Package: iterativeBMAsurv

Version: 1.36.0

Command: rm -rf iterativeBMAsurv.buildbin-libdir iterativeBMAsurv.Rcheck && mkdir iterativeBMAsurv.buildbin-libdir iterativeBMAsurv.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=iterativeBMAsurv.buildbin-libdir iterativeBMAsurv_1.36.0.tar.gz >iterativeBMAsurv.Rcheck\00install.out 2>&1 && cp iterativeBMAsurv.Rcheck\00install.out iterativeBMAsurv-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=iterativeBMAsurv.buildbin-libdir --install="check:iterativeBMAsurv-install.out" --force-multiarch --no-vignettes --timings iterativeBMAsurv_1.36.0.tar.gz

StartedAt: 2018-04-12 00:56:54 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:59:23 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 148.6 seconds

RetCode: 0

Status:  OK

CheckDir: iterativeBMAsurv.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf iterativeBMAsurv.buildbin-libdir iterativeBMAsurv.Rcheck && mkdir iterativeBMAsurv.buildbin-libdir iterativeBMAsurv.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=iterativeBMAsurv.buildbin-libdir iterativeBMAsurv_1.36.0.tar.gz >iterativeBMAsurv.Rcheck\00install.out 2>&1 && cp iterativeBMAsurv.Rcheck\00install.out iterativeBMAsurv-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=iterativeBMAsurv.buildbin-libdir --install="check:iterativeBMAsurv-install.out" --force-multiarch --no-vignettes --timings iterativeBMAsurv_1.36.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/iterativeBMAsurv.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'iterativeBMAsurv/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iterativeBMAsurv' version '1.36.0'
* 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 'iterativeBMAsurv' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'survival'
A package should be listed in only one of these fields.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  'BMA' 'leaps' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
iterateBMAsurv.train: no visible global function definition for
  'bic.surv'
iterateBMAsurv.train.wrapper: no visible global function definition for
  'bic.surv'
Undefined global functions or variables:
  bic.surv
* checking Rd files ... NOTE
prepare_Rd: predictBicSurv.Rd:46: Dropping empty section \note
prepare_Rd: predictiveAssessCategory.Rd:52: Dropping empty section \note
prepare_Rd: printTopGenes.Rd:49: Dropping empty section \note
prepare_Rd: singleGeneCoxph.Rd:54: Dropping empty section \note
prepare_Rd: testCens.Rd:13-14: Dropping empty section \details
prepare_Rd: testSurv.Rd:13-14: Dropping empty section \details
prepare_Rd: trainCens.Rd:13-14: Dropping empty section \details
prepare_Rd: trainSurv.Rd:13-14: Dropping empty section \details
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
imageplot.iterate.bma.surv 9.64   0.08    9.71
iterateBMAsurv.train       5.19   0.03    5.22
predictiveAssessCategory   5.19   0.03    5.21
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
imageplot.iterate.bma.surv   12.61   0.08   12.71
predictBicSurv                6.34   0.02    6.36
predictiveAssessCategory      6.00   0.04    6.05
iterateBMAsurv.train.wrapper  6.00   0.01    6.02
iterateBMAsurv.train          5.51   0.01    5.53
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/iterativeBMAsurv.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'iterativeBMAsurv' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'iterativeBMAsurv'
    finding HTML links ... done
    crossVal                                html  
    imageplot.iterate.bma.surv              html  
    iterateBMAsurv.train                    html  
    iterateBMAsurv.train.predict.assess     html  
    iterateBMAsurv.train.wrapper            html  
    iterativeBMAsurv-internal               html  
    iterativeBMAsurv-package                html  
    predictBicSurv                          html  
    predictiveAssessCategory                html  
    printTopGenes                           html  
    singleGeneCoxph                         html  
    testCens                                html  
    testData                                html  
    testSurv                                html  
    trainCens                               html  
    trainData                               html  
    trainSurv                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'iterativeBMAsurv' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iterativeBMAsurv' as iterativeBMAsurv_1.36.0.zip
* DONE (iterativeBMAsurv)
In R CMD INSTALL
In R CMD INSTALL