##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Clomial.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings Clomial_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/Clomial.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Clomial/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Clomial' version '1.24.0'
* 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 whether package 'Clomial' 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
Clomial: no visible global function definition for 'runif'
Clomial.generate.data: no visible global function definition for
  'runif'
Clomial.generate.data: no visible global function definition for
  'rbinom'
Clomial.likelihood: no visible global function definition for 'dbinom'
Phi: no visible global function definition for 'dbinom'
choose.best: no visible global function definition for 'tail'
compute.P.reparam : update.Wj: no visible global function definition
  for 'optim'
compute.q: no visible global function definition for 'dbinom'
Undefined global functions or variables:
  dbinom optim rbinom runif tail
Consider adding
  importFrom("stats", "dbinom", "optim", "rbinom", "runif")
  importFrom("utils", "tail")
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
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
choose.best        60.15   2.26   62.45
Clomial-package    23.92   0.80   24.72
Clomial            22.63   0.81   23.44
compute.bic        13.82   0.45   14.27
Clomial.iterate    12.94   0.50   13.44
Clomial.likelihood  9.78   0.35   10.13
compute.errors      6.56   0.21    6.77
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
choose.best        67.22   2.14   69.38
Clomial-package    24.20   0.78   25.03
Clomial            23.75   0.75   24.50
Clomial.likelihood 14.70   0.50   15.20
compute.bic        13.94   0.44   14.37
Clomial.iterate    11.47   0.31   11.78
compute.errors      5.89   0.28    6.18
* 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-3.11-bioc/meat/Clomial.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/Clomial_1.24.0.tar.gz && rm -rf Clomial.buildbin-libdir && mkdir Clomial.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Clomial.buildbin-libdir Clomial_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL Clomial_1.24.0.zip && rm Clomial_1.24.0.tar.gz Clomial_1.24.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1290k  100 1290k    0     0  17.9M      0 --:--:-- --:--:-- --:--:-- 20.0M

install for i386

* installing *source* package 'Clomial' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Clomial'
    finding HTML links ... done
    Clomial-package                         html  
    Clomial                                 html  
    Clomial.generate.data                   html  
    Clomial.iterate                         html  
    Clomial.likelihood                      html  
    Clomial1000                             html  
    breastCancer                            html  
    choose.best                             html  
    compute.bic                             html  
    compute.errors                          html  
** 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

install for x64

* installing *source* package 'Clomial' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Clomial' as Clomial_1.24.0.zip
* DONE (Clomial)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'Clomial' successfully unpacked and MD5 sums checked