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CHECK report for Glimma on tokay2

This page was generated on 2019-10-16 12:35:36 -0400 (Wed, 16 Oct 2019).

Package 684/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Glimma 1.12.0
Shian Su
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/Glimma
Branch: RELEASE_3_9
Last Commit: d021742
Last Changed Date: 2019-05-02 11:54:01 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Glimma
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Glimma.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Glimma_1.12.0.tar.gz
StartedAt: 2019-10-16 04:05:56 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:07:58 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 122.3 seconds
RetCode: 0
Status:  OK  
CheckDir: Glimma.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Glimma.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Glimma_1.12.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Glimma.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Glimma/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Glimma' version '1.12.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'Glimma' 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 ... OK
* 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
Examples with CPU or elapsed time > 5s
         user system elapsed
glMDPlot 9.58   0.08     9.7
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
glMDPlot 6.64   0.04    6.67
* 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-3.9-bioc/meat/Glimma.Rcheck/00check.log'
for details.



Installation output

Glimma.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/Glimma_1.12.0.tar.gz && rm -rf Glimma.buildbin-libdir && mkdir Glimma.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Glimma.buildbin-libdir Glimma_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Glimma_1.12.0.zip && rm Glimma_1.12.0.tar.gz Glimma_1.12.0.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3339k  100 3339k    0     0  8777k      0 --:--:-- --:--:-- --:--:-- 8906k

install for i386

* installing *source* package 'Glimma' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Glimma'
    finding HTML links ... done
    arraydata                               html  
    as.hexcol                               html  
    glBar                                   html  
    glBar.default                           html  
    glMDPlot.DESeqDataSet                   html  
    glMDPlot.DESeqResults                   html  
    glMDPlot.DGEExact                       html  
    glMDPlot.DGELRT                         html  
    glMDPlot.MArrayLM                       html  
    glMDPlot                                html  
    glMDPlot.default                        html  
    glMDRmd                                 html  
    glMDSPlot.DESeqDataSet                  html  
    glMDSPlot.DGEList                       html  
    glMDSPlot                               html  
    glMDSPlot.default                       html  
    glScatter                               html  
    glScatter.default                       html  
    glTable                                 html  
    glXYPlot                                html  
    glimma                                  html  
    gllink                                  html  
    gltablink                               html  
    is.hex                                  html  
    lymphomaRNAseq                          html  
    makeJson                                html  
    makeJson.data.frame                     html  
    makeJson.jschart                        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 'Glimma' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Glimma' as Glimma_1.12.0.zip
* DONE (Glimma)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'Glimma' successfully unpacked and MD5 sums checked

Tests output

Glimma.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(Glimma)
> 
> test_check("Glimma")
== testthat results  ===========================================================
[ OK: 143 | SKIPPED: 0 | WARNINGS: 12 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  16.54    1.75   19.65 

Glimma.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(Glimma)
> 
> test_check("Glimma")
== testthat results  ===========================================================
[ OK: 143 | SKIPPED: 0 | WARNINGS: 12 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  18.60    1.23   19.84 

Example timings

Glimma.Rcheck/examples_i386/Glimma-Ex.timings

nameusersystemelapsed
as.hexcol000
glBar0.070.010.07
glBar.default000
glMDPlot.MArrayLM000
glMDPlot9.580.089.70
glMDRmd000
glMDSPlot0.070.020.09
glScatter000
glScatter.default000
glXYPlot000
glimma000
gllink0.000.010.01

Glimma.Rcheck/examples_x64/Glimma-Ex.timings

nameusersystemelapsed
as.hexcol000
glBar0.030.000.04
glBar.default0.020.000.01
glMDPlot.MArrayLM000
glMDPlot6.640.046.67
glMDRmd000
glMDSPlot0.050.010.06
glScatter000
glScatter.default000
glXYPlot000
glimma000
gllink000