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CHECK report for mfa on tokay1

This page was generated on 2018-04-12 13:30:02 -0400 (Thu, 12 Apr 2018).

Package 846/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mfa 1.0.0
Kieran Campbell
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/mfa
Branch: RELEASE_3_6
Last Commit: 2994eb7
Last Changed Date: 2017-10-30 12:41:31 -0400 (Mon, 30 Oct 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: mfa
Version: 1.0.0
Command: rm -rf mfa.buildbin-libdir mfa.Rcheck && mkdir mfa.buildbin-libdir mfa.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mfa.buildbin-libdir mfa_1.0.0.tar.gz >mfa.Rcheck\00install.out 2>&1 && cp mfa.Rcheck\00install.out mfa-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=mfa.buildbin-libdir --install="check:mfa-install.out" --force-multiarch --no-vignettes --timings mfa_1.0.0.tar.gz
StartedAt: 2018-04-12 01:24:21 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:26:43 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 142.2 seconds
RetCode: 0
Status:  OK  
CheckDir: mfa.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf mfa.buildbin-libdir mfa.Rcheck && mkdir mfa.buildbin-libdir mfa.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mfa.buildbin-libdir mfa_1.0.0.tar.gz >mfa.Rcheck\00install.out 2>&1 && cp mfa.Rcheck\00install.out mfa-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=mfa.buildbin-libdir --install="check:mfa-install.out" --force-multiarch --no-vignettes --timings mfa_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/mfa.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 'mfa/DESCRIPTION' ... OK
* this is package 'mfa' version '1.0.0'
* 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 'mfa' 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/mfa.buildbin-libdir/mfa/libs/i386/mfa.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/mfa.Rcheck/00check.log'
for details.

Installation output

mfa.Rcheck/00install.out


install for i386

* installing *source* package 'mfa' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c gibbs.cpp -o gibbs.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o mfa.dll tmp.def RcppExports.o gibbs.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/mfa.buildbin-libdir/mfa/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'mfa'
    finding HTML links ... done
    calculate_chi                           html  
    create_synthetic                        html  
    cs_sigmoid                              html  
    empirical_lambda                        html  
    log_sum_exp                             html  
    map_branch                              html  
    mcmcify                                 html  
    mfa                                     html  
    plot_chi                                html  
    plot_dropout_relationship               html  
    plot_mfa_autocorr                       html  
    plot_mfa_trace                          html  
    posterior                               html  
    print.mfa                               html  
    summary.mfa                             html  
    to_ggmcmc                               html  
    transient                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'mfa' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c gibbs.cpp -o gibbs.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o mfa.dll tmp.def RcppExports.o gibbs.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/mfa.buildbin-libdir/mfa/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mfa' as mfa_1.0.0.zip
* DONE (mfa)
In R CMD INSTALL
In R CMD INSTALL

Tests output

mfa.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(mfa)
> 
> test_check("mfa")
== testthat results  ===========================================================
OK: 21 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   3.12    0.23    3.34

mfa.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(mfa)
> 
> test_check("mfa")
== testthat results  ===========================================================
OK: 21 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   4.01    0.25    4.25

Example timings

mfa.Rcheck/examples_i386/mfa-Ex.timings

nameusersystemelapsed
calculate_chi1.590.031.64
create_synthetic0.080.000.08
empirical_lambda000
mfa1.290.001.30
plot_chi1.710.001.70
plot_dropout_relationship0.610.000.61
plot_mfa_autocorr1.750.002.37
plot_mfa_trace1.420.001.42
print.mfa1.340.001.35
summary.mfa1.220.001.21

mfa.Rcheck/examples_x64/mfa-Ex.timings

nameusersystemelapsed
calculate_chi2.560.022.58
create_synthetic0.110.000.11
empirical_lambda000
mfa1.820.001.83
plot_chi2.190.002.18
plot_dropout_relationship0.870.000.87
plot_mfa_autocorr1.920.011.94
plot_mfa_trace1.680.001.67
print.mfa1.480.001.49
summary.mfa1.570.001.58