Package: vbmp

Version: 1.50.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:vbmp.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings vbmp_1.50.0.tar.gz

StartedAt: 2019-04-13 06:08:56 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 06:10:24 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 88.6 seconds

RetCode: 0

Status:  OK

CheckDir: vbmp.Rcheck

Warnings: 0

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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:vbmp.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings vbmp_1.50.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/vbmp.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 'vbmp/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'vbmp' version '1.50.0'
* 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 'vbmp' 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
* 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
genCPP.classic: no visible global function definition for 'rnorm'
plotDiagnostics: no visible global function definition for 'par'
plotDiagnostics: no visible global function definition for 'plot'
plotDiagnostics: no visible global function definition for 'lines'
printTrace: no visible global function definition for 'flush.console'
rexponential: no visible global function definition for 'rexp'
safeNormCDF: no visible global function definition for 'pnorm'
safeNormPDF: no visible global function definition for 'dnorm'
tmean: no visible global function definition for 'rnorm'
tmean.classic: no visible global function definition for 'rnorm'
vbmp: no visible global function definition for 'rnorm'
vbmp: no visible global function definition for 'runif'
vbmp: no visible global function definition for 'par'
vbmp: no visible global function definition for 'plot'
vbmp: no visible global function definition for 'lines'
Undefined global functions or variables:
  dnorm flush.console lines par plot pnorm rexp rnorm runif
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "dnorm", "pnorm", "rexp", "rnorm", "runif")
  importFrom("utils", "flush.console")
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 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/vbmp.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/vbmp_1.50.0.tar.gz && rm -rf vbmp.buildbin-libdir && mkdir vbmp.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=vbmp.buildbin-libdir vbmp_1.50.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL vbmp_1.50.0.zip && rm vbmp_1.50.0.tar.gz vbmp_1.50.0.zip
###
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100 1546k  100 1546k    0     0  2837k      0 --:--:-- --:--:-- --:--:-- 2906k

install for i386

* installing *source* package 'vbmp' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'vbmp'
    finding HTML links ... done
    BRCA12                                  html  
    covParams                               html  
    lowerBound                              html  
    plotDiagnostics                         html  
    predClass                               html  
    predError                               html  
    predLik                                 html  
    predictCPP                              html  
    vbmp                                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'vbmp' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'vbmp' as vbmp_1.50.0.zip
* DONE (vbmp)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'vbmp' successfully unpacked and MD5 sums checked
In R CMD INSTALL