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BioC 3.4: CHECK report for iterativeBMAsurv on tokay1

This page was generated on 2017-04-15 16:15:41 -0400 (Sat, 15 Apr 2017).

Package 653/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iterativeBMAsurv 1.32.0
Ka Yee Yeung
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/iterativeBMAsurv
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: iterativeBMAsurv
Version: 1.32.0
Command: rm -rf iterativeBMAsurv.buildbin-libdir iterativeBMAsurv.Rcheck && mkdir iterativeBMAsurv.buildbin-libdir iterativeBMAsurv.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=iterativeBMAsurv.buildbin-libdir iterativeBMAsurv_1.32.0.tar.gz >iterativeBMAsurv.Rcheck\00install.out 2>&1 && cp iterativeBMAsurv.Rcheck\00install.out iterativeBMAsurv-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=iterativeBMAsurv.buildbin-libdir --install="check:iterativeBMAsurv-install.out" --force-multiarch --no-vignettes --timings iterativeBMAsurv_1.32.0.tar.gz
StartedAt: 2017-04-14 23:09:23 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:11:39 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 135.6 seconds
RetCode: 0
Status:  OK  
CheckDir: iterativeBMAsurv.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf iterativeBMAsurv.buildbin-libdir iterativeBMAsurv.Rcheck && mkdir iterativeBMAsurv.buildbin-libdir iterativeBMAsurv.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=iterativeBMAsurv.buildbin-libdir iterativeBMAsurv_1.32.0.tar.gz >iterativeBMAsurv.Rcheck\00install.out 2>&1 && cp iterativeBMAsurv.Rcheck\00install.out iterativeBMAsurv-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=iterativeBMAsurv.buildbin-libdir --install="check:iterativeBMAsurv-install.out" --force-multiarch --no-vignettes --timings iterativeBMAsurv_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/iterativeBMAsurv.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.32.0'
* 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 7.58   0.02     7.6
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
imageplot.iterate.bma.surv 10.11   0.03   10.14
predictBicSurv              6.14   0.04    6.18
predictiveAssessCategory    5.73   0.04    5.78
iterateBMAsurv.train        5.17   0.02    5.19
* 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-3.4-bioc/meat/iterativeBMAsurv.Rcheck/00check.log'
for details.


iterativeBMAsurv.Rcheck/00install.out:


install for i386

* installing *source* package 'iterativeBMAsurv' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'iterativeBMAsurv' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iterativeBMAsurv' as iterativeBMAsurv_1.32.0.zip
* DONE (iterativeBMAsurv)

iterativeBMAsurv.Rcheck/examples_i386/iterativeBMAsurv-Ex.timings:

nameusersystemelapsed
crossVal1.130.001.12
imageplot.iterate.bma.surv7.580.027.60
iterateBMAsurv.train3.790.003.79
iterateBMAsurv.train.predict.assess0.550.050.60
iterateBMAsurv.train.wrapper3.800.003.79
iterativeBMAsurv-package1.580.041.63
predictBicSurv3.730.023.75
predictiveAssessCategory4.000.054.05
printTopGenes0.220.010.23
singleGeneCoxph0.230.000.23

iterativeBMAsurv.Rcheck/examples_x64/iterativeBMAsurv-Ex.timings:

nameusersystemelapsed
crossVal1.310.001.33
imageplot.iterate.bma.surv10.11 0.0310.14
iterateBMAsurv.train5.170.025.19
iterateBMAsurv.train.predict.assess0.610.010.62
iterateBMAsurv.train.wrapper4.940.004.94
iterativeBMAsurv-package2.500.032.53
predictBicSurv6.140.046.18
predictiveAssessCategory5.730.045.78
printTopGenes0.360.000.36
singleGeneCoxph0.270.030.29