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This page was generated on 2021-10-22 12:04:33 -0400 (Fri, 22 Oct 2021).

CHECK results for MLSeq on riesling1

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: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MLSeq.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MLSeq_2.11.1.tar.gz
StartedAt: 2021-10-22 02:05:22 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 02:09:19 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 236.4 seconds
RetCode: 0
Status:   OK  
CheckDir: MLSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MLSeq.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MLSeq_2.11.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/MLSeq.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'D:/biocbuild/bbs-3.14-bioc/meat/MLSeq.Rcheck/00check.log'
for details.



Installation output

MLSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MLSeq_2.11.1.tar.gz && rm -rf MLSeq.buildbin-libdir && mkdir MLSeq.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MLSeq.buildbin-libdir MLSeq_2.11.1.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MLSeq_2.11.1.zip && rm MLSeq_2.11.1.tar.gz MLSeq_2.11.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0  155k    0  1137    0     0  14212      0  0:00:11 --:--:--  0:00:11 14037
100  155k  100  155k    0     0   823k      0 --:--:-- --:--:-- --:--:--  819k

install for i386

* installing *source* package 'MLSeq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MLSeq'
    finding HTML links ... done
    Available-classifiers                   html  
    MLSeq-class                             html  
    MLSeq-package                           html  
    MLSeqMetaData-class                     html  
    MLSeqModelInfo-class                    html  
    cervical                                html  
    classify                                html  
    confusionMat                            html  
    control                                 html  
    discrete.train-class                    html  
    discreteControl                         html  
    input                                   html  
    isUpdated                               html  
    metaData                                html  
    method                                  html  
    modelInfo                               html  
    normalization                           html  
    plot                                    html  
    preProcessing                           html  
    predict                                 html  
    print                                   html  
    ref                                     html  
    selectedGenes                           html  
    show                                    html  
    trainParameters                         html  
    trained                                 html  
    transformation                          html  
    update                                  html  
    voom.train-class                        html  
    voomControl                             html  
** 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

install for x64

* installing *source* package 'MLSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MLSeq' as MLSeq_2.11.1.zip
* DONE (MLSeq)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'MLSeq' successfully unpacked and MD5 sums checked

Tests output

MLSeq.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  12.01    0.43   12.42 

MLSeq.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  12.12    0.50   12.62 

Example timings

MLSeq.Rcheck/examples_i386/MLSeq-Ex.timings

nameusersystemelapsed
cervical000
classify000
confusionMat000
control000
discreteControl000
input000
isUpdated000
metaData000
method000
modelInfo000
normalization000
preProcessing000
predict000
ref000
selectedGenes000
trainParameters000
trained000
transformation000
update000
voomControl000

MLSeq.Rcheck/examples_x64/MLSeq-Ex.timings

nameusersystemelapsed
cervical000
classify000
confusionMat000
control000
discreteControl000
input000
isUpdated000
metaData000
method000
modelInfo000
normalization000
preProcessing000
predict000
ref000
selectedGenes000
trainParameters000
trained000
transformation000
update000
voomControl000