Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-09 12:04 -0400 (Sat, 09 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
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 403/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CNVRanger 1.25.4 (landing page) Ludwig Geistlinger
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the CNVRanger package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNVRanger.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: CNVRanger |
Version: 1.25.4 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CNVRanger.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CNVRanger_1.25.4.tar.gz |
StartedAt: 2025-08-08 21:09:48 -0400 (Fri, 08 Aug 2025) |
EndedAt: 2025-08-08 21:16:33 -0400 (Fri, 08 Aug 2025) |
EllapsedTime: 405.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CNVRanger.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CNVRanger.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CNVRanger_1.25.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CNVRanger.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘CNVRanger/DESCRIPTION’ ... OK * this is package ‘CNVRanger’ version ‘1.25.4’ * 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 ‘CNVRanger’ 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 code 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 ... NOTE Unexported object imported by a ':::' call: 'rappdirs:::get_os' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE plotRecurrentRegions: no visible binding for global variable ‘type’ plotRecurrentRegions: no visible binding for global variable ‘pvalue’ Undefined global functions or variables: pvalue type * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: cnvEQTL.Rd: GRanges-class, GRangesList-class, RaggedExperiment-class, RangedSummarizedExperiment-class, qreduceAssay, filterByExpr, DataFrame-class, findOverlaps, glmQLFit, glmQLFTest cnvOncoPrint.Rd: GRangesList-class, RaggedExperiment-class, GRanges-class, qreduceAssay plotEQTL.Rd: GRanges-class plotManhattan.Rd: GRanges-class plotRecurrentRegions.Rd: GRanges-class populationRanges.Rd: GRangesList-class, GRanges-class, findOverlaps setupCnvGWAS.Rd: RaggedExperiment-class, GRangesList-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotEQTL 18.668 0.614 30.159 plotRecurrentRegions 14.714 0.074 17.547 plotManhattan 6.404 0.130 6.535 cnvGWAS 5.284 0.111 5.400 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/CNVRanger.Rcheck/00check.log’ for details.
CNVRanger.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL CNVRanger ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘CNVRanger’ ... ** this is package ‘CNVRanger’ version ‘1.25.4’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (CNVRanger)
CNVRanger.Rcheck/CNVRanger-Ex.timings
name | user | system | elapsed | |
cnvEQTL | 1.851 | 0.081 | 1.932 | |
cnvGWAS | 5.284 | 0.111 | 5.400 | |
cnvOncoPrint | 1.322 | 0.030 | 1.353 | |
generateGDS | 1.237 | 0.002 | 1.239 | |
importLrrBaf | 0.688 | 0.000 | 0.688 | |
plotEQTL | 18.668 | 0.614 | 30.159 | |
plotManhattan | 6.404 | 0.130 | 6.535 | |
plotRecurrentRegions | 14.714 | 0.074 | 17.547 | |
populationRanges | 1.386 | 0.002 | 1.389 | |
setupCnvGWAS | 0.007 | 0.000 | 0.008 | |