Wen Yao
| Snapshot Date: 2025-10-31 13:45 -0400 (Fri, 31 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/intansv |
| git_branch: RELEASE_3_22 |
| git_last_commit: 0bb1a74 |
| git_last_commit_date: 2025-10-29 10:15:39 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-01 12:03 -0400 (Sat, 01 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 1067/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| intansv 1.50.0 (landing page) Wen Yao
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 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: 1.50.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:intansv.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings intansv_1.50.0.tar.gz |
| StartedAt: 2025-11-01 00:48:21 -0400 (Sat, 01 Nov 2025) |
| EndedAt: 2025-11-01 00:55:28 -0400 (Sat, 01 Nov 2025) |
| EllapsedTime: 427.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: intansv.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:intansv.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings intansv_1.50.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/intansv.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘intansv/DESCRIPTION’ ... OK
* this is package ‘intansv’ version ‘1.50.0’
* 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 20.303 0.433 20.737
* 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/intansv.Rcheck/00check.log’
for details.
intansv.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL intansv ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘intansv’ ... ** this is package ‘intansv’ version ‘1.50.0’ ** 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 | 20.303 | 0.433 | 20.737 | |
| plotChromosome | 4.514 | 0.049 | 4.564 | |
| plotRegion | 3.629 | 0.027 | 3.657 | |
| readBreakDancer | 0.965 | 0.001 | 0.967 | |
| readCnvnator | 0.503 | 0.002 | 0.505 | |
| readDelly | 2.595 | 0.022 | 2.618 | |
| readLumpy | 2.998 | 0.003 | 3.001 | |
| readPindel | 2.324 | 0.057 | 2.381 | |
| readSoftSearch | 0.265 | 0.001 | 0.266 | |
| readSvseq | 0.260 | 0.002 | 0.262 | |
| svAnnotation | 1.092 | 0.001 | 1.093 | |