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BioC 3.1: CHECK report for birte on moscato2

This page was generated on 2015-10-09 09:32:02 -0700 (Fri, 09 Oct 2015).

Package 109/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
birte 1.2.0
Holger Froehlich
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/birte
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: birte
Version: 1.2.0
Command: rm -rf birte.buildbin-libdir birte.Rcheck && mkdir birte.buildbin-libdir birte.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=birte.buildbin-libdir birte_1.2.0.tar.gz >birte.Rcheck\00install.out 2>&1 && cp birte.Rcheck\00install.out birte-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=birte.buildbin-libdir --install="check:birte-install.out" --force-multiarch --no-vignettes --timings birte_1.2.0.tar.gz
StartedAt: 2015-10-08 23:49:58 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:53:20 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 202.0 seconds
RetCode: 0
Status:  OK  
CheckDir: birte.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf birte.buildbin-libdir birte.Rcheck && mkdir birte.buildbin-libdir birte.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=birte.buildbin-libdir birte_1.2.0.tar.gz >birte.Rcheck\00install.out 2>&1 && cp birte.Rcheck\00install.out birte-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=birte.buildbin-libdir --install="check:birte-install.out" --force-multiarch --no-vignettes --timings birte_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/birte.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'birte/DESCRIPTION' ... OK
* this is package 'birte' 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 'birte' 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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 'E:/biocbld/bbs-3.1-bioc/meat/birte.buildbin-libdir/birte/libs/i386/birte.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-3.1-bioc/meat/birte.buildbin-libdir/birte/libs/x64/birte.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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' ... [44s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
birteFitRidge 11.93   0.11   12.04
birteRun      10.26   0.06   10.33
birtePredict  10.08   0.09   10.17
simulateData   7.77   0.08    7.84
** running examples for arch 'x64' ... [40s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
birtePredict  9.37   0.05    9.42
birteRun      9.02   0.13    9.16
birteFitRidge 8.52   0.12    8.65
simulateData  7.78   0.11    7.90
* 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
  'E:/biocbld/bbs-3.1-bioc/meat/birte.Rcheck/00check.log'
for details.

birte.Rcheck/00install.out:


install for i386

* installing *source* package 'birte' ...
** libs
g++ -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/RcppArmadillo/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c BayesNetwork.cpp -o BayesNetwork.o
In file included from BayesNetwork.cpp:26:0:
BayesNetwork.h:203:3: warning: "/*" within comment [-Wcomment]
BayesNetwork.cpp: In constructor 'BayesNetwork::BayesNetwork(int, int, int, int, int, int**, double***, double***, double***, double***, int, int, int, int, int, double*, double*, double*, double*, std::list<int>*, std::list<int>*, std::list<int>*, std::list<int>*, std::list<int>*, std::list<int>*, double, double, double, double, double, double, double, double, double, double*, double*, double*, double*, double*, double*, int, int, std::list<int>*, std::list<int>*, std::list<int>*, double*, double*, double*, double**, int**, int**, int**, int**, double**, double**, double**)':
BayesNetwork.cpp:96:8: warning: unused variable 'j' [-Wunused-variable]
BayesNetwork.cpp:96:12: warning: unused variable 'r' [-Wunused-variable]
BayesNetwork.cpp: In destructor 'virtual BayesNetwork::˜BayesNetwork()':
BayesNetwork.cpp:221:8: warning: unused variable 'i' [-Wunused-variable]
BayesNetwork.cpp:221:10: warning: unused variable 'j' [-Wunused-variable]
BayesNetwork.cpp: In member function 'virtual int BayesNetwork::expandDesignMatrix(int, int, int, std::list<int>*, double**, int)':
BayesNetwork.cpp:357:6: warning: unused variable 'found' [-Wunused-variable]
BayesNetwork.cpp:357:30: warning: unused variable 'i' [-Wunused-variable]
BayesNetwork.cpp: In member function 'virtual int BayesNetwork::shrinkDesignMatrix(int, int, int)':
BayesNetwork.cpp:383:40: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
BayesNetwork.cpp:380:11: warning: unused variable 'k' [-Wunused-variable]
BayesNetwork.cpp: In member function 'virtual void BayesNetwork::updateEvidence2(int, int, int, arma::colvec&)':
BayesNetwork.cpp:599:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
BayesNetwork.cpp: In member function 'virtual double BayesNetwork::swap_states(int**, int, int, std::set<int>*, std::list<int>*, std::set<int>**, double)':
BayesNetwork.cpp:669:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
BayesNetwork.cpp:665:6: warning: unused variable 'pos_swaps' [-Wunused-variable]
BayesNetwork.cpp: In member function 'virtual void BayesNetwork::MCMC(long int, long int, int, double*)':
BayesNetwork.cpp:842:6: warning: unused variable 'mir' [-Wunused-variable]
BayesNetwork.cpp:842:11: warning: unused variable 'tf' [-Wunused-variable]
BayesNetwork.cpp:847:7: warning: unused variable 'eff_samples' [-Wunused-variable]
BayesNetwork.cpp:909:23: warning: unused variable 'u' [-Wunused-variable]
BayesNetwork.cpp:909:26: warning: unused variable 'delta_prior' [-Wunused-variable]
BayesNetwork.cpp:909:39: warning: unused variable 'eps_new' [-Wunused-variable]
BayesNetwork.cpp:909:48: warning: unused variable 'eps_old' [-Wunused-variable]
BayesNetwork.cpp:909:57: warning: unused variable 'delta_eps' [-Wunused-variable]
BayesNetwork.cpp:910:102: warning: unused variable 'make_move_eps' [-Wunused-variable]
BayesNetwork.cpp:910:119: warning: unused variable 'cond' [-Wunused-variable]
BayesNetwork.cpp: In member function 'virtual double BayesNetwork::likelihood()':
BayesNetwork.cpp:1074:12: warning: unused variable 'j' [-Wunused-variable]
BayesNetwork.cpp:1075:9: warning: unused variable 'bn' [-Wunused-variable]
BayesNetwork.cpp:1078:9: warning: unused variable 'z' [-Wunused-variable]
BayesNetwork.cpp: In member function 'virtual void BayesNetwork::MCMC(long int, long int, int, double*)':
BayesNetwork.cpp:1026:26: warning: 'delta_loglik' may be used uninitialized in this function [-Wuninitialized]
g++ -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/RcppArmadillo/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c getStates.cpp -o getStates.o
In file included from getStates.cpp:24:0:
BayesNetwork.h:203:3: warning: "/*" within comment [-Wcomment]
getStates.cpp: In function 'SEXPREC* getStates(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
getStates.cpp:349:36: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
getStates.cpp:366:36: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
getStates.cpp:384:36: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
Loading required package: Rcpp
Loading required package: Rcpp
Loading required package: Rcpp
Loading required package: Rcpp
g++ -m32 -shared -s -static-libgcc -o birte.dll tmp.def BayesNetwork.o getStates.o -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lRlapack -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lRblas -lgfortran -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/birte.buildbin-libdir/birte/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'birte' ...
** libs
g++ -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/RcppArmadillo/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c BayesNetwork.cpp -o BayesNetwork.o
In file included from BayesNetwork.cpp:26:0:
BayesNetwork.h:203:3: warning: "/*" within comment [-Wcomment]
BayesNetwork.cpp: In constructor 'BayesNetwork::BayesNetwork(int, int, int, int, int, int**, double***, double***, double***, double***, int, int, int, int, int, double*, double*, double*, double*, std::list<int>*, std::list<int>*, std::list<int>*, std::list<int>*, std::list<int>*, std::list<int>*, double, double, double, double, double, double, double, double, double, double*, double*, double*, double*, double*, double*, int, int, std::list<int>*, std::list<int>*, std::list<int>*, double*, double*, double*, double**, int**, int**, int**, int**, double**, double**, double**)':
BayesNetwork.cpp:96:8: warning: unused variable 'j' [-Wunused-variable]
BayesNetwork.cpp:96:12: warning: unused variable 'r' [-Wunused-variable]
BayesNetwork.cpp: In destructor 'virtual BayesNetwork::˜BayesNetwork()':
BayesNetwork.cpp:221:8: warning: unused variable 'i' [-Wunused-variable]
BayesNetwork.cpp:221:10: warning: unused variable 'j' [-Wunused-variable]
BayesNetwork.cpp: In member function 'virtual int BayesNetwork::expandDesignMatrix(int, int, int, std::list<int>*, double**, int)':
BayesNetwork.cpp:357:6: warning: unused variable 'found' [-Wunused-variable]
BayesNetwork.cpp:357:30: warning: unused variable 'i' [-Wunused-variable]
BayesNetwork.cpp: In member function 'virtual int BayesNetwork::shrinkDesignMatrix(int, int, int)':
BayesNetwork.cpp:383:40: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
BayesNetwork.cpp:380:11: warning: unused variable 'k' [-Wunused-variable]
BayesNetwork.cpp: In member function 'virtual void BayesNetwork::updateEvidence2(int, int, int, arma::colvec&)':
BayesNetwork.cpp:599:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
BayesNetwork.cpp: In member function 'virtual double BayesNetwork::swap_states(int**, int, int, std::set<int>*, std::list<int>*, std::set<int>**, double)':
BayesNetwork.cpp:669:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
BayesNetwork.cpp:665:6: warning: unused variable 'pos_swaps' [-Wunused-variable]
BayesNetwork.cpp: In member function 'virtual void BayesNetwork::MCMC(long int, long int, int, double*)':
BayesNetwork.cpp:842:6: warning: unused variable 'mir' [-Wunused-variable]
BayesNetwork.cpp:842:11: warning: unused variable 'tf' [-Wunused-variable]
BayesNetwork.cpp:847:7: warning: unused variable 'eff_samples' [-Wunused-variable]
BayesNetwork.cpp:909:23: warning: unused variable 'u' [-Wunused-variable]
BayesNetwork.cpp:909:26: warning: unused variable 'delta_prior' [-Wunused-variable]
BayesNetwork.cpp:909:39: warning: unused variable 'eps_new' [-Wunused-variable]
BayesNetwork.cpp:909:48: warning: unused variable 'eps_old' [-Wunused-variable]
BayesNetwork.cpp:909:57: warning: unused variable 'delta_eps' [-Wunused-variable]
BayesNetwork.cpp:910:102: warning: unused variable 'make_move_eps' [-Wunused-variable]
BayesNetwork.cpp:910:119: warning: unused variable 'cond' [-Wunused-variable]
BayesNetwork.cpp: In member function 'virtual double BayesNetwork::likelihood()':
BayesNetwork.cpp:1074:12: warning: unused variable 'j' [-Wunused-variable]
BayesNetwork.cpp:1075:9: warning: unused variable 'bn' [-Wunused-variable]
BayesNetwork.cpp:1078:9: warning: unused variable 'z' [-Wunused-variable]
BayesNetwork.cpp: In member function 'virtual void BayesNetwork::MCMC(long int, long int, int, double*)':
BayesNetwork.cpp:1026:26: warning: 'delta_loglik' may be used uninitialized in this function [-Wuninitialized]
g++ -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/RcppArmadillo/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c getStates.cpp -o getStates.o
In file included from getStates.cpp:24:0:
BayesNetwork.h:203:3: warning: "/*" within comment [-Wcomment]
getStates.cpp: In function 'SEXPREC* getStates(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
getStates.cpp:349:36: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
getStates.cpp:366:36: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
getStates.cpp:384:36: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
Loading required package: Rcpp
Loading required package: Rcpp
Loading required package: Rcpp
Loading required package: Rcpp
g++ -m64 -shared -s -static-libgcc -o birte.dll tmp.def BayesNetwork.o getStates.o -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lRlapack -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lRblas -lgfortran -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/birte.buildbin-libdir/birte/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'birte' as birte_1.2.0.zip
* DONE (birte)

birte.Rcheck/examples_i386/birte-Ex.timings:

nameusersystemelapsed
birteFitRidge11.93 0.1112.04
birtePredict10.08 0.0910.17
birteRun10.26 0.0610.33
estimateNetwork000
getPotentialSwaps0.520.050.56
limmaAnalysis000
plotConvergence000
proposeInteractions0.260.030.29
simplify0.190.050.24
simulateData7.770.087.84
suggestThreshold0.510.000.52

birte.Rcheck/examples_x64/birte-Ex.timings:

nameusersystemelapsed
birteFitRidge8.520.128.65
birtePredict9.370.059.42
birteRun9.020.139.16
estimateNetwork000
getPotentialSwaps0.640.060.70
limmaAnalysis000
plotConvergence000
proposeInteractions0.320.010.33
simplify0.170.030.20
simulateData7.780.117.90
suggestThreshold0.600.000.59