Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-04 12:04 -0400 (Sat, 04 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4853 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
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 441/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
conumee 1.43.1 (landing page) Volker Hovestadt
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the conumee package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/conumee.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: conumee |
Version: 1.43.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:conumee.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings conumee_1.43.1.tar.gz |
StartedAt: 2025-10-03 20:42:08 -0400 (Fri, 03 Oct 2025) |
EndedAt: 2025-10-03 21:06:54 -0400 (Fri, 03 Oct 2025) |
EllapsedTime: 1485.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: conumee.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:conumee.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings conumee_1.43.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/conumee.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘conumee/DESCRIPTION’ ... OK * this is package ‘conumee’ version ‘1.43.1’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘conumee’ 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 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 CNV.load,GenomicRatioSet: no visible global function definition for ‘assays’ CNV.load,matrix: no visible binding for global variable ‘anno’ Undefined global functions or variables: anno assays * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed CNV.write 67.074 4.044 75.945 CNV.detailplot 67.358 3.042 70.958 CNV.genomeplot 65.019 4.004 70.808 CNV.detailplot_wrap 64.661 3.395 68.708 CNV.analysis-class 63.061 3.370 69.775 CNV.segment 56.961 2.227 61.551 CNV.fit 41.820 2.304 44.934 CNV.bin 35.760 1.739 37.739 CNV.detail 35.519 1.822 37.574 CNV.anno-class 33.187 2.057 35.563 CNV.create_anno 29.345 1.903 31.472 read.450k.url 8.339 1.578 25.262 * 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-3.22-bioc/meat/conumee.Rcheck/00check.log’ for details.
conumee.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL conumee ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘conumee’ ... ** this is package ‘conumee’ version ‘1.43.1’ ** using staged installation ** R ** data ** 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 (conumee)
conumee.Rcheck/conumee-Ex.timings
name | user | system | elapsed | |
CNV.analysis-class | 63.061 | 3.370 | 69.775 | |
CNV.anno-class | 33.187 | 2.057 | 35.563 | |
CNV.bin | 35.760 | 1.739 | 37.739 | |
CNV.create_anno | 29.345 | 1.903 | 31.472 | |
CNV.data-class | 2.225 | 0.119 | 2.353 | |
CNV.detail | 35.519 | 1.822 | 37.574 | |
CNV.detailplot | 67.358 | 3.042 | 70.958 | |
CNV.detailplot_wrap | 64.661 | 3.395 | 68.708 | |
CNV.fit | 41.820 | 2.304 | 44.934 | |
CNV.genomeplot | 65.019 | 4.004 | 70.808 | |
CNV.load | 2.065 | 0.405 | 2.558 | |
CNV.segment | 56.961 | 2.227 | 61.551 | |
CNV.write | 67.074 | 4.044 | 75.945 | |
read.450k.url | 8.339 | 1.578 | 25.262 | |