Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-09 17:43 -0400 (Tue, 09 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4709 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
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 434/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
conumee 1.38.0 (landing page) Volker Hovestadt
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.38.0 |
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_1.38.0.tar.gz |
StartedAt: 2024-07-08 15:44:02 -0400 (Mon, 08 Jul 2024) |
EndedAt: 2024-07-08 16:12:53 -0400 (Mon, 08 Jul 2024) |
EllapsedTime: 1730.6 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_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/conumee.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-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 Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘conumee/DESCRIPTION’ ... OK * this is package ‘conumee’ version ‘1.38.0’ * 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 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 72.596 2.970 75.959 CNV.detailplot 71.793 2.772 74.867 CNV.analysis-class 67.769 2.771 71.254 CNV.detailplot_wrap 67.475 2.978 70.976 CNV.write 67.189 2.964 70.479 CNV.segment 59.929 1.639 61.969 CNV.fit 37.307 1.589 39.331 CNV.bin 34.812 1.590 36.534 CNV.detail 33.677 2.002 35.999 CNV.create_anno 30.199 1.992 32.351 CNV.anno-class 27.338 1.648 29.106 read.450k.url 8.132 0.430 14.292 * 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/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/4.4-arm64/Resources/library’ * installing *source* package ‘conumee’ ... ** 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 | 67.769 | 2.771 | 71.254 | |
CNV.anno-class | 27.338 | 1.648 | 29.106 | |
CNV.bin | 34.812 | 1.590 | 36.534 | |
CNV.create_anno | 30.199 | 1.992 | 32.351 | |
CNV.data-class | 3.380 | 0.208 | 3.600 | |
CNV.detail | 33.677 | 2.002 | 35.999 | |
CNV.detailplot | 71.793 | 2.772 | 74.867 | |
CNV.detailplot_wrap | 67.475 | 2.978 | 70.976 | |
CNV.fit | 37.307 | 1.589 | 39.331 | |
CNV.genomeplot | 72.596 | 2.970 | 75.959 | |
CNV.load | 2.689 | 0.208 | 2.911 | |
CNV.segment | 59.929 | 1.639 | 61.969 | |
CNV.write | 67.189 | 2.964 | 70.479 | |
read.450k.url | 8.132 | 0.430 | 14.292 | |