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Package 330/671HostnameOS / ArchBUILDCHECKBUILD BIN
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 

Summary

Package: iBMQ
Version: 1.0.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch iBMQ_1.0.1.tar.gz
StartedAt: 2013-05-01 06:58:37 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 06:59:50 -0700 (Wed, 01 May 2013)
EllapsedTime: 72.0 seconds
RetCode: 0
Status:  OK 
CheckDir: iBMQ.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/iBMQ.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'iBMQ/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iBMQ' version '1.0.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'iBMQ' can be installed ... [10s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/Users/biocbuild/bbs-2.12-bioc/meat/iBMQ.Rcheck/iBMQ/libs/iBMQ.so':
  Found '_printf', possibly from 'printf' (C)
    Objects: 'RngStream.o', 'sparse.o'
File '/Users/biocbuild/bbs-2.12-bioc/meat/iBMQ.Rcheck/iBMQ/libs/iBMQ.so':
  Found non-API call to R: 'R_CStackLimit'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking examples ... [12s/12s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
eqtlClassifier 5.993  0.308   6.364
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/iBMQ.Rcheck/00check.log'
for details.

iBMQ.Rcheck/00install.out:

* 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 -ggdb -O0 -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 -ggdb -O0 -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 -ggdb -O0 -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 -ggdb -O0 -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 -ggdb -O0 -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 -ggdb -O0 -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 -ggdb -O0 -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.Rcheck/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)

iBMQ.Rcheck/iBMQ-Ex.timings:

nameusersystemelapsed
PPA.liver0.3430.0470.398
calculateThreshold0.8970.0901.005
eqtlClassifier5.9930.3086.364
eqtlFinder0.8450.0890.934
eqtlMcmc0.0900.0280.119
gene0.0610.0070.071
genepos0.0060.0050.012
genotype.liver0.0130.0050.018
hotspotFinder0.7720.0940.875
map.liver0.0040.0020.006
phenotype.liver0.0790.0150.099
probe.liver0.0180.0060.024
snp0.0230.0110.035
snppos0.0080.0070.014