Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1036/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
intansv 1.46.0 (landing page) Wen Yao
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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. |
Package: intansv |
Version: 1.46.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:intansv.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings intansv_1.46.0.tar.gz |
StartedAt: 2024-12-20 01:26:19 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 01:35:58 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 578.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: intansv.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:intansv.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings intansv_1.46.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/intansv.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘intansv/DESCRIPTION’ ... OK * this is package ‘intansv’ version ‘1.46.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 19.054 0.524 19.581 * 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-3.20-bioc/meat/intansv.Rcheck/00check.log’ for details.
intansv.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL intansv ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/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 | 19.054 | 0.524 | 19.581 | |
plotChromosome | 3.842 | 0.028 | 3.870 | |
plotRegion | 3.066 | 0.002 | 3.069 | |
readBreakDancer | 0.850 | 0.001 | 0.850 | |
readCnvnator | 0.461 | 0.000 | 0.460 | |
readDelly | 2.404 | 0.002 | 2.407 | |
readLumpy | 2.688 | 0.000 | 2.689 | |
readPindel | 2.140 | 0.014 | 2.154 | |
readSoftSearch | 0.266 | 0.000 | 0.265 | |
readSvseq | 0.231 | 0.000 | 0.230 | |
svAnnotation | 0.976 | 0.001 | 0.977 | |