iBMQ 1.0.1
Marie-Pier Scott-Boyer
| 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/iBMQ | | Last Changed Rev: 75531 / Revision: 76155 | | Last Changed Date: 2013-04-10 13:41:32 -0700 (Wed, 10 Apr 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| 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=iBMQ.buildbin-libdir iBMQ_1.0.1.tar.gz'
>>>>>>>
* installing *source* package 'iBMQ' ...
checking for gcc... clang
checking for C compiler default output file name... rm: a.out.dSYM: is a directory
a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking omp.h usability... no
checking omp.h presence... no
checking for omp.h... no
configure: no parallelism
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ARS.c -o ARS.o
ARS.c:64:6: warning: unused variable 'accept' [-Wunused-variable]
int accept = 0;
^
ARS.c:404:9: warning: unused variable 'R' [-Wunused-variable]
double R, y;
^
ARS.c:405:9: warning: unused variable 'a' [-Wunused-variable]
double a, b, pstar;
^
ARS.c:424:15: warning: unused variable 'z_j' [-Wunused-variable]
const double z_j = z[j];
^
ARS.c:460:9: warning: unused variable 'tmp' [-Wunused-variable]
double tmp;
^
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c RngStream.c -o RngStream.o
RngStream.c:221:11: warning: implicit conversion turns floating-point number into integer: 'double' to 'long' [-Wconversion]
k = p1 / m1;
˜ ˜˜˜^˜˜˜
RngStream.c:231:11: warning: implicit conversion turns floating-point number into integer: 'double' to 'long' [-Wconversion]
k = p2 / m2;
˜ ˜˜˜^˜˜˜
RngStream.c:437:17: warning: implicit conversion turns floating-point number into integer: 'double' to 'unsigned long' [-Wconversion]
seed[i] = g->Cg[i];
˜ ^˜˜˜˜˜˜˜
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c iBMQ_common.c -o iBMQ_common.o
iBMQ_common.c:275:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp = gsl_matrix_column(Y, g);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
iBMQ_common.c:276:70: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
expr_means[g] = gsl_stats_mean(tmp.vector.data, tmp.vector.stride, n_indivs);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
iBMQ_common.c:277:75: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
expr_vars[g] = gsl_stats_variance_m(tmp.vector.data, tmp.vector.stride, n_indivs,
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
iBMQ_common.c:284:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp = gsl_matrix_column(X, j);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
iBMQ_common.c:269:24: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int g,j, n_genes = Y->size2, n_indivs = Y->size1, n_snps = X->size2;
˜˜˜˜˜˜˜ ˜˜˜^˜˜˜˜
iBMQ_common.c:269:45: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int g,j, n_genes = Y->size2, n_indivs = Y->size1, n_snps = X->size2;
˜˜˜˜˜˜˜˜ ˜˜˜^˜˜˜˜
iBMQ_common.c:269:64: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int g,j, n_genes = Y->size2, n_indivs = Y->size1, n_snps = X->size2;
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c main_parallel_sparse.c -o main_parallel_sparse.o
main_parallel_sparse.c:73:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix* Y_t = gsl_matrix_calloc(*n_genes, *n_indivs);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
main_parallel_sparse.c:73:48: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix* Y_t = gsl_matrix_calloc(*n_genes, *n_indivs);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
main_parallel_sparse.c:74:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix* Y = gsl_matrix_calloc(*n_indivs, *n_genes);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
main_parallel_sparse.c:74:47: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix* Y = gsl_matrix_calloc(*n_indivs, *n_genes);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
main_parallel_sparse.c:80:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix* X_t = gsl_matrix_calloc(*n_snps, *n_indivs);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
main_parallel_sparse.c:80:47: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix* X_t = gsl_matrix_calloc(*n_snps, *n_indivs);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
main_parallel_sparse.c:81:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix* X = gsl_matrix_calloc(*n_indivs, *n_snps);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
main_parallel_sparse.c:81:47: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix* X = gsl_matrix_calloc(*n_indivs, *n_snps);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
main_parallel_sparse.c:105:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
Beta = (ptr_m_el*) R_alloc(*n_genes, sizeof(ptr_m_el));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
main_parallel_sparse.c:117:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
W_Logit = (double**) R_alloc(*n_snps, sizeof(double*));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
main_parallel_sparse.c:118:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
W_Ind = (int**) R_alloc(*n_snps, sizeof(int*));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
main_parallel_sparse.c:119:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
xA = (double**) R_alloc(*n_snps, sizeof(double*));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
main_parallel_sparse.c:120:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
xB = (double**) R_alloc(*n_snps, sizeof(double*));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
main_parallel_sparse.c:121:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
Gamma = (int**) R_alloc(*n_snps, sizeof(int*));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
main_parallel_sparse.c:122:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ProbSum = (int**) R_alloc(*n_snps, sizeof(int*));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
main_parallel_sparse.c:126:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
W_Logit[j] = (double*) R_alloc(*n_genes, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
main_parallel_sparse.c:127:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
W_Ind[j] = (int*) R_alloc(*n_genes, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
main_parallel_sparse.c:128:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
xA[j] = (double*) R_alloc(*nmax, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜
main_parallel_sparse.c:129:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
xB[j] = (double*) R_alloc(*nmax, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜
main_parallel_sparse.c:130:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
Gamma[j] = (int*) R_alloc(*n_genes, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
main_parallel_sparse.c:131:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ProbSum[j] = (int*) R_alloc(*n_genes, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
main_parallel_sparse.c:137:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
A = (double*) R_alloc (*n_snps, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
main_parallel_sparse.c:138:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
B = (double*) R_alloc(*n_snps, sizeof(double));;
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
main_parallel_sparse.c:139:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
P = (double*) R_alloc(*n_snps, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
main_parallel_sparse.c:140:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
C = (double*) R_alloc(*n_genes, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
main_parallel_sparse.c:141:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
Mu = (double*) R_alloc(*n_genes, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
main_parallel_sparse.c:142:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
Sig2 = (double*) R_alloc(*n_genes, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
main_parallel_sparse.c:145:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
expr_means = (double*) R_alloc(*n_genes, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
main_parallel_sparse.c:146:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
expr_vars = (double*) R_alloc(*n_genes, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
main_parallel_sparse.c:149:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
alpha2_beta = (double*) R_alloc(*n_snps, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
main_parallel_sparse.c:201:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector* one = gsl_vector_calloc(*n_indivs);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
main_parallel_sparse.c:215:11: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma omp parallel private(th_id, Y_g, workspace, chunk_g) num_threads(*nP)
^
main_parallel_sparse.c:100:16: warning: unused variable 'workspace' [-Wunused-variable]
ARS_workspace workspace;
^
main_parallel_sparse.c:200:18: warning: unused variable 'Y_g' [-Wunused-variable]
gsl_vector_view Y_g;
^
main_parallel_sparse.c:61:21: warning: unused variable 'th_id' [-Wunused-variable]
int iter, i, j, g, th_id = 0;
^
main_parallel_sparse.c:203:15: warning: unused variable 'chunk_g' [-Wunused-variable]
ptr_memChunk chunk_g;
^
main_parallel_sparse.c:290:47: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector* Y_minus_mu_g = gsl_vector_calloc(*n_indivs);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
main_parallel_sparse.c:291:46: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector* Xbeta_sum_g = gsl_vector_calloc(*n_indivs);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
main_parallel_sparse.c:292:48: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector* Resid_minus_j = gsl_vector_calloc(*n_indivs);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
main_parallel_sparse.c:310:47: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_view X_j = gsl_matrix_column(X, j);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
main_parallel_sparse.c:373:49: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
G_g += gsl_pow_2(gsl_vector_get(Y_minus_mu_g, i) - gsl_vector_get(Xbeta_sum_g, i));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
main_parallel_sparse.c:373:82: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
G_g += gsl_pow_2(gsl_vector_get(Y_minus_mu_g, i) - gsl_vector_get(Xbeta_sum_g, i));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
main_parallel_sparse.c:299:26: warning: unused variable 'w_jg' [-Wunused-variable]
double S_j, v1, v2, p1, w_jg, temp, logodds;
^
main_parallel_sparse.c:299:22: warning: unused variable 'p1' [-Wunused-variable]
double S_j, v1, v2, p1, w_jg, temp, logodds;
^
44 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c main_parallel_sparse_constC.c -o main_parallel_sparse_constC.o
main_parallel_sparse_constC.c:76:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix* Y_t = gsl_matrix_calloc(*n_genes, *n_indivs);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:76:48: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix* Y_t = gsl_matrix_calloc(*n_genes, *n_indivs);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:77:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix* Y = gsl_matrix_calloc(*n_indivs, *n_genes);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:77:47: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix* Y = gsl_matrix_calloc(*n_indivs, *n_genes);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:83:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix* X_t = gsl_matrix_calloc(*n_snps, *n_indivs);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
main_parallel_sparse_constC.c:83:47: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix* X_t = gsl_matrix_calloc(*n_snps, *n_indivs);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:84:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix* X = gsl_matrix_calloc(*n_indivs, *n_snps);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:84:47: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix* X = gsl_matrix_calloc(*n_indivs, *n_snps);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
main_parallel_sparse_constC.c:105:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Beta = (ptr_m_el*) malloc(*n_genes*sizeof(ptr_m_el));
^˜˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:126:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
W_Logit = (double**) malloc(*n_snps*sizeof(double*));
^˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:127:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
W_Ind = (int**) malloc(*n_snps*sizeof(int*));
^˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:128:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
xA = (double**) malloc(*n_snps*sizeof(double*));
^˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:129:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
xB = (double**) malloc(*n_snps*sizeof(double*));
^˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:130:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Gamma = (int**) malloc(*n_snps*sizeof(int*));
^˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:131:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ProbSum = (int**) malloc(*n_snps*sizeof(int*));
^˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:140:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
W_Logit[j] = (double*) malloc(*n_genes*sizeof(double));
^˜˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:141:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
W_Ind[j] = (int*) malloc(*n_genes*sizeof(int));
^˜˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:142:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
xA[j] = (double*) malloc(*nmax*sizeof(double));
^˜˜˜˜˜
main_parallel_sparse_constC.c:143:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
xB[j] = (double*) malloc(*nmax*sizeof(double));
^˜˜˜˜˜
main_parallel_sparse_constC.c:144:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Gamma[j] = (int*) malloc(*n_genes*sizeof(int));
^˜˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:145:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ProbSum[j] = (int*) malloc(*n_genes*sizeof(int));
^˜˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:156:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
A = (double*)malloc(*n_snps*sizeof(double));
^˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:157:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
B = (double*)malloc(*n_snps*sizeof(double));;
^˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:158:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
P = (double*)malloc(*n_snps*sizeof(double));
^˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:159:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
C = (double*)malloc(*n_genes*sizeof(double));
^˜˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:160:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Mu = (double*)malloc(*n_genes*sizeof(double));
^˜˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:161:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
Sig2 = (double*)malloc(*n_genes*sizeof(double));
^˜˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:164:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
expr_means = (double*)malloc(*n_genes*sizeof(double));
^˜˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:165:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
expr_vars = (double*)malloc(*n_genes*sizeof(double));
^˜˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:168:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
alpha2_beta = (double*)malloc(*n_snps*sizeof(double));
^˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:226:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector* one = gsl_vector_calloc(*n_indivs);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:240:11: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma omp parallel private(th_id, Y_g, workspace, chunk_g) num_threads(*nP)
^
main_parallel_sparse_constC.c:100:16: warning: unused variable 'workspace' [-Wunused-variable]
ARS_workspace workspace;
^
main_parallel_sparse_constC.c:228:15: warning: unused variable 'chunk_g' [-Wunused-variable]
ptr_memChunk chunk_g;
^
main_parallel_sparse_constC.c:154:10: warning: unused variable 'Astart' [-Wunused-variable]
double *Astart, *Bstart;
^
main_parallel_sparse_constC.c:154:19: warning: unused variable 'Bstart' [-Wunused-variable]
double *Astart, *Bstart;
^
main_parallel_sparse_constC.c:59:21: warning: unused variable 'th_id' [-Wunused-variable]
int iter, i, j, g, th_id = 0;
^
main_parallel_sparse_constC.c:225:18: warning: unused variable 'Y_g' [-Wunused-variable]
gsl_vector_view Y_g;
^
main_parallel_sparse_constC.c:339:47: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector* Y_minus_mu_g = gsl_vector_calloc(*n_indivs);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:344:46: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector* Xbeta_sum_g = gsl_vector_calloc(*n_indivs);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:347:48: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector* Resid_minus_j = gsl_vector_calloc(*n_indivs);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
main_parallel_sparse_constC.c:361:47: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_view X_j = gsl_matrix_column(X, j);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
main_parallel_sparse_constC.c:424:49: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
G_g += gsl_pow_2(gsl_vector_get(Y_minus_mu_g, i) - gsl_vector_get(Xbeta_sum_g, i));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
main_parallel_sparse_constC.c:424:82: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
G_g += gsl_pow_2(gsl_vector_get(Y_minus_mu_g, i) - gsl_vector_get(Xbeta_sum_g, i));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
44 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c norm_gamma_generation.c -o norm_gamma_generation.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c sparse.c -o sparse.o
sparse.c:17:49: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ptr_pool->array_head = (ptr_memChunk*) R_alloc(n_chunks, sizeof(ptr_memChunk));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
sparse.c:47:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
el_array = (ptr_m_el) R_alloc(n_els, sizeof(m_el));
˜˜˜˜˜˜˜ ^˜˜˜˜
sparse.c:39:27: warning: unused variable 'tmp' [-Wunused-variable]
ptr_m_el el_array, last, tmp;
^
sparse.c:39:21: warning: unused variable 'last' [-Wunused-variable]
ptr_m_el el_array, last, tmp;
^
sparse.c:220:44: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
const double mat_el = gsl_matrix_get(X, i, indx);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
sparse.c:220:47: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
const double mat_el = gsl_matrix_get(X, i, indx);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
6 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 iBMQ.so ARS.o RngStream.o iBMQ_common.o main_parallel_sparse.o main_parallel_sparse_constC.o norm_gamma_generation.o sparse.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/iBMQ.buildbin-libdir/iBMQ/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 (iBMQ)
>>>>>>>
>>>>>>> FIXING LINKS FOR iBMQ.buildbin-libdir/iBMQ/libs//iBMQ.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" "iBMQ.buildbin-libdir/iBMQ/libs//iBMQ.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "iBMQ.buildbin-libdir/iBMQ/libs//iBMQ.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" "iBMQ.buildbin-libdir/iBMQ/libs//iBMQ.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "iBMQ.buildbin-libdir/iBMQ/libs//iBMQ.so"