Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-29 11:35:55 -0400 (Fri, 29 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
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 581/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DMRcate 2.16.1 (landing page) Tim Peters
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the DMRcate package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DMRcate.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: DMRcate |
Version: 2.16.1 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:DMRcate.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings DMRcate_2.16.1.tar.gz |
StartedAt: 2024-03-27 22:01:23 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 22:34:42 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 1999.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DMRcate.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:DMRcate.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings DMRcate_2.16.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/DMRcate.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘DMRcate/DESCRIPTION’ ... OK * this is package ‘DMRcate’ version ‘2.16.1’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘DMRcate’ 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: DSS dependency removed Cannot process chunk/lines: CITATION updated. Cannot process chunk/lines: BUG FIXES • annotate() renamed to cpg.annotate to avoid clashes with same-named function in ggplot2 Cannot process chunk/lines: NEW FEATURES • Kernel estimator has been rewritten from scratch without the need for ks:::kde. Now only takes moderated t-values as cpg weights, as required by the chi-square transformation. • Now allows for multi-level factor experiments, as allowed by limma. Contrasts should be specified with a contrast matrix, otherwise the design matrix MUST have an intercept. (Thanks to Tim Triche Jr. and David Martino for their advice). • A GRanges object can be produced from the results. • XY probes can also be filtered out using rmSNPandCH(). • DMR.plot() allows group median lines to be plotted to better visualise distances between groups (Thanks to Susan van Dijk and Magnus Tobiasson for their advice). * 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 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 ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed DMR.plot 174.854 9.679 202.134 DMRcate-package 133.875 6.132 143.132 rmSNPandCH 118.941 5.896 125.554 extractRanges 117.571 5.085 123.620 cpg.annotate 112.510 6.032 119.218 dmrcate 112.787 3.176 116.521 changeFDR 51.651 7.404 59.393 sequencing.annotate 46.362 4.896 51.511 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘DMRcate.Rnw’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.18-bioc/meat/DMRcate.Rcheck/00check.log’ for details.
DMRcate.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL DMRcate ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ * installing *source* package ‘DMRcate’ ... ** 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 (DMRcate)
DMRcate.Rcheck/DMRcate-Ex.timings
name | user | system | elapsed | |
DMR.plot | 174.854 | 9.679 | 202.134 | |
DMRcate-package | 133.875 | 6.132 | 143.132 | |
changeFDR | 51.651 | 7.404 | 59.393 | |
cpg.annotate | 112.510 | 6.032 | 119.218 | |
dmrcate | 112.787 | 3.176 | 116.521 | |
extractRanges | 117.571 | 5.085 | 123.620 | |
rmSNPandCH | 118.941 | 5.896 | 125.554 | |
sequencing.annotate | 46.362 | 4.896 | 51.511 | |