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CHECK report for iterativeBMA on merida1

This page was generated on 2021-05-06 12:35:25 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the iterativeBMA package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 925/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iterativeBMA 1.48.0  (landing page)
Ka Yee Yeung
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/iterativeBMA
Branch: RELEASE_3_12
Last Commit: 23ef7f4
Last Changed Date: 2020-10-27 10:33:57 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: iterativeBMA
Version: 1.48.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:iterativeBMA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings iterativeBMA_1.48.0.tar.gz
StartedAt: 2021-05-06 03:00:47 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:02:06 -0400 (Thu, 06 May 2021)
EllapsedTime: 79.3 seconds
RetCode: 0
Status:   OK  
CheckDir: iterativeBMA.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:iterativeBMA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings iterativeBMA_1.48.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/iterativeBMA.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iterativeBMA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iterativeBMA’ version ‘1.48.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘iterativeBMA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* 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’ ‘Biobase’ ‘leaps’
  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
convertSingleName: no visible global function definition for ‘exprs’
imageplot.bma.mod: no visible global function definition for ‘par’
imageplot.bma.mod: no visible global function definition for ‘image’
imageplot.bma.mod: no visible global function definition for ‘axis’
iterateBMAglm: no visible global function definition for ‘bic.glm’
iterateBMAglm.train: no visible global function definition for ‘exprs’
iterateBMAglm.train.predict: no visible global function definition for
  ‘exprs’
iterateBMAglm.train.predict.test: no visible global function definition
  for ‘exprs’
iterateBMAglm.wrapper: no visible global function definition for
  ‘bic.glm’
Undefined global functions or variables:
  axis bic.glm exprs image par
Consider adding
  importFrom("graphics", "axis", "image", "par")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: BssWssFast.Rd:39: Dropping empty section \note
prepare_Rd: bma_predict.Rd:36: Dropping empty section \note
prepare_Rd: brier_score.Rd:34: Dropping empty section \note
prepare_Rd: testClass.Rd:13-14: Dropping empty section \details
prepare_Rd: trainClass.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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/iterativeBMA.Rcheck/00check.log’
for details.



Installation output

iterativeBMA.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL iterativeBMA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘iterativeBMA’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (iterativeBMA)

Tests output


Example timings

iterativeBMA.Rcheck/iterativeBMA-Ex.timings

nameusersystemelapsed
BssWssFast0.0280.0070.035
bma_predict1.8670.0531.925
brier_score1.6160.0331.650
imageplot_iterate_bma1.6550.0301.686
iterateBMAglm_train1.7060.0301.738
iterateBMAglm_train_predict1.7460.0502.157
iterateBMAglm_train_predict_test1.6100.0281.639
iterateBMAglm_wrapper1.8540.0381.969
iterativeBMA-package1.9430.0352.021