Package: pickgene

Version: 1.59.0

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_1.59.0.tar.gz

StartedAt: 2020-01-16 07:27:42 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 07:28:20 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 38.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: pickgene.Rcheck

Warnings: 1

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### Running command:
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###   /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_1.59.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/pickgene.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.59.0’
* 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-3.11-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-3.11-bioc/meat/pickgene.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pickgene
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘pickgene’ ...
** using staged installation
** 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 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 (pickgene)

name	user	system	elapsed
Simulation.pickgene	0.729	0.064	0.799
em.ggb	0.001	0.000	0.000
model.pickgene	0.012	0.001	0.013
oddsplot	0.000	0.001	0.001
pickgene	0.000	0.001	0.001
robustscale	0.000	0.001	0.001