Package: survtype

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:survtype.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings survtype_1.0.0.tar.gz

StartedAt: 2019-10-16 07:26:46 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:30:31 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 225.0 seconds

RetCode: 0

Status:  OK

CheckDir: survtype.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:survtype.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings survtype_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/survtype.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'survtype/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'survtype' version '1.0.0'
* 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 'survtype' 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.survtype
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* 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
** 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-3.9-bioc/meat/survtype.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/survtype_1.0.0.tar.gz && rm -rf survtype.buildbin-libdir && mkdir survtype.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=survtype.buildbin-libdir survtype_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL survtype_1.0.0.zip && rm survtype_1.0.0.tar.gz survtype_1.0.0.zip
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install for i386

* installing *source* package 'survtype' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'survtype'
    finding HTML links ... done
    Exprs.survtype                          html  
    MAF.survgroup                           html  
    Single.survgroup                        html  
    Surv.survtype                           html  
    gene.clust                              html  
    maf2matrix                              html  
    plot.survtype                           html  
    quantile_normalization                  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 'survtype' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'survtype' as survtype_1.0.0.zip
* DONE (survtype)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'survtype' successfully unpacked and MD5 sums checked