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This page was generated on 2022-01-21 13:07:57 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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

CHECK results for iterativeBMAsurv on machv2


To the developers/maintainers of the iterativeBMAsurv package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iterativeBMAsurv.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 969/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iterativeBMAsurv 1.52.0  (landing page)
Ka Yee Yeung
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/iterativeBMAsurv
git_branch: RELEASE_3_14
git_last_commit: 9eebd34
git_last_commit_date: 2021-10-26 11:52:44 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 1.52.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iterativeBMAsurv.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iterativeBMAsurv_1.52.0.tar.gz
StartedAt: 2022-01-20 14:19:57 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 14:22:30 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 153.1 seconds
RetCode: 0
Status:   OK  
CheckDir: iterativeBMAsurv.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iterativeBMAsurv.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iterativeBMAsurv_1.52.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/iterativeBMAsurv.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iterativeBMAsurv/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iterativeBMAsurv’ version ‘1.52.0’
* 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 ‘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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
imageplot.iterate.bma.surv   23.538  0.121  23.670
predictiveAssessCategory     11.312  0.174  11.496
iterateBMAsurv.train         11.314  0.095  11.416
predictBicSurv               11.217  0.095  11.320
iterateBMAsurv.train.wrapper 10.675  0.046  10.729
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/iterativeBMAsurv.Rcheck/00check.log’
for details.



Installation output

iterativeBMAsurv.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL iterativeBMAsurv
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘iterativeBMAsurv’ ...
** 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 (iterativeBMAsurv)

Tests output


Example timings

iterativeBMAsurv.Rcheck/iterativeBMAsurv-Ex.timings

nameusersystemelapsed
crossVal3.2750.1013.378
imageplot.iterate.bma.surv23.538 0.12123.670
iterateBMAsurv.train11.314 0.09511.416
iterateBMAsurv.train.predict.assess1.2640.0591.324
iterateBMAsurv.train.wrapper10.675 0.04610.729
iterativeBMAsurv-package4.4330.1224.557
predictBicSurv11.217 0.09511.320
predictiveAssessCategory11.312 0.17411.496
printTopGenes0.6430.0080.652
singleGeneCoxph0.6370.0080.646