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BioC 3.5: CHECK report for pickgene on veracruz2

This page was generated on 2017-08-16 13:27:11 -0400 (Wed, 16 Aug 2017).

Package 982/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pickgene 1.48.0
Brian S. Yandell
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/pickgene
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: pickgene
Version: 1.48.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pickgene_1.48.0.tar.gz
StartedAt: 2017-08-16 06:30:08 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 06:30:30 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 21.7 seconds
RetCode: 0
Status:  OK 
CheckDir: pickgene.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pickgene_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/pickgene.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.48.0’
* 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 ... 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 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 ... 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 installed files from ‘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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/pickgene.Rcheck/00check.log’
for details.


pickgene.Rcheck/00install.out:

* installing *source* package ‘pickgene’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pickgene)

pickgene.Rcheck/pickgene-Ex.timings:

nameusersystemelapsed
Simulation.pickgene0.5870.0210.631
em.ggb0.0010.0000.001
model.pickgene0.0090.0010.010
oddsplot000
pickgene000
robustscale0.0000.0000.001