Back to Multiple platform build/check report for BioC 3.8 |
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This page was generated on 2019-04-16 11:54:05 -0400 (Tue, 16 Apr 2019).
Package 1158/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
pickgene 1.54.0 Brian S. Yandell
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK |
Package: pickgene |
Version: 1.54.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pickgene.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pickgene_1.54.0.tar.gz |
StartedAt: 2019-04-16 01:54:54 -0400 (Tue, 16 Apr 2019) |
EndedAt: 2019-04-16 01:55:19 -0400 (Tue, 16 Apr 2019) |
EllapsedTime: 25.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: pickgene.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pickgene.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pickgene_1.54.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/pickgene.Rcheck’ * using R version 3.5.3 (2019-03-11) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘pickgene/DESCRIPTION’ ... OK * this is package ‘pickgene’ version ‘1.54.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘pickgene’ can be installed ... WARNING Found the following significant warnings: Note: possible error in 'oddsplot(exp(data[[x]]), ': unused argument (chip = "") See ‘/Users/biocbuild/bbs-3.8-bioc/meat/pickgene.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. * 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 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 do.oddsplot: warning in em.ggb(data[[conditions[1]]], data[[conditions[2]]], theta, theta[1:3], print = TRUE): partial argument match of 'print' to 'printit' pickgene.poly: warning in pickgene.two(y[, i], intensity, geneid = geneID, singlelevel = singlelevel, npick = npickgene, ylab = ylabs[i], ...): partial argument match of 'npick' to 'npickgene' lod.plot: possible error in oddsplot(exp(data[[x]]), exp(data[[y]]), theta, col = col, xlab = xlab, ylab = ylab, chip = ""): unused argument (chip = "") nloglik: no visible binding for global variable ‘.fit.xx’ nloglik: no visible binding for global variable ‘.fit.yy’ nploglik: no visible binding for global variable ‘.fit.xx’ nploglik: no visible binding for global variable ‘.fit.yy’ nploglik: no visible binding for global variable ‘.fit.zz’ s.check1: no visible global function definition for ‘lod’ s.marg: no visible binding for global variable ‘x’ shrinkplot: no visible global function definition for ‘s.fits’ shrinkplot: no visible binding for global variable ‘lims’ Undefined global functions or variables: .fit.xx .fit.yy .fit.zz lims lod s.fits x * checking Rd files ... NOTE prepare_Rd: Simulation.pickgene.Rd:8: Dropping empty section \keyword prepare_Rd: Simulation.pickgene.Rd:5-6: Dropping empty section \usage prepare_Rd: Simulation.pickgene.Rd:7: Dropping empty section \details * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.8-bioc/meat/pickgene.Rcheck/00check.log’ for details.
pickgene.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pickgene ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘pickgene’ ... ** R ** byte-compile and prepare package for lazy loading Note: possible error in 'oddsplot(exp(data[[x]]), ': unused argument (chip = "") ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (pickgene)
pickgene.Rcheck/pickgene-Ex.timings
name | user | system | elapsed | |
Simulation.pickgene | 0.528 | 0.030 | 0.569 | |
em.ggb | 0 | 0 | 0 | |
model.pickgene | 0.009 | 0.000 | 0.010 | |
oddsplot | 0.000 | 0.000 | 0.001 | |
pickgene | 0 | 0 | 0 | |
robustscale | 0.000 | 0.001 | 0.001 | |