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CHECK report for a4Classif on malbec1

This page was generated on 2020-09-19 10:14:20 -0400 (Sat, 19 Sep 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE a4Classif PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 3/1912HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
a4Classif 1.37.0
Tobias Verbeke
Snapshot Date: 2020-09-18 14:43:25 -0400 (Fri, 18 Sep 2020)
URL: https://git.bioconductor.org/packages/a4Classif
Branch: master
Last Commit: a9ae689
Last Changed Date: 2020-04-27 14:25:23 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: a4Classif
Version: 1.37.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:a4Classif.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings a4Classif_1.37.0.tar.gz
StartedAt: 2020-09-19 00:31:50 -0400 (Sat, 19 Sep 2020)
EndedAt: 2020-09-19 00:33:36 -0400 (Sat, 19 Sep 2020)
EllapsedTime: 106.8 seconds
RetCode: 0
Status:  OK 
CheckDir: a4Classif.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:a4Classif.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings a4Classif_1.37.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/a4Classif.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘a4Classif/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4Classif’ version ‘1.37.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'a4Core', 'a4Preproc', 'MLInterfaces', 'ROCR', 'pamr', 'glmnet',
  'varSelRF'
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 ‘a4Classif’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘a4Core’
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:
  ‘MLInterfaces’ ‘ROCR’ ‘a4Preproc’ ‘glmnet’ ‘methods’ ‘pamr’
  ‘varSelRF’
  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
.onAttach: no visible global function definition for
  ‘packageDescription’
ROCcurve: no visible global function definition for ‘exprs’
ROCcurve: no visible global function definition for ‘featureData’
ROCcurve: no visible global function definition for ‘featureNames’
ROCcurve: no visible global function definition for ‘pData’
ROCcurve: no visible global function definition for ‘prediction’
ROCcurve: no visible global function definition for ‘performance’
confusionMatrix.pamClass: no visible global function definition for
  ‘pamr.confusion’
lassoClass: no visible global function definition for ‘pData’
lassoClass: no visible global function definition for ‘glmnet’
lassoClass: no visible global function definition for ‘exprs’
lassoClass: no visible global function definition for ‘featureData’
pamClass: no visible global function definition for ‘pData’
pamClass: no visible global function definition for ‘featureNames’
pamClass: no visible global function definition for ‘exprs’
pamClass: no visible global function definition for ‘capture.output’
pamClass: no visible global function definition for ‘pamr.train’
pamClass: no visible global function definition for ‘pamr.cv’
pamClass: no visible global function definition for ‘featureData’
plot.pamClass: no visible binding for global variable ‘var’
plot.pamClass: no visible global function definition for ‘par’
plot.pamClass: no visible global function definition for ‘lines’
plot.pamClass: no visible global function definition for ‘segments’
plot.pamClass: no visible global function definition for ‘axis’
plot.pamClass: no visible global function definition for ‘points’
plot.rfClass: no visible global function definition for ‘par’
plot.rfClass: no visible global function definition for ‘lines’
plot.rfClass: no visible global function definition for ‘segments’
plot.rfClass: no visible global function definition for ‘axis’
plot.rfClass: no visible global function definition for ‘points’
rfClass: no visible global function definition for ‘pData’
rfClass: no visible global function definition for ‘varSelRF’
rfClass: no visible global function definition for ‘exprs’
rfClass: no visible global function definition for ‘featureData’
rfClass: no visible global function definition for ‘featureNames’
topTable,pamClass: no visible global function definition for
  ‘capture.output’
topTable,pamClass: no visible global function definition for
  ‘pamr.listgenes’
Undefined global functions or variables:
  axis capture.output exprs featureData featureNames glmnet lines pData
  packageDescription pamr.confusion pamr.cv pamr.listgenes pamr.train
  par performance points prediction segments var varSelRF
Consider adding
  importFrom("graphics", "axis", "lines", "par", "points", "segments")
  importFrom("stats", "var")
  importFrom("utils", "capture.output", "packageDescription")
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 examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/a4Classif.Rcheck/00check.log’
for details.



Installation output

a4Classif.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL a4Classif
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘a4Classif’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (a4Classif)

Tests output


Example timings

a4Classif.Rcheck/a4Classif-Ex.timings

nameusersystemelapsed
ROCcurve2.7600.0482.816
lassoClass3.5840.1203.723