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CHECK report for MLSeq on tokay1

This page was generated on 2019-04-13 11:23:38 -0400 (Sat, 13 Apr 2019).

Package 984/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MLSeq 2.0.1
Gokmen Zararsiz
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/MLSeq
Branch: RELEASE_3_8
Last Commit: 2b99386
Last Changed Date: 2019-01-04 13:15:37 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MLSeq
Version: 2.0.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MLSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MLSeq_2.0.1.tar.gz
StartedAt: 2019-04-13 03:55:50 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:00:48 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 298.2 seconds
RetCode: 0
Status:  OK  
CheckDir: MLSeq.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MLSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MLSeq_2.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MLSeq.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '2.0.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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
Namespace in Imports field not imported from: 'xtable'
  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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/MLSeq.Rcheck/00check.log'
for details.



Installation output

MLSeq.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/MLSeq_2.0.1.tar.gz && rm -rf MLSeq.buildbin-libdir && mkdir MLSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MLSeq.buildbin-libdir MLSeq_2.0.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL MLSeq_2.0.1.zip && rm MLSeq_2.0.1.tar.gz MLSeq_2.0.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  153k  100  153k    0     0  3945k      0 --:--:-- --:--:-- --:--:-- 4376k

install for i386

* installing *source* package 'MLSeq' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'MLSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MLSeq' as MLSeq_2.0.1.zip
* DONE (MLSeq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'MLSeq' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

MLSeq.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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: lattice
Loading required package: ggplot2


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")
== testthat results  ===========================================================
OK: 0 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   7.07    0.53    7.59 

MLSeq.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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: lattice
Loading required package: ggplot2


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")
== testthat results  ===========================================================
OK: 0 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   7.59    0.51    8.10 

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