DirichletMultinomial 1.2.0
Martin Morgan
| Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/DirichletMultinomial | | Last Changed Rev: 75263 / Revision: 76155 | | Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
| pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DirichletMultinomial.buildbin-libdir DirichletMultinomial_1.2.0.tar.gz'
>>>>>>>
* installing *source* package 'DirichletMultinomial' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c R_init_DirichletMultinomial.c -o R_init_DirichletMultinomial.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c dirichlet_fit.c -o dirichlet_fit.o
dirichlet_fit.c:14:21: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
data->verbose = LOGICAL(verbose)[0];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c dirichlet_fit_main.c -o dirichlet_fit_main.o
dirichlet_fit_main.c:35:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
aadY = (double *) calloc(N *S, sizeof(double));
˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
dirichlet_fit_main.c:11:40: note: expanded from macro 'calloc'
#define calloc(_nelm, _elsize) R_alloc(_nelm, _elsize)
^
dirichlet_fit_main.c:37:30: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
adMu = (double *) calloc(S, sizeof(double));
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
dirichlet_fit_main.c:11:40: note: expanded from macro 'calloc'
#define calloc(_nelm, _elsize) R_alloc(_nelm, _elsize)
^
dirichlet_fit_main.c:49:44: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
k = gsl_rng_uniform_int (ptGSLRNG, K);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
dirichlet_fit_main.c:49:13: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
k = gsl_rng_uniform_int (ptGSLRNG, K);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
dirichlet_fit_main.c:121:55: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
const double dLambda = gsl_vector_get(lambda, j);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
dirichlet_fit_main.c:163:51: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
adAlpha[j] = exp(gsl_vector_get(ptLambda, j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
dirichlet_fit_main.c:184:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(g, j, value);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
dirichlet_fit_main.c:209:33: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ptLambda = gsl_vector_alloc(S);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
dirichlet_fit_main.c:211:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(ptLambda, i, adLambdaK[i]);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
dirichlet_fit_main.c:215:13: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fdf.n = S;
˜ ^
dirichlet_fit_main.c:222:44: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
s = gsl_multimin_fdfminimizer_alloc(T, S);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
dirichlet_fit_main.c:235:45: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
adLambdaK[i] = gsl_vector_get(s->x, i);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
dirichlet_fit_main.c:273:50: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double *aadLngammaLambda0 = (double*)calloc(S*K,sizeof(double));
˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
dirichlet_fit_main.c:11:40: note: expanded from macro 'calloc'
#define calloc(_nelm, _elsize) R_alloc(_nelm, _elsize)
^
dirichlet_fit_main.c:312:50: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double *aadLngammaLambda0 = (double*)calloc(S*K,sizeof(double));
˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
dirichlet_fit_main.c:11:40: note: expanded from macro 'calloc'
#define calloc(_nelm, _elsize) R_alloc(_nelm, _elsize)
^
dirichlet_fit_main.c:421:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(ptHessian, i, j, dVal);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
dirichlet_fit_main.c:421:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(ptHessian, i, j, dVal);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
dirichlet_fit_main.c:472:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
gsl_rng_set(ptGSLRNG, rseed);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
dirichlet_fit_main.c:476:29: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
adW = (double *) calloc(K, sizeof(double));
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
dirichlet_fit_main.c:11:40: note: expanded from macro 'calloc'
#define calloc(_nelm, _elsize) R_alloc(_nelm, _elsize)
^
dirichlet_fit_main.c:478:31: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
aadZ = (double **) calloc(K, sizeof(double *));
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
dirichlet_fit_main.c:11:40: note: expanded from macro 'calloc'
#define calloc(_nelm, _elsize) R_alloc(_nelm, _elsize)
^
dirichlet_fit_main.c:479:36: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
aadLambda = (double **) calloc(K, sizeof(double *));
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
dirichlet_fit_main.c:11:40: note: expanded from macro 'calloc'
#define calloc(_nelm, _elsize) R_alloc(_nelm, _elsize)
^
dirichlet_fit_main.c:480:33: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
aadErr = (double **) calloc(K, sizeof(double*));
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
dirichlet_fit_main.c:11:40: note: expanded from macro 'calloc'
#define calloc(_nelm, _elsize) R_alloc(_nelm, _elsize)
^
dirichlet_fit_main.c:482:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
aadZ[0] = (double *) calloc(K * N, sizeof(double));
˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
dirichlet_fit_main.c:11:40: note: expanded from macro 'calloc'
#define calloc(_nelm, _elsize) R_alloc(_nelm, _elsize)
^
dirichlet_fit_main.c:483:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
aadLambda[0] = (double *) calloc(K * S, sizeof(double));
˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
dirichlet_fit_main.c:11:40: note: expanded from macro 'calloc'
#define calloc(_nelm, _elsize) R_alloc(_nelm, _elsize)
^
dirichlet_fit_main.c:484:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
aadErr[0] = (double *) calloc(K * S, sizeof(double));
˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
dirichlet_fit_main.c:11:40: note: expanded from macro 'calloc'
#define calloc(_nelm, _elsize) R_alloc(_nelm, _elsize)
^
dirichlet_fit_main.c:538:46: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix *ptHessian = gsl_matrix_alloc(S, S),
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
dirichlet_fit_main.c:538:49: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix *ptHessian = gsl_matrix_alloc(S, S),
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
dirichlet_fit_main.c:539:46: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
*ptInverseHessian = gsl_matrix_alloc(S, S);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
dirichlet_fit_main.c:539:49: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
*ptInverseHessian = gsl_matrix_alloc(S, S);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
dirichlet_fit_main.c:540:48: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_permutation *p = gsl_permutation_alloc(S);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
dirichlet_fit_main.c:553:61: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
aadErr[k][j] = gsl_matrix_get(ptInverseHessian, j, j);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
dirichlet_fit_main.c:553:64: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
aadErr[k][j] = gsl_matrix_get(ptInverseHessian, j, j);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
dirichlet_fit_main.c:554:47: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
dTemp = gsl_matrix_get(ptHessian, j, j);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
dirichlet_fit_main.c:554:50: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
dTemp = gsl_matrix_get(ptHessian, j, j);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
33 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o DirichletMultinomial.so R_init_DirichletMultinomial.o dirichlet_fit.o dirichlet_fit_main.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/DirichletMultinomial.buildbin-libdir/DirichletMultinomial/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 (DirichletMultinomial)
>>>>>>>
>>>>>>> FIXING LINKS FOR DirichletMultinomial.buildbin-libdir/DirichletMultinomial/libs//DirichletMultinomial.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "DirichletMultinomial.buildbin-libdir/DirichletMultinomial/libs//DirichletMultinomial.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "DirichletMultinomial.buildbin-libdir/DirichletMultinomial/libs//DirichletMultinomial.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "DirichletMultinomial.buildbin-libdir/DirichletMultinomial/libs//DirichletMultinomial.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "DirichletMultinomial.buildbin-libdir/DirichletMultinomial/libs//DirichletMultinomial.so"