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CHECK report for phenopath on tokay1

This page was generated on 2018-04-12 13:30:06 -0400 (Thu, 12 Apr 2018).

Package 1030/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phenopath 1.2.0
Kieran Campbell
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/phenopath
Branch: RELEASE_3_6
Last Commit: 3e38a3b
Last Changed Date: 2017-10-30 12:41:32 -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: phenopath
Version: 1.2.0
Command: rm -rf phenopath.buildbin-libdir phenopath.Rcheck && mkdir phenopath.buildbin-libdir phenopath.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phenopath.buildbin-libdir phenopath_1.2.0.tar.gz >phenopath.Rcheck\00install.out 2>&1 && cp phenopath.Rcheck\00install.out phenopath-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=phenopath.buildbin-libdir --install="check:phenopath-install.out" --force-multiarch --no-vignettes --timings phenopath_1.2.0.tar.gz
StartedAt: 2018-04-12 02:07:53 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:11:32 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 219.1 seconds
RetCode: 0
Status:  OK  
CheckDir: phenopath.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf phenopath.buildbin-libdir phenopath.Rcheck && mkdir phenopath.buildbin-libdir phenopath.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phenopath.buildbin-libdir phenopath_1.2.0.tar.gz >phenopath.Rcheck\00install.out 2>&1 && cp phenopath.Rcheck\00install.out phenopath-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=phenopath.buildbin-libdir --install="check:phenopath-install.out" --force-multiarch --no-vignettes --timings phenopath_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/phenopath.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 'phenopath/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'phenopath' version '1.2.0'
* 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 'phenopath' 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/phenopath.buildbin-libdir/phenopath/libs/i386/phenopath.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/phenopath.Rcheck/00check.log'
for details.

Installation output

phenopath.Rcheck/00install.out


install for i386

* installing *source* package 'phenopath' ...
** 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 cavi.cpp -o cavi.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o phenopath.dll tmp.def RcppExports.o cavi.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/phenopath.buildbin-libdir/phenopath/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'phenopath'
    finding HTML links ... done
    clvm                                    html  
    interaction_effects                     html  
    interaction_sds                         html  
    interactions                            html  
    phenopath                               html  
    finding level-2 HTML links ... done

    plot_elbo                               html  
    print.phenopath_fit                     html  
    sample_fns                              html  
    scale_vec                               html  
    significant_interactions                html  
    simulate_one_gene                       html  
    simulate_phenopath                      html  
    trajectory                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'phenopath' ...
** 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 cavi.cpp -o cavi.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o phenopath.dll tmp.def RcppExports.o cavi.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/phenopath.buildbin-libdir/phenopath/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'phenopath' as phenopath_1.2.0.zip
* DONE (phenopath)
In R CMD INSTALL
In R CMD INSTALL

Tests output

phenopath.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(phenopath)
> 
> test_check("phenopath")
== testthat results  ===========================================================
OK: 26 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   6.87    0.21    7.07

phenopath.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(phenopath)
> 
> test_check("phenopath")
== testthat results  ===========================================================
OK: 26 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   8.00    0.28    8.26

Example timings

phenopath.Rcheck/examples_i386/phenopath-Ex.timings

nameusersystemelapsed
clvm2.030.032.06
interaction_effects0.30.00.3
interaction_sds0.220.000.22
interactions0.720.000.72
phenopath0.090.010.11
plot_elbo3.240.063.30
print.phenopath_fit0.120.000.12
significant_interactions0.110.000.11
simulate_phenopath0.020.000.02
trajectory0.150.000.15

phenopath.Rcheck/examples_x64/phenopath-Ex.timings

nameusersystemelapsed
clvm1.730.001.74
interaction_effects0.300.000.29
interaction_sds0.170.000.17
interactions0.610.000.61
phenopath0.110.000.11
plot_elbo2.520.002.52
print.phenopath_fit0.480.000.48
significant_interactions0.140.000.14
simulate_phenopath000
trajectory0.120.000.12