Package: pickgene

Version: 1.54.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pickgene.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings pickgene_1.54.0.tar.gz

StartedAt: 2019-04-13 04:33:16 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 04:34:42 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 86.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: pickgene.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pickgene.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings pickgene_1.54.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/pickgene.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 whether package 'pickgene' can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'oddsplot(exp(data[[x]]), ': unused argument (chip = "") 
See 'C:/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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/pickgene.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/pickgene_1.54.0.tar.gz && rm -rf pickgene.buildbin-libdir && mkdir pickgene.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pickgene.buildbin-libdir pickgene_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL pickgene_1.54.0.zip && rm pickgene_1.54.0.tar.gz pickgene_1.54.0.zip
###
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install for i386

* 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
  converting help for package 'pickgene'
    finding HTML links ... done
    Simulation.pickgene                     html  
    em.ggb                                  html  
    model.pickgene                          html  
    oddsplot                                html  
    pickgene-internal                       html  
    pickgene                                html  
    robustscale                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'pickgene' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pickgene' as pickgene_1.54.0.zip
* DONE (pickgene)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'pickgene' successfully unpacked and MD5 sums checked
In R CMD INSTALL