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This page was generated on 2024-03-28 11:32:23 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4376
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 1144/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maPredictDSC 1.40.0  (landing page)
Adi Laurentiu Tarca
Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/maPredictDSC
git_branch: RELEASE_3_18
git_last_commit: 20ea6c6
git_last_commit_date: 2023-10-24 09:54:43 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for maPredictDSC on kjohnson1


To the developers/maintainers of the maPredictDSC 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: maPredictDSC
Version: 1.40.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maPredictDSC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maPredictDSC_1.40.0.tar.gz
StartedAt: 2024-03-27 17:50:33 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 17:54:48 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 255.2 seconds
RetCode: 0
Status:   OK  
CheckDir: maPredictDSC.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maPredictDSC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maPredictDSC_1.40.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/maPredictDSC.Rcheck’
* using R version 4.3.3 (2024-02-29)
* 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 Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maPredictDSC/DESCRIPTION’ ... OK
* this is package ‘maPredictDSC’ version ‘1.40.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'MASS', 'affy', 'limma', 'gcrma', 'ROC', 'class', 'e1071', 'caret',
  'hgu133plus2.db', 'ROCR', 'AnnotationDbi', 'LungCancerACvsSCCGEO'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘maPredictDSC’ 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
'library' or 'require' calls to packages already attached by Depends:
  ‘ROC’ ‘ROCR’ ‘affy’ ‘caret’ ‘class’ ‘e1071’ ‘gcrma’ ‘limma’
  Please remove these calls from your code.
'library' or 'require' call to ‘parallel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘LungCancerACvsSCCGEO’ ‘ROC’ ‘ROCR’ ‘affy’ ‘caret’ ‘class’ ‘e1071’
  ‘gcrma’ ‘hgu133plus2.db’ ‘limma’
  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
maPredictDSC: no visible global function definition for
  ‘installed.packages’
maPredictDSC: no visible global function definition for ‘ReadAffy’
maPredictDSC: no visible global function definition for ‘rma’
maPredictDSC: no visible global function definition for ‘mas5’
maPredictDSC: no visible global function definition for ‘gcrma’
maPredictDSC: no visible global function definition for ‘exprs’
maPredictDSC: no visible global function definition for ‘mas5calls’
maPredictDSC: no visible global function definition for ‘createFolds’
maPredictDSC : mff: no visible global function definition for
  ‘model.matrix’
maPredictDSC : mff: no visible global function definition for ‘formula’
maPredictDSC : mff: no visible global function definition for ‘lmFit’
maPredictDSC : mff: no visible global function definition for
  ‘makeContrasts’
maPredictDSC : mff: no visible global function definition for
  ‘contrasts.fit’
maPredictDSC : mff: no visible global function definition for ‘eBayes’
maPredictDSC : mff: no visible global function definition for
  ‘topTable’
maPredictDSC : mff: no visible global function definition for ‘pt’
maPredictDSC : mff : wf: no visible global function definition for
  ‘wilcox.test’
maPredictDSC : mff: no visible global function definition for ‘predict’
maPredictDSC : mff: no visible global function definition for ‘knn’
maPredictDSC : mff: no visible global function definition for ‘svm’
maPredictDSC : mff: no visible global function definition for
  ‘rocdemo.sca’
maPredictDSC : mff: no visible binding for global variable ‘dxrule.sca’
maPredictDSC : mff: no visible global function definition for ‘AUC’
maPredictDSC: no visible global function definition for ‘mclapply’
maPredictDSC: no visible global function definition for ‘sd’
maPredictDSC: no visible global function definition for ‘model.matrix’
maPredictDSC: no visible global function definition for ‘formula’
maPredictDSC: no visible global function definition for ‘lmFit’
maPredictDSC: no visible global function definition for ‘makeContrasts’
maPredictDSC: no visible global function definition for ‘contrasts.fit’
maPredictDSC: no visible global function definition for ‘eBayes’
maPredictDSC: no visible global function definition for ‘topTable’
maPredictDSC: no visible global function definition for ‘pt’
maPredictDSC : wf: no visible global function definition for
  ‘wilcox.test’
maPredictDSC: no visible global function definition for ‘predict’
maPredictDSC: no visible global function definition for ‘knn’
maPredictDSC: no visible global function definition for ‘svm’
perfDSC: no visible global function definition for ‘prediction’
perfDSC: no visible global function definition for ‘performance’
perfDSC: no visible global function definition for ‘na.omit’
perfDSC: no visible global function definition for ‘trapezint’
perfDSC: no visible global function definition for ‘rocdemo.sca’
perfDSC: no visible binding for global variable ‘dxrule.sca’
perfDSC: no visible global function definition for ‘AUC’
Undefined global functions or variables:
  AUC ReadAffy contrasts.fit createFolds dxrule.sca eBayes exprs
  formula gcrma installed.packages knn lmFit makeContrasts mas5
  mas5calls mclapply model.matrix na.omit performance predict
  prediction pt rma rocdemo.sca sd svm topTable trapezint wilcox.test
Consider adding
  importFrom("stats", "formula", "model.matrix", "na.omit", "predict",
             "pt", "sd", "wilcox.test")
  importFrom("utils", "installed.packages")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 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
predictDSC 158.336 12.809 116.588
* 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-3.18-bioc-mac-arm64/meat/maPredictDSC.Rcheck/00check.log’
for details.



Installation output

maPredictDSC.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL maPredictDSC
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘maPredictDSC’ ...
** using staged installation
** R
** 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 (maPredictDSC)

Tests output


Example timings

maPredictDSC.Rcheck/maPredictDSC-Ex.timings

nameusersystemelapsed
aggregateDSC0.0000.0010.001
perfDSC0.0300.0010.031
predictDSC158.336 12.809116.588