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This page was generated on 2024-04-18 11:32:19 -0400 (Thu, 18 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
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 1998/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SOMNiBUS 1.10.0 (landing page) Kathleen Klein
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the SOMNiBUS package: - 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: SOMNiBUS |
Version: 1.10.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SOMNiBUS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SOMNiBUS_1.10.0.tar.gz |
StartedAt: 2024-04-18 04:32:42 -0400 (Thu, 18 Apr 2024) |
EndedAt: 2024-04-18 04:56:55 -0400 (Thu, 18 Apr 2024) |
EllapsedTime: 1453.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SOMNiBUS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SOMNiBUS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SOMNiBUS_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/SOMNiBUS.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: aarch64-apple-darwin20 (64-bit) * 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 13.6.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SOMNiBUS/DESCRIPTION’ ... OK * this is package ‘SOMNiBUS’ version ‘1.10.0’ * package encoding: UTF-8 * 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 ‘SOMNiBUS’ 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 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 startup messages can be suppressed ... 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 testStat: no visible global function definition for ‘pf’ Undefined global functions or variables: pf Consider adding importFrom("stats", "pf") to your NAMESPACE file. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed binomRegMethModel 430.838 20.046 462.876 runSOMNiBUS 356.213 20.716 384.072 binomRegMethPredPlot 43.920 4.908 49.445 binomRegMethModelPred 41.025 5.121 46.307 binomRegMethModelPlot 41.154 4.659 46.158 splitDataByGene 15.586 1.311 17.666 splitDataByChromatin 10.610 0.347 12.897 formatFromBismark 5.846 0.373 6.356 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/SOMNiBUS.Rcheck/00check.log’ for details.
SOMNiBUS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SOMNiBUS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘SOMNiBUS’ ... ** 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 (SOMNiBUS)
SOMNiBUS.Rcheck/SOMNiBUS-Ex.timings
name | user | system | elapsed | |
binomRegMethModel | 430.838 | 20.046 | 462.876 | |
binomRegMethModelPlot | 41.154 | 4.659 | 46.158 | |
binomRegMethModelPred | 41.025 | 5.121 | 46.307 | |
binomRegMethModelSim | 2.289 | 0.328 | 2.618 | |
binomRegMethPredPlot | 43.920 | 4.908 | 49.445 | |
formatFromBSmooth | 0.299 | 0.014 | 0.321 | |
formatFromBSseq | 0.050 | 0.001 | 0.050 | |
formatFromBismark | 5.846 | 0.373 | 6.356 | |
runSOMNiBUS | 356.213 | 20.716 | 384.072 | |
splitDataByChromatin | 10.610 | 0.347 | 12.897 | |
splitDataByDensity | 2.180 | 0.047 | 2.323 | |
splitDataByGRanges | 0.192 | 0.010 | 0.203 | |
splitDataByGene | 15.586 | 1.311 | 17.666 | |
splitDataByRegion | 0.017 | 0.003 | 0.021 | |