##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gwasurvivr.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings gwasurvivr_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/gwasurvivr.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 'gwasurvivr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gwasurvivr' version '1.8.0'
* package encoding: UTF-8
* 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 'gwasurvivr' 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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
michiganCoxSurv 1.70   0.72   21.26
impute2CoxSurv  1.17   0.05   19.62
plinkCoxSurv    1.14   0.08   20.58
sangerCoxSurv   1.11   0.01   20.92
gdsCoxSurv      0.09   0.01   18.77
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
michiganCoxSurv 1.64   0.12   23.48
gdsCoxSurv      1.35   0.03   23.41
impute2CoxSurv  1.36   0.02   23.67
plinkCoxSurv    1.17   0.02   19.33
sangerCoxSurv   0.82   0.00   18.92
* 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: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/gwasurvivr_1.8.0.tar.gz && rm -rf gwasurvivr.buildbin-libdir && mkdir gwasurvivr.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gwasurvivr.buildbin-libdir gwasurvivr_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL gwasurvivr_1.8.0.zip && rm gwasurvivr_1.8.0.tar.gz gwasurvivr_1.8.0.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 42679  100 42679    0     0  2177k      0 --:--:-- --:--:-- --:--:-- 2315k

install for i386

* installing *source* package 'gwasurvivr' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** help
*** installing help indices
  converting help for package 'gwasurvivr'
    finding HTML links ... done
    gdsCoxSurv                              html  
    impute2CoxSurv                          html  
    michiganCoxSurv                         html  
    plinkCoxSurv                            html  
    sangerCoxSurv                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** testing if installed package can be loaded from final location
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'gwasurvivr' ...
** testing if installed package can be loaded
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
* MD5 sums
packaged installation of 'gwasurvivr' as gwasurvivr_1.8.0.zip
* DONE (gwasurvivr)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'gwasurvivr' successfully unpacked and MD5 sums checked