Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 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" | 4833 |
merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
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 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.7.5 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: conumee |
Version: 1.42.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:conumee.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings conumee_1.42.0.tar.gz |
StartedAt: 2025-10-14 07:47:53 -0000 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 08:20:04 -0000 (Tue, 14 Oct 2025) |
EllapsedTime: 1931.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: conumee.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:conumee.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings conumee_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/conumee.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * 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.genomeplot 112.102 0.933 113.268 CNV.write 101.241 1.122 102.543 CNV.detailplot 101.372 0.874 102.421 CNV.detailplot_wrap 100.789 0.946 101.922 CNV.analysis-class 98.529 1.489 100.259 CNV.segment 91.644 0.646 92.436 CNV.fit 58.576 0.565 59.266 CNV.detail 50.337 0.610 51.061 CNV.bin 49.563 0.371 50.045 CNV.create_anno 44.797 0.667 45.567 CNV.anno-class 42.025 0.539 42.660 read.450k.url 8.349 1.122 54.026 CNV.load 6.799 0.248 7.059 * 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 ‘/home/biocbuild/bbs-3.21-bioc/meat/conumee.Rcheck/00check.log’ for details.
conumee.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL conumee ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/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 | 98.529 | 1.489 | 100.259 | |
CNV.anno-class | 42.025 | 0.539 | 42.660 | |
CNV.bin | 49.563 | 0.371 | 50.045 | |
CNV.create_anno | 44.797 | 0.667 | 45.567 | |
CNV.data-class | 2.125 | 0.044 | 2.173 | |
CNV.detail | 50.337 | 0.610 | 51.061 | |
CNV.detailplot | 101.372 | 0.874 | 102.421 | |
CNV.detailplot_wrap | 100.789 | 0.946 | 101.922 | |
CNV.fit | 58.576 | 0.565 | 59.266 | |
CNV.genomeplot | 112.102 | 0.933 | 113.268 | |
CNV.load | 6.799 | 0.248 | 7.059 | |
CNV.segment | 91.644 | 0.646 | 92.436 | |
CNV.write | 101.241 | 1.122 | 102.543 | |
read.450k.url | 8.349 | 1.122 | 54.026 | |