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BioC 3.5: BUILD BIN report for birte on veracruz2

This page was generated on 2017-08-16 13:32:53 -0400 (Wed, 16 Aug 2017).

Package 141/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
birte 1.12.0
Holger Froehlich
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/birte
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: birte
Version: 1.12.0
Command: rm -rf birte.buildbin-libdir && mkdir birte.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh birte_1.12.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R birte.buildbin-libdir
StartedAt: 2017-08-16 09:47:33 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 09:47:51 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 18.7 seconds
RetCode: 0
Status:  OK 
PackageFile: birte_1.12.0.tgz
PackageFileSize: 575.8 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf birte.buildbin-libdir && mkdir birte.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh birte_1.12.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R birte.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=birte.buildbin-libdir birte_1.12.0.tar.gz'
>>>>>>> 

* installing *source* package ‘birte’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c BayesNetwork.cpp -o BayesNetwork.o
In file included from BayesNetwork.cpp:26:
./BayesNetwork.h:203:3: warning: '/*' within block comment [-Wcomment]
                /**
                ^
BayesNetwork.cpp:96:8: warning: unused variable 'j' [-Wunused-variable]
        int i,j,c,r;
              ^
BayesNetwork.cpp:96:12: warning: unused variable 'r' [-Wunused-variable]
        int i,j,c,r;
                  ^
BayesNetwork.cpp:221:8: warning: unused variable 'i' [-Wunused-variable]
        int c,i,j;
              ^
BayesNetwork.cpp:221:10: warning: unused variable 'j' [-Wunused-variable]
        int c,i,j;
                ^
BayesNetwork.cpp:357:6: warning: unused variable 'found' [-Wunused-variable]
        int found, omega_index = 0, i, j;
            ^
BayesNetwork.cpp:357:30: warning: unused variable 'i' [-Wunused-variable]
        int found, omega_index = 0, i, j;
                                    ^
BayesNetwork.cpp:380:11: warning: unused variable 'k' [-Wunused-variable]
        int j=1, k, del=-1;      // j startet bei 1, weil die 1. Spalte der Intercept ist
                 ^
BayesNetwork.cpp:665:6: warning: unused variable 'pos_swaps' [-Wunused-variable]
        int pos_swaps = 0, condition, condition1, condition2, counter;
            ^
BayesNetwork.cpp:909:57: warning: unused variable 'delta_eps' [-Wunused-variable]
        double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY;        
                                                               ^
BayesNetwork.cpp:909:48: warning: unused variable 'eps_old' [-Wunused-variable]
        double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY;        
                                                      ^
BayesNetwork.cpp:909:39: warning: unused variable 'eps_new' [-Wunused-variable]
        double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY;        
                                             ^
BayesNetwork.cpp:909:26: warning: unused variable 'delta_prior' [-Wunused-variable]
        double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY;        
                                ^
BayesNetwork.cpp:909:23: warning: unused variable 'u' [-Wunused-variable]
        double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY;        
                             ^
BayesNetwork.cpp:910:119: warning: unused variable 'cond' [-Wunused-variable]
        int nall_possible_ops, n_Tpos_swaps_total=0, n_Spos_swaps_total=0, n_Qpos_swaps_total=0, make_move, make_move_eps=0, cond=0;
                                                                                                                             ^
BayesNetwork.cpp:842:11: warning: unused variable 'tf' [-Wunused-variable]
        int mir, tf;
                 ^
BayesNetwork.cpp:910:102: warning: unused variable 'make_move_eps' [-Wunused-variable]
        int nall_possible_ops, n_Tpos_swaps_total=0, n_Spos_swaps_total=0, n_Qpos_swaps_total=0, make_move, make_move_eps=0, cond=0;
                                                                                                            ^
BayesNetwork.cpp:847:7: warning: unused variable 'eff_samples' [-Wunused-variable]
        long eff_samples = niter / thin + 1;
             ^
BayesNetwork.cpp:842:6: warning: unused variable 'mir' [-Wunused-variable]
        int mir, tf;
            ^
BayesNetwork.cpp:1075:9: warning: unused variable 'bn' [-Wunused-variable]
        double bn; 
               ^
BayesNetwork.cpp:1078:9: warning: unused variable 'z' [-Wunused-variable]
        double z;
               ^
BayesNetwork.cpp:1074:12: warning: unused variable 'j' [-Wunused-variable]
        int c, i, j, r;
                  ^
22 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c getStates.cpp -o getStates.o
In file included from getStates.cpp:24:
./BayesNetwork.h:203:3: warning: '/*' within block comment [-Wcomment]
                /**
                ^
1 warning generated.
Loading required package: Rcpp
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o birte.so BayesNetwork.o getStates.o -llapack -lblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Loading required package: Rcpp
installing to /Users/biocbuild/bbs-3.5-bioc/meat/birte.buildbin-libdir/birte/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (birte)


>>>>>>> 
>>>>>>> FIXING LINKS FOR birte.buildbin-libdir/birte/libs//birte.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "birte.buildbin-libdir/birte/libs//birte.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "birte.buildbin-libdir/birte/libs//birte.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "birte.buildbin-libdir/birte/libs//birte.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "birte.buildbin-libdir/birte/libs//birte.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "birte.buildbin-libdir/birte/libs//birte.so"