| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:28 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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: - 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 341/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| circRNAprofiler 1.15.0 (landing page) Simona Aufiero
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: circRNAprofiler |
| Version: 1.15.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings circRNAprofiler_1.15.0.tar.gz |
| StartedAt: 2023-06-05 19:30:18 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 19:47:45 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 1046.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: circRNAprofiler.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings circRNAprofiler_1.15.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/circRNAprofiler.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘circRNAprofiler/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘circRNAprofiler’ version ‘1.15.0’
* 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 25.267 1.261 30.499
plotMotifs 19.608 0.555 25.625
mergeMotifs 12.427 0.340 14.762
getMotifs 11.615 0.302 15.118
mergeBSJunctions 6.430 0.171 6.625
getDeseqRes 5.749 0.171 5.929
* 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-3.18-bioc/meat/circRNAprofiler.Rcheck/00check.log’
for details.
circRNAprofiler.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL circRNAprofiler ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 ═══════════════════════════════════════════════════════════════
• empty test (1)
[ FAIL 0 | WARN 31 | SKIP 1 | PASS 255 ]
>
> proc.time()
user system elapsed
436.707 8.183 455.275
circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings
| name | user | system | elapsed | |
| ahChainFiles | 0.131 | 0.004 | 0.135 | |
| ahRepeatMasker | 0.002 | 0.000 | 0.001 | |
| annotateBSJs | 0.573 | 0.008 | 0.582 | |
| annotateRepeats | 1.085 | 0.024 | 1.111 | |
| annotateSNPsGWAS | 0.819 | 0.044 | 0.864 | |
| attractSpecies | 0.001 | 0.000 | 0.001 | |
| backSplicedJunctions | 0.546 | 0.008 | 0.555 | |
| checkProjectFolder | 0.002 | 0.000 | 0.002 | |
| filterCirc | 0.391 | 0.004 | 0.396 | |
| formatGTF | 0.000 | 0.000 | 0.001 | |
| getBackSplicedJunctions | 0.001 | 0.000 | 0.001 | |
| getCircSeqs | 0.733 | 0.024 | 0.757 | |
| getDeseqRes | 5.749 | 0.171 | 5.929 | |
| getDetectionTools | 0.003 | 0.000 | 0.002 | |
| getEdgerRes | 0.750 | 0.012 | 0.762 | |
| getMiRsites | 0.769 | 0.004 | 0.775 | |
| getMotifs | 11.615 | 0.302 | 15.118 | |
| getRandomBSJunctions | 0.185 | 0.008 | 0.193 | |
| getRegexPattern | 0.002 | 0.000 | 0.002 | |
| getSeqsAcrossBSJs | 0.738 | 0.028 | 0.768 | |
| getSeqsFromGRs | 0.845 | 0.016 | 0.863 | |
| gtf | 0.020 | 0.000 | 0.019 | |
| gwasTraits | 0.005 | 0.000 | 0.005 | |
| importCircExplorer2 | 0.034 | 0.000 | 0.035 | |
| importCircMarker | 0.148 | 0.004 | 0.153 | |
| importKnife | 0.034 | 0.000 | 0.035 | |
| importMapSplice | 0.084 | 0.000 | 0.085 | |
| importNCLscan | 0.029 | 0.004 | 0.034 | |
| importOther | 0.031 | 0.000 | 0.031 | |
| importUroborus | 0.031 | 0.000 | 0.032 | |
| initCircRNAprofiler | 0 | 0 | 0 | |
| iupac | 0.001 | 0.000 | 0.001 | |
| liftBSJcoords | 25.267 | 1.261 | 30.499 | |
| memeDB | 0.001 | 0.000 | 0.001 | |
| mergeBSJunctions | 6.430 | 0.171 | 6.625 | |
| mergeMotifs | 12.427 | 0.340 | 14.762 | |
| mergedBSJunctions | 0.384 | 0.000 | 0.385 | |
| miRspeciesCodes | 0.002 | 0.000 | 0.002 | |
| plotExBetweenBSEs | 1.153 | 0.056 | 1.213 | |
| plotExPosition | 1.116 | 0.004 | 1.123 | |
| plotHostGenes | 1.047 | 0.028 | 1.077 | |
| plotLenBSEs | 2.154 | 0.016 | 2.173 | |
| plotLenIntrons | 2.052 | 0.024 | 2.079 | |
| plotMiR | 0.742 | 0.012 | 0.757 | |
| plotMotifs | 19.608 | 0.555 | 25.625 | |
| plotTotExons | 1.121 | 0.020 | 1.142 | |
| rearrangeMiRres | 0.764 | 0.032 | 0.797 | |
| volcanoPlot | 4.568 | 0.128 | 4.708 | |