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This page was generated on 2021-10-15 15:06:09 -0400 (Fri, 15 Oct 2021).

CHECK results for iterativeBMAsurv on tokay2

To the developers/maintainers of the iterativeBMAsurv package:
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reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 957/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iterativeBMAsurv 1.50.0  (landing page)
Ka Yee Yeung
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/iterativeBMAsurv
git_branch: RELEASE_3_13
git_last_commit: 9637225
git_last_commit_date: 2021-05-19 11:41:26 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: iterativeBMAsurv
Version: 1.50.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iterativeBMAsurv.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings iterativeBMAsurv_1.50.0.tar.gz
StartedAt: 2021-10-15 00:58:43 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 01:01:36 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 172.4 seconds
RetCode: 0
Status:   OK  
CheckDir: iterativeBMAsurv.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iterativeBMAsurv.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings iterativeBMAsurv_1.50.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/iterativeBMAsurv.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.50.0'
* 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   15.08   0.05   15.13
predictBicSurv                6.66   0.07    6.71
iterateBMAsurv.train          6.67   0.01    6.69
predictiveAssessCategory      6.09   0.06    6.16
iterateBMAsurv.train.wrapper  5.81   0.00    5.82
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
imageplot.iterate.bma.surv   12.10   0.03   12.13
predictiveAssessCategory      7.16   0.02    7.17
predictBicSurv                6.40   0.04    6.46
iterateBMAsurv.train          5.98   0.00    5.98
iterateBMAsurv.train.wrapper  5.86   0.01    5.88
* 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-3.13-bioc/meat/iterativeBMAsurv.Rcheck/00check.log'
for details.



Installation output

iterativeBMAsurv.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/iterativeBMAsurv_1.50.0.tar.gz && rm -rf iterativeBMAsurv.buildbin-libdir && mkdir iterativeBMAsurv.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iterativeBMAsurv.buildbin-libdir iterativeBMAsurv_1.50.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL iterativeBMAsurv_1.50.0.zip && rm iterativeBMAsurv_1.50.0.tar.gz iterativeBMAsurv_1.50.0.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 60354  100 60354    0     0   378k      0 --:--:-- --:--:-- --:--:--  380k

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_1.50.0.zip
* DONE (iterativeBMAsurv)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'iterativeBMAsurv' successfully unpacked and MD5 sums checked

Tests output


Example timings

iterativeBMAsurv.Rcheck/examples_i386/iterativeBMAsurv-Ex.timings

nameusersystemelapsed
crossVal1.820.051.87
imageplot.iterate.bma.surv15.08 0.0515.13
iterateBMAsurv.train6.670.016.69
iterateBMAsurv.train.predict.assess0.950.051.00
iterateBMAsurv.train.wrapper5.810.005.82
iterativeBMAsurv-package2.530.042.58
predictBicSurv6.660.076.71
predictiveAssessCategory6.090.066.16
printTopGenes0.420.020.44
singleGeneCoxph0.410.010.42

iterativeBMAsurv.Rcheck/examples_x64/iterativeBMAsurv-Ex.timings

nameusersystemelapsed
crossVal2.430.052.48
imageplot.iterate.bma.surv12.10 0.0312.13
iterateBMAsurv.train5.980.005.98
iterateBMAsurv.train.predict.assess0.770.000.77
iterateBMAsurv.train.wrapper5.860.015.88
iterativeBMAsurv-package2.640.042.67
predictBicSurv6.400.046.46
predictiveAssessCategory7.160.027.17
printTopGenes0.450.010.47
singleGeneCoxph0.460.020.47