bridge 1.39.0
Raphael Gottardo
| Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bridge | | Last Changed Rev: 122712 / Revision: 127142 | | Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 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 | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | [ OK ] | |
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### Running command:
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### rm -rf bridge.buildbin-libdir && mkdir bridge.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bridge_1.39.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R bridge.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=bridge.buildbin-libdir bridge_1.39.0.tar.gz'
>>>>>>>
* installing *source* package ‘bridge’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c bridge2.affy.c -o bridge2.affy.o
bridge2.affy.c:37:7: warning: unused variable 'count_model' [-Wunused-variable]
int count_model=0;
^
bridge2.affy.c:36:7: warning: unused variable 'old_model' [-Wunused-variable]
int old_model;
^
bridge2.affy.c:302:3: warning: implicit declaration of function 'dirichlet' is invalid in C99 [-Wimplicit-function-declaration]
dirichlet(gamma, 2, w);
^
bridge2.affy.c:282:10: warning: unused variable 'w_new' [-Wunused-variable]
double w_new[2];
^
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c bridge2.c -o bridge2.o
bridge2.c:143:10: warning: unused variable 'dens_rho' [-Wunused-variable]
double dens_rho,dens_rho_new;
^
bridge2.c:143:19: warning: unused variable 'dens_rho_new' [-Wunused-variable]
double dens_rho,dens_rho_new;
^
bridge2.c:162:28: warning: unused variable 'post_prec_delta' [-Wunused-variable]
double post_mean_delta=0,post_prec_delta=0;
^
bridge2.c:162:10: warning: unused variable 'post_mean_delta' [-Wunused-variable]
double post_mean_delta=0,post_prec_delta=0;
^
bridge2.c:142:20: warning: unused variable 'sum_rho_new' [-Wunused-variable]
double sum_rho=0,sum_rho_new=0;
^
bridge2.c:199:18: warning: unused variable 'width_a' [-Wunused-variable]
double old_a=0,width_a=5;
^
bridge2.c:163:26: warning: unused variable 'post_prec_eta' [-Wunused-variable]
double post_mean_eta=0,post_prec_eta=0;
^
bridge2.c:163:10: warning: unused variable 'post_mean_eta' [-Wunused-variable]
double post_mean_eta=0,post_prec_eta=0;
^
bridge2.c:165:17: warning: unused variable 'l_ab_new' [-Wunused-variable]
double l_ab=0,l_ab_new=0;
^
bridge2.c:165:10: warning: unused variable 'l_ab' [-Wunused-variable]
double l_ab=0,l_ab_new=0;
^
bridge2.c:142:10: warning: unused variable 'sum_rho' [-Wunused-variable]
double sum_rho=0,sum_rho_new=0;
^
bridge2.c:166:22: warning: unused variable 'b_eps_new' [-Wunused-variable]
double a_eps_new=0,b_eps_new=0;
^
bridge2.c:166:10: warning: unused variable 'a_eps_new' [-Wunused-variable]
double a_eps_new=0,b_eps_new=0;
^
bridge2.c:192:10: warning: unused variable 'sum_res2' [-Wunused-variable]
double sum_res2;
^
bridge2.c:171:7: warning: unused variable 'countrho' [-Wunused-variable]
int countrho=0;
^
bridge2.c:173:7: warning: unused variable 'counta' [-Wunused-variable]
int counta=0;
^
bridge2.c:138:10: warning: unused variable 'rho_new' [-Wunused-variable]
double rho_new;
^
bridge2.c:175:7: warning: unused variable 'countb_eps' [-Wunused-variable]
int countb_eps=0;
^
bridge2.c:191:10: warning: unused variable 'sum_res1' [-Wunused-variable]
double sum_res1;
^
bridge2.c:174:7: warning: unused variable 'counta_eps' [-Wunused-variable]
int counta_eps=0;
^
bridge2.c:154:10: warning: unused variable 'dens_t' [-Wunused-variable]
double dens_t=0,dens_t_new=0;
^
bridge2.c:154:19: warning: unused variable 'dens_t_new' [-Wunused-variable]
double dens_t=0,dens_t_new=0;
^
bridge2.c:159:25: warning: unused variable 'post_prec_mu' [-Wunused-variable]
double post_mean_mu=0,post_prec_mu=0;
^
bridge2.c:198:18: warning: unused variable 'width_b' [-Wunused-variable]
double old_b=0,width_b=5;
^
bridge2.c:160:10: warning: unused variable 'post_mean_beta' [-Wunused-variable]
double post_mean_beta=0,post_prec_beta=0;
^
bridge2.c:159:10: warning: unused variable 'post_mean_mu' [-Wunused-variable]
double post_mean_mu=0,post_prec_mu=0;
^
bridge2.c:145:10: warning: unused variable 'pi' [-Wunused-variable]
double pi=3.14;
^
bridge2.c:177:7: warning: unused variable 'countp' [-Wunused-variable]
int countp=0;
^
bridge2.c:199:10: warning: unused variable 'old_a' [-Wunused-variable]
double old_a=0,width_a=5;
^
bridge2.c:161:10: warning: unused variable 'post_mean_alpha' [-Wunused-variable]
double post_mean_alpha=0,post_prec_alpha=0;
^
bridge2.c:161:28: warning: unused variable 'post_prec_alpha' [-Wunused-variable]
double post_mean_alpha=0,post_prec_alpha=0;
^
bridge2.c:160:27: warning: unused variable 'post_prec_beta' [-Wunused-variable]
double post_mean_beta=0,post_prec_beta=0;
^
bridge2.c:198:10: warning: unused variable 'old_b' [-Wunused-variable]
double old_b=0,width_b=5;
^
33 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c bridge2_util.c -o bridge2_util.o
bridge2_util.c:570:5: warning: implicit declaration of function 'dqrdc2_' is invalid in C99 [-Wimplicit-function-declaration]
F77_CALL(dqrdc2)(xt, &n, &n, &p, &tol, &rank,qraux, pivot, work);
^
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:92:22: note: expanded from macro 'F77_CALL'
# define F77_CALL(x) x ## _
^
<scratch space>:198:1: note: expanded from here
dqrdc2_
^
bridge2_util.c:585:5: warning: implicit declaration of function 'dqrcf_' is invalid in C99 [-Wimplicit-function-declaration]
F77_CALL(dqrcf)(xt, &n, &rank, qraux,yt, &n, coeft, &info);
^
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:92:22: note: expanded from macro 'F77_CALL'
# define F77_CALL(x) x ## _
^
<scratch space>:198:1: note: expanded from here
dqrcf_
^
bridge2_util.c:549:11: warning: unused variable 'vmax' [-Wunused-variable]
char *vmax;
^
bridge2_util.c:608:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
bridge2_util.c:655:11: warning: unused variable 'k' [-Wunused-variable]
int i,j,k;
^
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c bridge3.c -o bridge3.o
bridge3.c:38:7: warning: unused variable 'count_model' [-Wunused-variable]
int count_model=0;
^
bridge3.c:37:7: warning: unused variable 'old_model' [-Wunused-variable]
int old_model;
^
bridge3.c:332:25: warning: & has lower precedence than <; < will be evaluated first [-Wparentheses]
else if((w_star[3]<u) & u<w_star[4])
^˜˜˜˜˜˜˜˜˜˜˜˜
bridge3.c:332:25: note: place parentheses around the '<' expression to silence this warning
else if((w_star[3]<u) & u<w_star[4])
^
( )
bridge3.c:332:25: note: place parentheses around the & expression to evaluate it first
else if((w_star[3]<u) & u<w_star[4])
^
( )
bridge3.c:362:10: warning: unused variable 'w_new' [-Wunused-variable]
double w_new[5];
^
4 warnings generated.
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 bridge.so bridge2.affy.o bridge2.o bridge2_util.o bridge3.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/bridge.buildbin-libdir/bridge/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 (bridge)
>>>>>>>
>>>>>>> FIXING LINKS FOR bridge.buildbin-libdir/bridge/libs//bridge.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" "bridge.buildbin-libdir/bridge/libs//bridge.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "bridge.buildbin-libdir/bridge/libs//bridge.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" "bridge.buildbin-libdir/bridge/libs//bridge.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "bridge.buildbin-libdir/bridge/libs//bridge.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "bridge.buildbin-libdir/bridge/libs//bridge.so"