Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-09-29 11:37 -0400 (Mon, 29 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4827 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4580 |
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 439/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
conumee 1.42.0 (landing page) Volker Hovestadt
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | 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: 1.42.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:conumee.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings conumee_1.42.0.tar.gz |
StartedAt: 2025-09-28 22:13:04 -0400 (Sun, 28 Sep 2025) |
EndedAt: 2025-09-28 22:38:28 -0400 (Sun, 28 Sep 2025) |
EllapsedTime: 1524.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: conumee.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:conumee.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings conumee_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/conumee.Rcheck’ * using R version 4.5.1 (2025-06-13) * 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 ‘conumee/DESCRIPTION’ ... OK * this is package ‘conumee’ version ‘1.42.0’ * 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 ... 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 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 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.detailplot_wrap 57.886 2.048 59.937 CNV.analysis-class 57.267 2.183 59.469 CNV.genomeplot 56.960 1.796 58.758 CNV.detailplot 55.559 1.799 57.361 CNV.write 52.885 1.882 54.769 CNV.segment 48.553 0.930 49.486 CNV.fit 32.720 0.531 33.314 CNV.bin 28.640 0.433 29.076 CNV.detail 28.586 0.372 28.994 CNV.create_anno 26.952 1.110 28.067 CNV.anno-class 25.343 1.342 26.688 read.450k.url 6.378 1.031 13.399 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/conumee.Rcheck/00check.log’ for details.
conumee.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL conumee ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘conumee’ ... ** this is package ‘conumee’ version ‘1.42.0’ ** 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 | 57.267 | 2.183 | 59.469 | |
CNV.anno-class | 25.343 | 1.342 | 26.688 | |
CNV.bin | 28.640 | 0.433 | 29.076 | |
CNV.create_anno | 26.952 | 1.110 | 28.067 | |
CNV.data-class | 1.543 | 0.080 | 1.623 | |
CNV.detail | 28.586 | 0.372 | 28.994 | |
CNV.detailplot | 55.559 | 1.799 | 57.361 | |
CNV.detailplot_wrap | 57.886 | 2.048 | 59.937 | |
CNV.fit | 32.720 | 0.531 | 33.314 | |
CNV.genomeplot | 56.960 | 1.796 | 58.758 | |
CNV.load | 1.650 | 0.085 | 1.735 | |
CNV.segment | 48.553 | 0.930 | 49.486 | |
CNV.write | 52.885 | 1.882 | 54.769 | |
read.450k.url | 6.378 | 1.031 | 13.399 | |