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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iterativeBMAsurv.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings iterativeBMAsurv_1.46.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/iterativeBMAsurv.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.46.0'
* 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
* 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
imageplot.iterate.bma.surv   19.22   0.05   19.28
predictiveAssessCategory     10.22   0.08   10.29
predictBicSurv                9.95   0.01    9.97
iterateBMAsurv.train          8.87   0.00    8.89
iterateBMAsurv.train.wrapper  7.56   0.02    7.58
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
imageplot.iterate.bma.surv   14.08   0.04   14.12
predictiveAssessCategory      6.42   0.02    6.44
iterateBMAsurv.train.wrapper  6.37   0.03    6.42
iterateBMAsurv.train          6.09   0.02    6.11
predictBicSurv                5.77   0.01    5.79
* 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-3.11-bioc/meat/iterativeBMAsurv.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/iterativeBMAsurv_1.46.0.tar.gz && rm -rf iterativeBMAsurv.buildbin-libdir && mkdir iterativeBMAsurv.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iterativeBMAsurv.buildbin-libdir iterativeBMAsurv_1.46.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL iterativeBMAsurv_1.46.0.zip && rm iterativeBMAsurv_1.46.0.tar.gz iterativeBMAsurv_1.46.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

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100 59433  100 59433    0     0   862k      0 --:--:-- --:--:-- --:--:--  967k

install for i386

* installing *source* package 'iterativeBMAsurv' ...
** using staged installation
** R
** data
** byte-compile and prepare 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 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 'iterativeBMAsurv' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iterativeBMAsurv' as iterativeBMAsurv_1.46.0.zip
* DONE (iterativeBMAsurv)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'iterativeBMAsurv' successfully unpacked and MD5 sums checked