Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:40:51 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
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 1031/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
intansv 1.43.0 (landing page) Wen Yao
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the intansv package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/intansv.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: intansv |
Version: 1.43.0 |
Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:intansv.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings intansv_1.43.0.tar.gz |
StartedAt: 2024-03-28 06:24:35 -0000 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 06:32:52 -0000 (Thu, 28 Mar 2024) |
EllapsedTime: 496.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: intansv.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:intansv.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings intansv_1.43.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/intansv.Rcheck’ * using R Under development (unstable) (2024-03-19 r86153) * using platform: aarch64-unknown-linux-gnu * 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 * using option ‘--no-vignettes’ * checking for file ‘intansv/DESCRIPTION’ ... OK * this is package ‘intansv’ version ‘1.43.0’ * 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 ‘intansv’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE DellyCluster: no visible global function definition for 'subjectHits' LumpyCluster: no visible global function definition for 'subjectHits' PindelCluster: no visible global function definition for 'subjectHits' breakDancerCluster: no visible global function definition for 'subjectHits' mergeOLCNVs: no visible global function definition for 'subjectHits' methodsMerge: no visible global function definition for 'subjectHits' plotChromosome: no visible global function definition for 'queryHits' plotChromosome: no visible global function definition for 'subjectHits' plotChromosome: no visible global function definition for 'seqlengths<-' plotChromosome: no visible global function definition for 'seqlengths' plotChromosome: no visible global function definition for 'aes' plotRegion: no visible global function definition for 'seqlengths<-' plotRegion: no visible global function definition for 'subjectHits' plotRegion: no visible global function definition for 'aes' plotRegion: no visible binding for global variable 'name' readCnvnator: no visible global function definition for 'subjectHits' readDelly: no visible global function definition for 'subjectHits' readLumpy: no visible global function definition for 'subjectHits' readPindel: no visible global function definition for 'subjectHits' readSoftSearch: no visible global function definition for 'subjectHits' readSvseq: no visible global function definition for 'subjectHits' readSvseq : <anonymous>: no visible global function definition for 'subjectHits' softSearchCluster: no visible global function definition for 'subjectHits' tellOLPercantage: no visible global function definition for 'queryHits' tellOLPercantage: no visible global function definition for 'subjectHits' Undefined global functions or variables: aes name queryHits seqlengths seqlengths<- subjectHits * checking Rd files ... NOTE checkRd: (-1) plotChromosome.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotChromosome.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotChromosome.Rd:36-37: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotChromosome.Rd:38-39: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotChromosome.Rd:40-41: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotRegion.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotRegion.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotRegion.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotRegion.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) svAnnotation.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) svAnnotation.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) svAnnotation.Rd:32: Lost braces in \itemize; meant \describe ? * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed methodsMerge 36.438 0.547 37.069 plotChromosome 6.928 0.024 6.966 plotRegion 5.286 0.060 5.358 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/intansv.Rcheck/00check.log’ for details.
intansv.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL intansv ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’ * installing *source* package ‘intansv’ ... ** using staged installation ** R ** 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 (intansv)
intansv.Rcheck/intansv-Ex.timings
name | user | system | elapsed | |
methodsMerge | 36.438 | 0.547 | 37.069 | |
plotChromosome | 6.928 | 0.024 | 6.966 | |
plotRegion | 5.286 | 0.060 | 5.358 | |
readBreakDancer | 1.441 | 0.056 | 1.501 | |
readCnvnator | 0.809 | 0.016 | 0.826 | |
readDelly | 4.201 | 0.020 | 4.229 | |
readLumpy | 4.698 | 0.000 | 4.708 | |
readPindel | 3.672 | 0.004 | 3.684 | |
readSoftSearch | 0.437 | 0.004 | 0.444 | |
readSvseq | 0.414 | 0.008 | 0.423 | |
svAnnotation | 1.642 | 0.016 | 1.662 | |