Package: Clomial

Version: 1.18.1

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Clomial.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings Clomial_1.18.1.tar.gz

StartedAt: 2019-04-13 01:16:18 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 01:22:47 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 389.0 seconds

RetCode: 0

Status:  OK

CheckDir: Clomial.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:Clomial.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings Clomial_1.18.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/Clomial.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 'Clomial/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Clomial' version '1.18.1'
* 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 '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.P.reparam : plot.obj: no visible global function definition for
  'plot'
compute.q: no visible global function definition for 'dbinom'
Undefined global functions or variables:
  dbinom optim plot rbinom runif tail
Consider adding
  importFrom("graphics", "plot")
  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 or elapsed time > 5s
                    user system elapsed
choose.best        52.00   2.03   54.03
Clomial-package    20.18   0.73   20.94
Clomial            16.24   0.66   16.91
Clomial.iterate    10.27   0.47   10.74
compute.bic        10.16   0.35   10.50
Clomial.likelihood 10.00   0.47   10.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
choose.best        56.30   1.75   58.05
Clomial-package    22.93   0.66   23.60
Clomial            21.67   0.50   22.17
compute.bic        13.36   0.57   13.94
Clomial.likelihood 10.54   0.37   10.94
Clomial.iterate     9.74   0.14    9.87
compute.errors      6.81   0.19    7.00
* 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/Clomial.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/Clomial_1.18.1.tar.gz && rm -rf Clomial.buildbin-libdir && mkdir Clomial.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Clomial.buildbin-libdir Clomial_1.18.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL Clomial_1.18.1.zip && rm Clomial_1.18.1.tar.gz Clomial_1.18.1.zip
###
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install for i386

* installing *source* package 'Clomial' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'Clomial' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Clomial' as Clomial_1.18.1.zip
* DONE (Clomial)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'Clomial' successfully unpacked and MD5 sums checked
In R CMD INSTALL