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This page was generated on 2021-10-22 12:05:04 -0400 (Fri, 22 Oct 2021).

CHECK results for MLSeq on merida1

To the developers/maintainers of the MLSeq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MLSeq.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 1177/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MLSeq 2.11.1  (landing page)
Gokmen Zararsiz
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/MLSeq
git_branch: master
git_last_commit: e0cd2ac
git_last_commit_date: 2021-08-14 08:43:12 -0400 (Sat, 14 Aug 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: MLSeq
Version: 2.11.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MLSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MLSeq_2.11.1.tar.gz
StartedAt: 2021-10-22 06:17:38 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 06:23:16 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 338.3 seconds
RetCode: 0
Status:   OK  
CheckDir: MLSeq.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MLSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MLSeq_2.11.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/MLSeq.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MLSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MLSeq’ version ‘2.11.1’
* package encoding: UTF-8
* 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 ‘MLSeq’ 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
Namespaces in Imports field not imported from:
  ‘VennDiagram’ ‘pamr’ ‘testthat’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 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 ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/MLSeq.Rcheck/00check.log’
for details.



Installation output

MLSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MLSeq
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘MLSeq’ ...
** using staged installation
** R
** data
** inst
** 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 (MLSeq)

Tests output

MLSeq.Rcheck/tests/testthat.Rout


R version 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(MLSeq)
Loading required package: caret
Loading required package: ggplot2
Loading required package: lattice


NOTE: MLSeq has major changes after version 1.20.1 and this will bump following versions to 2.y.z in the next release of Bioconductor (ver. 3.8). Most of the functions from previous versions were changed and new functions are included. Please see Beginner's Guide before continue with the analysis.
> test_check("MLSeq")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
 28.017   1.006  29.001 

Example timings

MLSeq.Rcheck/MLSeq-Ex.timings

nameusersystemelapsed
cervical000
classify000
confusionMat0.0000.0000.001
control0.0000.0010.000
discreteControl000
input0.0000.0000.001
isUpdated000
metaData0.0000.0010.001
method0.0000.0000.001
modelInfo0.0000.0000.001
normalization0.0010.0000.000
preProcessing0.0000.0010.000
predict0.0000.0000.001
ref0.0000.0000.001
selectedGenes0.0000.0010.001
trainParameters0.0000.0000.001
trained0.0000.0000.001
transformation0.0000.0010.000
update0.0000.0000.001
voomControl000