Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:38 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the gprege package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gprege.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 800/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gprege 1.36.0 (landing page) Alfredo Kalaitzis
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: gprege |
Version: 1.36.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gprege.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gprege_1.36.0.tar.gz |
StartedAt: 2021-10-14 19:44:49 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 19:46:42 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 113.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gprege.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gprege.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gprege_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/gprege.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘gprege/DESCRIPTION’ ... OK * this is package ‘gprege’ version ‘1.36.0’ * 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: .git_fetch_output.txt .git_merge_output.txt 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 ‘gprege’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE BugReports field is not a suitable URL but appears to contain an email address not specified by mailto: nor contained in < > use the Contact field instead * 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 dependencies in R code ... NOTE Package in Depends field not imported from: ‘gptk’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE compareROC: no visible global function definition for ‘par’ compareROC: no visible global function definition for ‘lines’ compareROC: no visible global function definition for ‘legend’ demTp63Gp1: no visible global function definition for ‘data’ demTp63Gp1: no visible binding for global variable ‘FullDellaGattaData’ demTp63Gp1: no visible binding for global variable ‘FragmentDellaGattaData’ demTp63Gp1: no visible binding for global variable ‘DGdat_p63’ demTp63Gp1: no visible binding for global variable ‘DGdat_p63_case1_GL’ demTp63Gp1: no visible binding for global variable ‘DGdat_p63_case2_GL’ demTp63Gp1: no visible binding for global variable ‘DGdat_p63_case3_GL’ demTp63Gp1: no visible global function definition for ‘graphics.off’ exhaustivePlot: no visible global function definition for ‘sd’ exhaustivePlot: no visible global function definition for ‘gpCreate’ exhaustivePlot: no visible global function definition for ‘gpExpandParam’ exhaustivePlot: no visible global function definition for ‘gpLogLikelihood’ exhaustivePlot: no visible global function definition for ‘filled.contour’ exhaustivePlot: no visible binding for global variable ‘gray.colors’ exhaustivePlot: no visible global function definition for ‘axis’ exhaustivePlot: no visible global function definition for ‘points’ exhaustivePlot: no visible global function definition for ‘dev.set’ exhaustivePlot: no visible global function definition for ‘gpPlot’ gprege: no visible global function definition for ‘gpOptions’ gprege: no visible global function definition for ‘sd’ gprege: no visible global function definition for ‘pdf’ gprege: no visible global function definition for ‘close.screen’ gprege: no visible global function definition for ‘split.screen’ gprege: no visible global function definition for ‘gpCreate’ gprege: no visible global function definition for ‘gpExpandParam’ gprege: no visible global function definition for ‘gpOptimise’ gprege: no visible global function definition for ‘gpExtractParam’ gprege: no visible global function definition for ‘gpLogLikelihood’ gprege: no visible global function definition for ‘screen’ gprege: no visible global function definition for ‘erase.screen’ gprege: no visible global function definition for ‘gpPlot’ gprege: no visible global function definition for ‘gpPosteriorMeanVar’ gprege: no visible global function definition for ‘rnorm’ gprege: no visible global function definition for ‘points’ gprege: no visible global function definition for ‘dev.off’ Undefined global functions or variables: DGdat_p63 DGdat_p63_case1_GL DGdat_p63_case2_GL DGdat_p63_case3_GL FragmentDellaGattaData FullDellaGattaData axis close.screen data dev.off dev.set erase.screen filled.contour gpCreate gpExpandParam gpExtractParam gpLogLikelihood gpOptimise gpOptions gpPlot gpPosteriorMeanVar graphics.off gray.colors legend lines par pdf points rnorm screen sd split.screen Consider adding importFrom("grDevices", "dev.off", "dev.set", "graphics.off", "gray.colors", "pdf") importFrom("graphics", "axis", "close.screen", "erase.screen", "filled.contour", "legend", "lines", "par", "points", "screen", "split.screen") importFrom("stats", "rnorm", "sd") importFrom("utils", "data") 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed demTp63Gp1 13.438 0.163 13.667 exhaustivePlot 13.127 0.203 13.412 gprege 11.734 0.139 11.969 * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/gprege.Rcheck/00check.log’ for details.
gprege.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gprege ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘gprege’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘gprege_quick.Rnw’ ** 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 (gprege)
gprege.Rcheck/gprege-Ex.timings
name | user | system | elapsed | |
compareROC | 0.051 | 0.008 | 0.060 | |
demTp63Gp1 | 13.438 | 0.163 | 13.667 | |
exhaustivePlot | 13.127 | 0.203 | 13.412 | |
gprege-package | 0.001 | 0.000 | 0.001 | |
gprege | 11.734 | 0.139 | 11.969 | |
rocStats | 0.481 | 1.375 | 1.906 | |