| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:37 -0000 (Wed, 01 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
| 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 327/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| circRNAprofiler 1.13.7 (landing page) Simona Aufiero
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: circRNAprofiler |
| Version: 1.13.7 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings circRNAprofiler_1.13.7.tar.gz |
| StartedAt: 2023-02-27 23:31:25 -0000 (Mon, 27 Feb 2023) |
| EndedAt: 2023-02-27 23:49:02 -0000 (Mon, 27 Feb 2023) |
| EllapsedTime: 1056.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: circRNAprofiler.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings circRNAprofiler_1.13.7.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/circRNAprofiler.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* 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 ... ERROR
Running examples in ‘circRNAprofiler-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: liftBSJcoords
> ### Title: LiftOver back-spliced junction coordinates
> ### Aliases: liftBSJcoords
>
> ### ** Examples
>
> # Load a data frame containing detected back-spliced junctions
> data("mergedBSJunctions")
>
> # LiftOver the first 10 back-spliced junction coordinates
> liftedBSJcoords <- liftBSJcoords(mergedBSJunctions[1:10,], map = "hg19ToMm9")
snapshotDate(): 2022-12-16
loading from cache
require(“rtracklayer”)
Error: failed to load resource
name: AH14155
title: hg19ToMm9.over.chain.gz
reason: incomplete block
Execution halted
* 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 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/circRNAprofiler.Rcheck/00check.log’
for details.
circRNAprofiler.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL circRNAprofiler ### ############################################################################## ############################################################################## * installing to library ‘/home/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) (2023-01-14 r83615) -- "Unsuffered Consequences"
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 36 | SKIP 1 | PASS 255 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)
[ FAIL 0 | WARN 36 | SKIP 1 | PASS 255 ]
>
> proc.time()
user system elapsed
548.533 12.092 574.450
circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings
| name | user | system | elapsed | |
| ahChainFiles | 0.158 | 0.000 | 0.158 | |
| ahRepeatMasker | 0.001 | 0.000 | 0.001 | |
| annotateBSJs | 2.146 | 0.072 | 2.218 | |
| annotateRepeats | 1.585 | 0.108 | 1.693 | |
| annotateSNPsGWAS | 1.329 | 0.096 | 1.425 | |
| attractSpecies | 0.001 | 0.000 | 0.001 | |
| backSplicedJunctions | 0.619 | 0.008 | 0.627 | |
| checkProjectFolder | 0.002 | 0.000 | 0.002 | |
| filterCirc | 0.536 | 0.052 | 0.588 | |
| formatGTF | 0 | 0 | 0 | |
| getBackSplicedJunctions | 0.001 | 0.000 | 0.001 | |
| getCircSeqs | 1.29 | 0.02 | 1.31 | |
| getDeseqRes | 4.933 | 0.072 | 5.006 | |
| getDetectionTools | 0.000 | 0.003 | 0.003 | |
| getEdgerRes | 0.922 | 0.008 | 0.931 | |
| getMiRsites | 2.484 | 0.104 | 2.588 | |
| getMotifs | 20.042 | 0.808 | 26.702 | |
| getRandomBSJunctions | 0.362 | 0.020 | 0.382 | |
| getRegexPattern | 0.002 | 0.000 | 0.002 | |
| getSeqsAcrossBSJs | 1.360 | 0.072 | 1.432 | |
| getSeqsFromGRs | 1.428 | 0.040 | 1.468 | |
| gtf | 0.023 | 0.000 | 0.022 | |
| gwasTraits | 0.006 | 0.000 | 0.006 | |
| importCircExplorer2 | 0.053 | 0.000 | 0.054 | |
| importCircMarker | 0.183 | 0.008 | 0.191 | |
| importKnife | 0.043 | 0.000 | 0.043 | |
| importMapSplice | 0.095 | 0.008 | 0.104 | |
| importNCLscan | 0.043 | 0.008 | 0.051 | |
| importOther | 0.037 | 0.000 | 0.037 | |
| importUroborus | 0.033 | 0.004 | 0.038 | |
| initCircRNAprofiler | 0.000 | 0.000 | 0.001 | |
| iupac | 0.000 | 0.002 | 0.002 | |