
| annotateRepeats | 1.342 | 0.064 | 1.425 | |
| annotateSNPsGWAS | 1.005 | 0.049 | 1.086 | |
| attractSpecies | 0.001 | 0.003 | 0.005 | |
| backSplicedJunctions | 0.881 | 0.012 | 0.899 | |
| checkProjectFolder | 0.002 | 0.001 | 0.003 | |
| filterCirc | 0.671 | 0.012 | 0.688 | |
| formatGTF | 0.000 | 0.000 | 0.001 | |
| getBackSplicedJunctions | 0.001 | 0.000 | 0.001 | |
| getCircSeqs | 1.000 | 0.048 | 1.076 | |
| getDeseqRes | 5.146 | 0.186 | 5.391 | |
| getDetectionTools | 0.003 | 0.001 | 0.003 | |
| getEdgerRes | 0.796 | 0.030 | 0.831 | |
| getMiRsites | 0.875 | 0.050 | 0.980 | |
| getMotifs | 13.286 | 0.157 | 19.336 | |
| getRandomBSJunctions | 0.186 | 0.011 | 0.198 | |
| getRegexPattern | 0.002 | 0.002 | 0.005 | |
| getSeqsAcrossBSJs | 1.081 | 0.040 | 1.128 | |
| getSeqsFromGRs | 1.189 | 0.045 | 1.245 | |
| gtf | 0.022 | 0.004 | 0.026 | |
| gwasTraits | 0.005 | 0.003 | 0.008 | |
| importCircExplorer2 | 0.031 | 0.003 | 0.035 | |
| importCircMarker | 0.152 | 0.010 | 0.164 | |
| importKnife | 0.032 | 0.004 | 0.036 | |
| importMapSplice | 0.081 | 0.003 | 0.085 | |
| importNCLscan | 0.030 | 0.003 | 0.036 | |
| importOther | 0.030 | 0.003 | 0.033 | |
| importUroborus | 0.028 | 0.003 | 0.032 | |
| initCircRNAprofiler | 0.001 | 0.000 | 0.001 | |
| iupac | 0.001 | 0.002 | 0.003 | |
| liftBSJcoords | 24.459 | 2.387 | 32.262 | |
| memeDB | 0.001 | 0.002 | 0.003 | |
| mergeBSJunctions | 4.601 | 0.644 | 5.610 | |
| mergeMotifs | 12.837 | 0.219 | 19.534 | |
| mergedBSJunctions | 0.526 | 0.013 | 0.781 | |
| miRspeciesCodes | 0.002 | 0.004 | 0.028 | |
| plotExBetweenBSEs | 1.169 | 0.042 | 1.337 | |
| plotExPosition | 1.289 | 0.040 | 1.350 | |
| plotHostGenes | 1.100 | 0.028 | 1.143 | |
| plotLenBSEs | 2.039 | 0.086 | 2.164 | |
| plotLenIntrons | 1.885 | 0.048 | 1.954 | |
| plotMiR | 0.996 | 0.043 | 1.047 | |
| plotMotifs | 20.069 | 0.202 | 29.753 | |
| plotTotExons | 1.246 | 0.033 | 1.306 | |
| rearrangeMiRres | 0.906 | 0.034 | 0.944 | |
| volcanoPlot | 3.612 | 0.070 | 3.725 | |