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CHECK report for apeglm on tokay1

This page was generated on 2018-04-12 13:30:24 -0400 (Thu, 12 Apr 2018).

Package 62/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
apeglm 1.0.3
Anqi Zhu
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/apeglm
Branch: RELEASE_3_6
Last Commit: 11ecf17
Last Changed Date: 2017-12-20 14:51:38 -0400 (Wed, 20 Dec 2017)
malbec1 Linux (Ubuntu 16.04.1 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
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: apeglm
Version: 1.0.3
Command: rm -rf apeglm.buildbin-libdir apeglm.Rcheck && mkdir apeglm.buildbin-libdir apeglm.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=apeglm.buildbin-libdir apeglm_1.0.3.tar.gz >apeglm.Rcheck\00install.out 2>&1 && cp apeglm.Rcheck\00install.out apeglm-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=apeglm.buildbin-libdir --install="check:apeglm-install.out" --force-multiarch --no-vignettes --timings apeglm_1.0.3.tar.gz
StartedAt: 2018-04-11 22:14:15 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:17:16 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 181.0 seconds
RetCode: 0
Status:  OK  
CheckDir: apeglm.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf apeglm.buildbin-libdir apeglm.Rcheck && mkdir apeglm.buildbin-libdir apeglm.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=apeglm.buildbin-libdir apeglm_1.0.3.tar.gz >apeglm.Rcheck\00install.out 2>&1 && cp apeglm.Rcheck\00install.out apeglm-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=apeglm.buildbin-libdir --install="check:apeglm-install.out" --force-multiarch --no-vignettes --timings apeglm_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/apeglm.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'apeglm/DESCRIPTION' ... OK
* this is package 'apeglm' version '1.0.3'
* 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 'apeglm' 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 installed files from 'inst/doc' ... 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: OK


Installation output

apeglm.Rcheck/00install.out


install for i386

* installing *source* package 'apeglm' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'apeglm'
    finding HTML links ... done
    apeglm                                  html  
    bbEstDisp                               html  
    logLikNB                                html  
    svalue                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'apeglm' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'apeglm' as apeglm_1.0.3.zip
* DONE (apeglm)
In R CMD INSTALL
In R CMD INSTALL

Tests output

apeglm.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("apeglm")
> test_check("apeglm")
== testthat results  ===========================================================
OK: 7 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   9.01    0.10    9.10 

apeglm.Rcheck/tests_x64/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("apeglm")
> test_check("apeglm")
== testthat results  ===========================================================
OK: 7 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  10.31    0.15   10.45 

Example timings

apeglm.Rcheck/examples_i386/apeglm-Ex.timings

nameusersystemelapsed
apeglm0.250.000.25
bbEstDisp0.150.000.15
logLikNB0.020.000.02
svalue0.50.00.5

apeglm.Rcheck/examples_x64/apeglm-Ex.timings

nameusersystemelapsed
apeglm0.280.000.28
bbEstDisp0.110.020.12
logLikNB000
svalue0.390.000.39