birte 1.11.0
Holger Froehlich
| Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/birte | | Last Changed Rev: 125420 / Revision: 129046 | | Last Changed Date: 2016-12-23 07:15:30 -0500 (Fri, 23 Dec 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | [ OK ] | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf birte.buildbin-libdir && mkdir birte.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh birte_1.11.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R birte.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=birte.buildbin-libdir birte_1.11.0.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 -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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:221:10: warning: unused variable 'j' [-Wunused-variable]
int c,i,j;
^
BayesNetwork.cpp:221:8: warning: unused variable 'i' [-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:842:11: warning: unused variable 'tf' [-Wunused-variable]
int mir, tf;
^
BayesNetwork.cpp:842:6: warning: unused variable 'mir' [-Wunused-variable]
int mir, tf;
^
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:847:7: warning: unused variable 'eff_samples' [-Wunused-variable]
long eff_samples = niter / thin + 1;
^
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:910:102: 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: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:1078:9: warning: unused variable 'z' [-Wunused-variable]
double z;
^
BayesNetwork.cpp:1075:9: warning: unused variable 'bn' [-Wunused-variable]
double bn;
^
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 -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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"