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CHECK report for birta on tokay1

This page was generated on 2019-04-13 11:22:05 -0400 (Sat, 13 Apr 2019).

Package 164/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
birta 1.26.0
Benedikt Zacher
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/birta
Branch: RELEASE_3_8
Last Commit: 43cffee
Last Changed Date: 2018-10-30 11:41:48 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: birta
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:birta.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings birta_1.26.0.tar.gz
StartedAt: 2019-04-13 00:51:08 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 00:52:52 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 104.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: birta.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:birta.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings birta_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/birta.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'birta/DESCRIPTION' ... OK
* this is package 'birta' version '1.26.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'birta' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpmOOc6P/R.INSTALLd4c33ad4631/birta/man/plotConvergence.Rd:17: file link 'birta' in package 'birta' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/birta.Rcheck/00install.out' for details.
* 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 ... NOTE
Packages in Depends field not imported from:
  'Biobase' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
FisherPretest : <anonymous>: no visible global function definition for
  'fisher.test'
FisherPretest: no visible global function definition for 'p.adjust'
birtaRun: no visible global function definition for 'median'
birtaRun: no visible global function definition for 'var'
plotConvergence: no visible global function definition for 'plot'
plotConvergence: no visible global function definition for 'abline'
birta,ExpressionSet-ExpressionSet-ExpressionSet: no visible global
  function definition for 'exprs'
birta,ExpressionSet-ExpressionSet-ExpressionSet: no visible global
  function definition for 'callGeneric'
birta,ExpressionSet-ExpressionSet-missing: no visible global function
  definition for 'exprs'
birta,ExpressionSet-ExpressionSet-missing: no visible global function
  definition for 'callGeneric'
birta,ExpressionSet-missing-ExpressionSet: no visible global function
  definition for 'exprs'
birta,ExpressionSet-missing-ExpressionSet: no visible global function
  definition for 'callGeneric'
birta,ExpressionSet-missing-missing: no visible global function
  definition for 'exprs'
birta,ExpressionSet-missing-missing: no visible global function
  definition for 'callGeneric'
limmaAnalysis,ExpressionSet-matrix-character: no visible global
  function definition for 'exprs'
limmaAnalysis,ExpressionSet-matrix-character: no visible global
  function definition for 'callGeneric'
Undefined global functions or variables:
  abline callGeneric exprs fisher.test median p.adjust plot var
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("methods", "callGeneric")
  importFrom("stats", "fisher.test", "median", "p.adjust", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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-3.8-bioc/R/library/birta/libs/i386/birta.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/birta.Rcheck/00check.log'
for details.



Installation output

birta.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/birta_1.26.0.tar.gz && rm -rf birta.buildbin-libdir && mkdir birta.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=birta.buildbin-libdir birta_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL birta_1.26.0.zip && rm birta_1.26.0.tar.gz birta_1.26.0.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
100  432k  100  432k    0     0  5421k      0 --:--:-- --:--:-- --:--:-- 5686k

install for i386

* installing *source* package 'birta' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BayesNetwork.cpp -o BayesNetwork.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BayesNetworkNC.cpp -o BayesNetworkNC.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getStates.cpp -o getStates.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o birta.dll tmp.def BayesNetwork.o BayesNetworkNC.o getStates.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/birta.buildbin-libdir/birta/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'birta'
    finding HTML links ... done
    EColiNetwork                            html  
    EColiOxygen                             html  
    TFexpr                                  html  
    birta-methods                           html  
    birta-package                           html  
    birta.run                               html  
    genesets                                html  
    get_potential_swaps                     html  
    limmaAnalysis-methods                   html  
    limmaAnalysis                           html  
    plotConvergence                         html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpmOOc6P/R.INSTALLd4c33ad4631/birta/man/plotConvergence.Rd:17: file link 'birta' in package 'birta' does not exist and so has been treated as a topic
    potential_swaps                         html  
    sim                                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'birta' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BayesNetwork.cpp -o BayesNetwork.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BayesNetworkNC.cpp -o BayesNetworkNC.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getStates.cpp -o getStates.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o birta.dll tmp.def BayesNetwork.o BayesNetworkNC.o getStates.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/birta.buildbin-libdir/birta/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'birta' as birta_1.26.0.zip
* DONE (birta)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'birta' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

birta.Rcheck/examples_i386/birta-Ex.timings

nameusersystemelapsed
birta.run0.710.030.81
get_potential_swaps0.010.000.02
limmaAnalysis0.100.000.09
plotConvergence0.670.000.67

birta.Rcheck/examples_x64/birta-Ex.timings

nameusersystemelapsed
birta.run0.790.030.83
get_potential_swaps000
limmaAnalysis0.060.000.06
plotConvergence0.780.000.79