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This page was generated on 2023-10-20 09:38:05 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1035/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iterativeBMA 1.58.0  (landing page)
Ka Yee Yeung
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/iterativeBMA
git_branch: RELEASE_3_17
git_last_commit: a615aca
git_last_commit_date: 2023-04-25 09:47:14 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for iterativeBMA on kjohnson2


To the developers/maintainers of the iterativeBMA package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: iterativeBMA
Version: 1.58.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iterativeBMA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iterativeBMA_1.58.0.tar.gz
StartedAt: 2023-10-18 03:07:30 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 03:08:56 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 86.2 seconds
RetCode: 0
Status:   OK  
CheckDir: iterativeBMA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iterativeBMA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iterativeBMA_1.58.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/iterativeBMA.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iterativeBMA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iterativeBMA’ version ‘1.58.0’
* 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-3.17-bioc-mac-arm64/meat/iterativeBMA.Rcheck/00check.log’
for details.



Installation output

iterativeBMA.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL iterativeBMA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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
BssWssFast0.0210.0060.041
bma_predict1.2950.0502.056
brier_score1.3470.0442.134
imageplot_iterate_bma1.2790.0412.020
iterateBMAglm_train1.3070.0432.057
iterateBMAglm_train_predict1.3170.0412.119
iterateBMAglm_train_predict_test1.3300.0472.124
iterateBMAglm_wrapper1.3220.0452.084
iterativeBMA-package1.3010.0452.080