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CHECK report for alpine on tokay1

This page was generated on 2018-04-12 13:28:36 -0400 (Thu, 12 Apr 2018).

Package 36/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alpine 1.4.0
Michael Love
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/alpine
Branch: RELEASE_3_6
Last Commit: c85beb2
Last Changed Date: 2017-10-30 12:41:21 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: alpine
Version: 1.4.0
Command: rm -rf alpine.buildbin-libdir alpine.Rcheck && mkdir alpine.buildbin-libdir alpine.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=alpine.buildbin-libdir alpine_1.4.0.tar.gz >alpine.Rcheck\00install.out 2>&1 && cp alpine.Rcheck\00install.out alpine-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=alpine.buildbin-libdir --install="check:alpine-install.out" --force-multiarch --no-vignettes --timings alpine_1.4.0.tar.gz
StartedAt: 2018-04-11 22:09:36 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:17:19 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 463.4 seconds
RetCode: 0
Status:  OK  
CheckDir: alpine.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf alpine.buildbin-libdir alpine.Rcheck && mkdir alpine.buildbin-libdir alpine.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=alpine.buildbin-libdir alpine_1.4.0.tar.gz >alpine.Rcheck\00install.out 2>&1 && cp alpine.Rcheck\00install.out alpine-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=alpine.buildbin-libdir --install="check:alpine-install.out" --force-multiarch --no-vignettes --timings alpine_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/alpine.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 'alpine/DESCRIPTION' ... OK
* this is package 'alpine' version '1.4.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'alpine' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
fitBiasModels     13.54   0.79   17.57
estimateAbundance  9.83   0.64   10.89
predictCoverage    5.92   0.23    6.20
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
fitBiasModels     14.11   0.99   15.25
estimateAbundance 11.41   0.77   13.00
predictCoverage    5.42   0.45    5.96
* 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

alpine.Rcheck/00install.out


install for i386

* installing *source* package 'alpine' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'alpine'
    finding HTML links ... done
    alpine-package                          html  
    buildFragtypes                          html  
    estimateAbundance                       html  
    extractAlpine                           html  
    fitBiasModels                           html  
    getFragmentWidths                       html  
    getReadLength                           html  
    mergeGenes                              html  
    normalizeDESeq                          html  
    plotFragLen                             html  
    plotGC                                  html  
    plotGRL                                 html  
    plotOrder0                              html  
    plotRelPos                              html  
    predictCoverage                         html  
    preprocessedData                        html  
    splitGenesAcrossChroms                  html  
    splitLongGenes                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'alpine' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'alpine' as alpine_1.4.0.zip
* DONE (alpine)
In R CMD INSTALL
In R CMD INSTALL

Tests output

alpine.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(alpine)
> test_check("alpine")
== testthat results  ===========================================================
OK: 1 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  49.71    3.79   53.86 
[samopen] SAM header is present: 194 sequences.

alpine.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(alpine)
> test_check("alpine")
== testthat results  ===========================================================
OK: 1 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  50.12    3.01   53.51 
[samopen] SAM header is present: 194 sequences.

Example timings

alpine.Rcheck/examples_i386/alpine-Ex.timings

nameusersystemelapsed
buildFragtypes2.850.164.78
estimateAbundance 9.83 0.6410.89
extractAlpine0.030.000.04
fitBiasModels13.54 0.7917.57
getFragmentWidths1.970.102.22
getReadLength1.420.031.50
mergeGenes0.180.000.17
normalizeDESeq000
plotFragLen0.020.000.01
plotGC0.030.000.03
plotGRL0.120.000.13
plotOrder00.030.020.04
plotRelPos0.020.000.02
predictCoverage5.920.236.20
splitGenesAcrossChroms0.250.000.25
splitLongGenes0.220.030.25

alpine.Rcheck/examples_x64/alpine-Ex.timings

nameusersystemelapsed
buildFragtypes4.530.154.69
estimateAbundance11.41 0.7713.00
extractAlpine0.020.010.03
fitBiasModels14.11 0.9915.25
getFragmentWidths1.920.112.19
getReadLength1.150.031.25
mergeGenes0.170.010.18
normalizeDESeq000
plotFragLen0.000.020.02
plotGC0.020.010.03
plotGRL0.120.020.14
plotOrder00.050.000.05
plotRelPos0.020.000.01
predictCoverage5.420.455.96
splitGenesAcrossChroms0.330.000.33
splitLongGenes0.310.020.32