Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:39:22 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 1023/2251 | 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 | |||||||||
merida1 | 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. |
Package: intansv |
Version: 1.43.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:intansv.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings intansv_1.43.0.tar.gz |
StartedAt: 2024-03-02 05:33:14 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 05:47:16 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 841.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: intansv.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:intansv.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings intansv_1.43.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/intansv.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * 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 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 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed methodsMerge 55.177 0.785 68.246 plotChromosome 10.934 0.129 13.751 readLumpy 8.989 0.256 11.741 plotRegion 8.748 0.093 10.947 readDelly 6.998 0.065 9.014 readPindel 6.167 0.068 7.928 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/intansv.Rcheck/00check.log’ for details.
intansv.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL intansv ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 | 55.177 | 0.785 | 68.246 | |
plotChromosome | 10.934 | 0.129 | 13.751 | |
plotRegion | 8.748 | 0.093 | 10.947 | |
readBreakDancer | 2.381 | 0.024 | 2.950 | |
readCnvnator | 1.517 | 0.016 | 1.895 | |
readDelly | 6.998 | 0.065 | 9.014 | |
readLumpy | 8.989 | 0.256 | 11.741 | |
readPindel | 6.167 | 0.068 | 7.928 | |
readSoftSearch | 0.716 | 0.010 | 0.909 | |
readSvseq | 0.780 | 0.010 | 0.998 | |
svAnnotation | 2.637 | 0.032 | 3.408 | |