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Package 183/671HostnameOS / ArchBUILDCHECKBUILD BIN
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 

Summary

Package: DirichletMultinomial
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DirichletMultinomial_1.2.0.tar.gz
StartedAt: 2013-05-01 04:41:10 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 04:42:56 -0700 (Wed, 01 May 2013)
EllapsedTime: 105.9 seconds
RetCode: 0
Status:  OK 
CheckDir: DirichletMultinomial.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/DirichletMultinomial.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 'DirichletMultinomial/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DirichletMultinomial' version '1.2.0'
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'DirichletMultinomial' 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 ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [6s/6s] OK
* 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

DirichletMultinomial.Rcheck/00install.out:

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

DirichletMultinomial.Rcheck/DirichletMultinomial-Ex.timings:

nameusersystemelapsed
DMN-class0.0410.0040.045
DMNGroup-class0.0260.0020.029
cvdmngroup0.0270.0020.030
dataobjects0.0390.0030.044
dmn0.0210.0030.024
dmngroup0.0240.0010.026
fitted0.2210.0120.237
heatmapdmn0.2770.0110.291
roc0.4430.0230.489
util0.2310.0100.245