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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gespeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings gespeR_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/gespeR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gespeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gespeR' version '1.22.0'
* 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 'gespeR' 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
.gespeR.cv: no visible global function definition for 'coef'
.select.model: no visible global function definition for 'predict'
concordance: no visible global function definition for 'cor'
lasso.rand: no visible global function definition for 'runif'
plot.gespeR: no visible global function definition for 'hist'
stability.selection: no visible global function definition for 'lm'
Phenotypes,character: no visible global function definition for
  'read.delim'
Undefined global functions or variables:
  coef cor hist lm predict read.delim runif
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "coef", "cor", "lm", "predict", "runif")
  importFrom("utils", "read.delim")
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 ... WARNING
Codoc mismatches from documentation object 'c,Phenotypes-method':
\S4method{c}{Phenotypes}
  Code: function(x, ...)
  Docs: function(x, ..., recursive = FALSE)
  Argument names in docs not in code:
    recursive

* 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
gespeR-package    4.97   0.14   63.06
gespeR-class      0.33   0.06   15.00
stability-methods 0.17   0.02   12.91
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
gespeR-package    7.56   0.23   58.76
gespeR-class      0.41   0.00   14.25
stability-methods 0.14   0.02   11.06
* 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/gespeR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/gespeR_1.22.0.tar.gz && rm -rf gespeR.buildbin-libdir && mkdir gespeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gespeR.buildbin-libdir gespeR_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL gespeR_1.22.0.zip && rm gespeR_1.22.0.tar.gz gespeR_1.22.0.zip
###
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  % 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 24.1M  100 24.1M    0     0  98.7M      0 --:--:-- --:--:-- --:--:-- 99.3M

install for i386

* installing *source* package 'gespeR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'gespeR'
    finding HTML links ... done
    Phenotypes-class                        html  
    TargetRelations-class                   html  
    annotate.gsp-methods                    html  
    as.data.frame-Phenotypes-method         html  
    as.data.frame.concordance               html  
    c-Phenotypes-method                     html  
    concordance                             html  
    dim-Phenotypes-method                   html  
    gespeR-class                            html  
    finding level-2 HTML links ... done

    gespeR-package                          html  
    gspssp-methods                          html  
    join-methods                            html  
    lasso.rand                              html  
    na.rem-methods                          html  
    path-methods                            html  
    plot.Phenotypes                         html  
    plot.concordance                        html  
    plot.gespeR                             html  
    rbo                                     html  
    scores-methods                          html  
    simData                                 html  
    stability-methods                       html  
    stability.selection                     html  
    stabilityfits                           html  
    sub-Phenotypes-ANY-ANY-ANY-method       html  
    sub-TargetRelations-ANY-ANY-ANY-method
                                            html  
    target-relations-methods                html  
    trmatrix-methods                        html  
    values-methods                          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 'gespeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gespeR' as gespeR_1.22.0.zip
* DONE (gespeR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'gespeR' successfully unpacked and MD5 sums checked