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CHECK report for iterativeBMAsurv on tokay2

This page was generated on 2018-10-17 08:33:56 -0400 (Wed, 17 Oct 2018).

Package 761/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iterativeBMAsurv 1.38.0
Ka Yee Yeung
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/iterativeBMAsurv
Branch: RELEASE_3_7
Last Commit: 4714a1e
Last Changed Date: 2018-04-30 10:35:09 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: iterativeBMAsurv
Version: 1.38.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iterativeBMAsurv.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings iterativeBMAsurv_1.38.0.tar.gz
StartedAt: 2018-10-17 02:54:02 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:56:28 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 146.5 seconds
RetCode: 0
Status:  OK  
CheckDir: iterativeBMAsurv.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iterativeBMAsurv.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings iterativeBMAsurv_1.38.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/iterativeBMAsurv.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.38.0'
* 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 or elapsed time > 5s
                              user system elapsed
imageplot.iterate.bma.surv   13.25   0.03   13.28
predictiveAssessCategory      6.72   0.08    6.83
iterateBMAsurv.train.wrapper  6.66   0.02    6.67
predictBicSurv                6.50   0.03    6.69
iterateBMAsurv.train          6.41   0.07    6.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
imageplot.iterate.bma.surv 8.80   0.02    8.81
predictiveAssessCategory   5.72   0.04    5.77
iterateBMAsurv.train       5.04   0.04    5.08
* 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-3.7-bioc/meat/iterativeBMAsurv.Rcheck/00check.log'
for details.



Installation output

iterativeBMAsurv.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/iterativeBMAsurv_1.38.0.tar.gz && rm -rf iterativeBMAsurv.buildbin-libdir && mkdir iterativeBMAsurv.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iterativeBMAsurv.buildbin-libdir iterativeBMAsurv_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL iterativeBMAsurv_1.38.0.zip && rm iterativeBMAsurv_1.38.0.tar.gz iterativeBMAsurv_1.38.0.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 59430  100 59430    0     0  1206k      0 --:--:-- --:--:-- --:--:-- 1415k

install for i386

* installing *source* package 'iterativeBMAsurv' ...
** 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
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_1.38.0.zip
* DONE (iterativeBMAsurv)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'iterativeBMAsurv' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

iterativeBMAsurv.Rcheck/examples_i386/iterativeBMAsurv-Ex.timings

nameusersystemelapsed
crossVal1.830.081.91
imageplot.iterate.bma.surv13.25 0.0313.28
iterateBMAsurv.train6.410.076.47
iterateBMAsurv.train.predict.assess0.840.040.89
iterateBMAsurv.train.wrapper6.660.026.67
iterativeBMAsurv-package2.470.092.56
predictBicSurv6.500.036.69
predictiveAssessCategory6.720.086.83
printTopGenes0.360.030.39
singleGeneCoxph0.390.020.40

iterativeBMAsurv.Rcheck/examples_x64/iterativeBMAsurv-Ex.timings

nameusersystemelapsed
crossVal1.290.001.30
imageplot.iterate.bma.surv8.800.028.81
iterateBMAsurv.train5.040.045.08
iterateBMAsurv.train.predict.assess0.610.020.64
iterateBMAsurv.train.wrapper4.750.014.76
iterativeBMAsurv-package1.710.101.82
predictBicSurv4.350.004.34
predictiveAssessCategory5.720.045.77
printTopGenes0.250.020.26
singleGeneCoxph0.260.000.27