Package: ddgraph

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ddgraph_1.4.0.tar.gz

StartedAt: 2013-05-01 04:22:21 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 04:26:58 -0700 (Wed, 01 May 2013)

EllapsedTime: 277.7 seconds

RetCode: 0

Status:  OK

CheckDir: ddgraph.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ddgraph.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 'ddgraph/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ddgraph' version '1.4.0'
* 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 'ddgraph' can be installed ... [12s/14s] 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 ... [48s/49s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotPCalg      27.835  0.245  28.499
calcDependence 10.254  0.120  10.699
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-all.R' [130s/139s]
 [131s/139s] 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

* installing *source* package 'ddgraph' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c mcX2cloop.cpp -o mcX2cloop.o
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:130:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        switch (size - i){                          
                     ˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:190:44: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP x = PROTECT( Rf_allocVector( VECSXP, size ) );
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:209:44: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP x = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:237:48: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP names = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:245:26: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
                SET_STRING_ELT( names, i, Rf_mkChar(buf.c_str()) ) ;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:266:48: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP names = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:274:26: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
                SET_STRING_ELT( names, i, Rf_mkChar(buf.c_str()) ) ;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:311:44: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP x = PROTECT( Rf_allocVector( VECSXP, size ) );
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:312:48: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP names = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:319:22: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
                SET_VECTOR_ELT( x, i, element ) ;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜     ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:320:26: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
                SET_STRING_ELT( names, i, Rf_mkChar(buf.c_str()) ) ; 
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:343:44: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP x = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:344:48: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP names = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:484:44: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP x = PROTECT( Rf_allocVector( LGLSXP, size ) );
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:50:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/Language.h:173:76: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
        unary_call( Language call_, int index ) : call(call_), proxy(call_,index){}
                                                               ˜˜˜˜˜       ^˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/Language.h:190:91: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
        binary_call( Language call_, int index1, int index2 ) : call(call_), proxy1(call_,index1), proxy2(call_,index2){}
                                                                             ˜˜˜˜˜˜       ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/Language.h:190:113: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
        binary_call( Language call_, int index1, int index2 ) : call(call_), proxy1(call_,index1), proxy2(call_,index2){}
                                                                                                   ˜˜˜˜˜˜       ^˜˜˜˜˜
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:60:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/Datetime.h:40:40: warning: implicit conversion changes signedness: 'const unsigned int' to 'int' [-Wsign-conversion]
                int getMicroSeconds() const { return m_us; }
                                              ˜˜˜˜˜˜ ^˜˜˜
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:70:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:28:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/hash.h:27:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:197:16: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        return RCPP_HASH(value) ;
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:45:61: note: expanded from macro 'RCPP_HASH'
    #define RCPP_HASH(X) (3141592653U * ((unsigned int)(X)) >> (32 - k))
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:212:14: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      addr = RCPP_HASH(val_u.u[0] + val_u.u[1]);
           ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:45:61: note: expanded from macro 'RCPP_HASH'
    #define RCPP_HASH(X) (3141592653U * ((unsigned int)(X)) >> (32 - k))
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:221:18: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
          addr = RCPP_HASH((val & 0xffffffff) ^ (val >> 32));
               ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:45:61: note: expanded from macro 'RCPP_HASH'
    #define RCPP_HASH(X) (3141592653U * ((unsigned int)(X)) >> (32 - k))
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:70:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:28:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/hash.h:28:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/SelfHash.h:95:16: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        return RCPP_HASH(value) ;
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:45:61: note: expanded from macro 'RCPP_HASH'
    #define RCPP_HASH(X) (3141592653U * ((unsigned int)(X)) >> (32 - k))
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:70:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:28:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/hash.h:28:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/SelfHash.h:110:14: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      addr = RCPP_HASH(val_u.u[0] + val_u.u[1]);
           ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:45:61: note: expanded from macro 'RCPP_HASH'
    #define RCPP_HASH(X) (3141592653U * ((unsigned int)(X)) >> (32 - k))
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:70:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:28:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/hash.h:28:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/SelfHash.h:119:18: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
          addr = RCPP_HASH((val & 0xffffffff) ^ (val >> 32));
               ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:45:61: note: expanded from macro 'RCPP_HASH'
    #define RCPP_HASH(X) (3141592653U * ((unsigned int)(X)) >> (32 - k))
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:70:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/functions/functions.h:37:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/functions/seq_along.h:49:24: warning: implicit conversion loses integer precision: 'const size_t' (aka 'const unsigned long') to 'int' [-Wshorten-64-to-32]
        return sugar::SeqLen( n ) ;
               ˜˜˜˜˜          ^
mcX2cloop.cpp:39:19: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                vRowS[0] = rowS(i,0);
                           ˜˜˜˜ ^
mcX2cloop.cpp:40:19: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                vRowS[1] = rowS(i,1);
                           ˜˜˜˜ ^
mcX2cloop.cpp:41:19: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                vColS[0] = colS(i,0);
                           ˜˜˜˜ ^
mcX2cloop.cpp:42:19: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                vColS[1] = colS(i,1);
                           ˜˜˜˜ ^
mcX2cloop.cpp:51:13: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                        simTable(j,pos) = st(0,0);
                        ˜˜˜˜˜˜˜˜ ^
mcX2cloop.cpp:51:15: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                        simTable(j,pos) = st(0,0);
                        ˜˜˜˜˜˜˜˜   ^˜˜
mcX2cloop.cpp:52:13: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                        simTable(j,pos+1) = st(1,0);
                        ˜˜˜˜˜˜˜˜ ^
mcX2cloop.cpp:52:18: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                        simTable(j,pos+1) = st(1,0);
                        ˜˜˜˜˜˜˜˜   ˜˜˜^˜
mcX2cloop.cpp:53:13: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                        simTable(j,pos+2) = st(0,1);
                        ˜˜˜˜˜˜˜˜ ^
mcX2cloop.cpp:53:18: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                        simTable(j,pos+2) = st(0,1);
                        ˜˜˜˜˜˜˜˜   ˜˜˜^˜
mcX2cloop.cpp:54:13: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                        simTable(j,pos+3) = st(1,1);
                        ˜˜˜˜˜˜˜˜ ^
mcX2cloop.cpp:54:18: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                        simTable(j,pos+3) = st(1,1);
                        ˜˜˜˜˜˜˜˜   ˜˜˜^˜
mcX2cloop.cpp:59:5: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                E(i,0) = vRowS[0] * vColS[0] / total;
                ˜ ^
mcX2cloop.cpp:60:5: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                E(i,1) = vRowS[1] * vColS[0] / total;           
                ˜ ^
mcX2cloop.cpp:61:5: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                E(i,2) = vRowS[0] * vColS[1] / total;           
                ˜ ^
mcX2cloop.cpp:62:5: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                E(i,3) = vRowS[1] * vColS[1] / total;
                ˜ ^
mcX2cloop.cpp:70:20: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                        vRowS[0] = rowS(i,0);
                                   ˜˜˜˜ ^
mcX2cloop.cpp:71:20: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                        vRowS[1] = rowS(i,1);
                                   ˜˜˜˜ ^
mcX2cloop.cpp:72:20: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                        vColS[0] = colS(i,0);
                                   ˜˜˜˜ ^
mcX2cloop.cpp:73:20: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                        vColS[1] = colS(i,1);
                                   ˜˜˜˜ ^
mcX2cloop.cpp:80:50: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                Rprintf("simTable: %f,%f,%f,%f\\n", simTable(j,pos), simTable(j,pos+1), simTable(j,pos+2), simTable(j,pos+3));
                                                                    ˜˜˜˜˜˜˜˜ ^
mcX2cloop.cpp:80:52: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                Rprintf("simTable: %f,%f,%f,%f\\n", simTable(j,pos), simTable(j,pos+1), simTable(j,pos+2), simTable(j,pos+3));
                                                                    ˜˜˜˜˜˜˜˜   ^˜˜
mcX2cloop.cpp:80:67: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                Rprintf("simTable: %f,%f,%f,%f\\n", simTable(j,pos), simTable(j,pos+1), simTable(j,pos+2), simTable(j,pos+3));
                                                                                     ˜˜˜˜˜˜˜˜ ^
mcX2cloop.cpp:80:72: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                Rprintf("simTable: %f,%f,%f,%f\\n", simTable(j,pos), simTable(j,pos+1), simTable(j,pos+2), simTable(j,pos+3));
                                                                                     ˜˜˜˜˜˜˜˜   ˜˜˜^˜
mcX2cloop.cpp:80:86: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                Rprintf("simTable: %f,%f,%f,%f\\n", simTable(j,pos), simTable(j,pos+1), simTable(j,pos+2), simTable(j,pos+3));
                                                                                                        ˜˜˜˜˜˜˜˜ ^
mcX2cloop.cpp:80:91: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                Rprintf("simTable: %f,%f,%f,%f\\n", simTable(j,pos), simTable(j,pos+1), simTable(j,pos+2), simTable(j,pos+3));
                                                                                                        ˜˜˜˜˜˜˜˜   ˜˜˜^˜
mcX2cloop.cpp:80:105: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                Rprintf("simTable: %f,%f,%f,%f\\n", simTable(j,pos), simTable(j,pos+1), simTable(j,pos+2), simTable(j,pos+3));
                                                                                                                           ˜˜˜˜˜˜˜˜ ^
mcX2cloop.cpp:80:110: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                Rprintf("simTable: %f,%f,%f,%f\\n", simTable(j,pos), simTable(j,pos+1), simTable(j,pos+2), simTable(j,pos+3));
                                                                                                                           ˜˜˜˜˜˜˜˜   ˜˜˜^˜
mcX2cloop.cpp:82:54: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                Rprintf("calcula Sums: %f,%f,%f,%f\\n", simTable(j,pos)+simTable(j,pos+2), simTable(j,pos+1)+simTable(j,pos+3), 
                                                                        ˜˜˜˜˜˜˜˜ ^
mcX2cloop.cpp:82:56: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                Rprintf("calcula Sums: %f,%f,%f,%f\\n", simTable(j,pos)+simTable(j,pos+2), simTable(j,pos+1)+simTable(j,pos+3), 
                                                                        ˜˜˜˜˜˜˜˜   ^˜˜
mcX2cloop.cpp:82:70: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                Rprintf("calcula Sums: %f,%f,%f,%f\\n", simTable(j,pos)+simTable(j,pos+2), simTable(j,pos+1)+simTable(j,pos+3), 
                                                                                        ˜˜˜˜˜˜˜˜ ^
mcX2cloop.cpp:82:75: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                Rprintf("calcula Sums: %f,%f,%f,%f\\n", simTable(j,pos)+simTable(j,pos+2), simTable(j,pos+1)+simTable(j,pos+3), 
                                                                                        ˜˜˜˜˜˜˜˜   ˜˜˜^˜
mcX2cloop.cpp:82:89: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                Rprintf("calcula Sums: %f,%f,%f,%f\\n", simTable(j,pos)+simTable(j,pos+2), simTable(j,pos+1)+simTable(j,pos+3), 
                                                                                                           ˜˜˜˜˜˜˜˜ ^
mcX2cloop.cpp:82:94: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                Rprintf("calcula Sums: %f,%f,%f,%f\\n", simTable(j,pos)+simTable(j,pos+2), simTable(j,pos+1)+simTable(j,pos+3), 
                                                                                                           ˜˜˜˜˜˜˜˜   ˜˜˜^˜
mcX2cloop.cpp:82:107: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                Rprintf("calcula Sums: %f,%f,%f,%f\\n", simTable(j,pos)+simTable(j,pos+2), simTable(j,pos+1)+simTable(j,pos+3), 
                                                                                                                             ˜˜˜˜˜˜˜˜ ^
mcX2cloop.cpp:82:112: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                Rprintf("calcula Sums: %f,%f,%f,%f\\n", simTable(j,pos)+simTable(j,pos+2), simTable(j,pos+1)+simTable(j,pos+3), 
                                                                                                                             ˜˜˜˜˜˜˜˜   ˜˜˜^˜
mcX2cloop.cpp:83:15: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                        simTable(j,pos)+simTable(j,pos+1), simTable(j,pos+2)+simTable(j,pos+3));
                                        ˜˜˜˜˜˜˜˜ ^
mcX2cloop.cpp:83:17: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                        simTable(j,pos)+simTable(j,pos+1), simTable(j,pos+2)+simTable(j,pos+3));
                                        ˜˜˜˜˜˜˜˜   ^˜˜
mcX2cloop.cpp:83:31: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                        simTable(j,pos)+simTable(j,pos+1), simTable(j,pos+2)+simTable(j,pos+3));
                                                        ˜˜˜˜˜˜˜˜ ^
mcX2cloop.cpp:83:36: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                        simTable(j,pos)+simTable(j,pos+1), simTable(j,pos+2)+simTable(j,pos+3));
                                                        ˜˜˜˜˜˜˜˜   ˜˜˜^˜
mcX2cloop.cpp:83:50: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                        simTable(j,pos)+simTable(j,pos+1), simTable(j,pos+2)+simTable(j,pos+3));
                                                                           ˜˜˜˜˜˜˜˜ ^
mcX2cloop.cpp:83:55: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                        simTable(j,pos)+simTable(j,pos+1), simTable(j,pos+2)+simTable(j,pos+3));
                                                                           ˜˜˜˜˜˜˜˜   ˜˜˜^˜
mcX2cloop.cpp:83:68: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                        simTable(j,pos)+simTable(j,pos+1), simTable(j,pos+2)+simTable(j,pos+3));
                                                                                             ˜˜˜˜˜˜˜˜ ^
mcX2cloop.cpp:83:73: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                        simTable(j,pos)+simTable(j,pos+1), simTable(j,pos+2)+simTable(j,pos+3));
                                                                                             ˜˜˜˜˜˜˜˜   ˜˜˜^˜
mcX2cloop.cpp:84:36: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                Rprintf("E: %f,%f,%f,%f\\n", E(i,0), E(i,1), E(i,2), E(i,3));
                                                             ˜ ^
mcX2cloop.cpp:84:44: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                Rprintf("E: %f,%f,%f,%f\\n", E(i,0), E(i,1), E(i,2), E(i,3));
                                                                     ˜ ^
mcX2cloop.cpp:84:52: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                Rprintf("E: %f,%f,%f,%f\\n", E(i,0), E(i,1), E(i,2), E(i,3));
                                                                             ˜ ^
mcX2cloop.cpp:84:60: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                Rprintf("E: %f,%f,%f,%f\\n", E(i,0), E(i,1), E(i,2), E(i,3));
                                                                                     ˜ ^
mcX2cloop.cpp:93:14: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                simTable(j,pos) = st(0,0);
                                ˜˜˜˜˜˜˜˜ ^
mcX2cloop.cpp:93:16: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                simTable(j,pos) = st(0,0);
                                ˜˜˜˜˜˜˜˜   ^˜˜
mcX2cloop.cpp:94:14: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                simTable(j,pos+1) = st(1,0);
                                ˜˜˜˜˜˜˜˜ ^
mcX2cloop.cpp:94:19: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                simTable(j,pos+1) = st(1,0);
                                ˜˜˜˜˜˜˜˜   ˜˜˜^˜
mcX2cloop.cpp:95:14: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                simTable(j,pos+2) = st(0,1);
                                ˜˜˜˜˜˜˜˜ ^
mcX2cloop.cpp:95:19: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                simTable(j,pos+2) = st(0,1);
                                ˜˜˜˜˜˜˜˜   ˜˜˜^˜
mcX2cloop.cpp:96:14: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                simTable(j,pos+3) = st(1,1);
                                ˜˜˜˜˜˜˜˜ ^
mcX2cloop.cpp:96:19: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                simTable(j,pos+3) = st(1,1);
                                ˜˜˜˜˜˜˜˜   ˜˜˜^˜
mcX2cloop.cpp:104:15: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                        diff = E(i,k) - simTable(j,pos+k);
                                               ˜ ^
mcX2cloop.cpp:104:17: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                        diff = E(i,k) - simTable(j,pos+k);
                                               ˜   ^
mcX2cloop.cpp:104:31: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                        diff = E(i,k) - simTable(j,pos+k);
                                                        ˜˜˜˜˜˜˜˜ ^
mcX2cloop.cpp:104:36: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                        diff = E(i,k) - simTable(j,pos+k);
                                                        ˜˜˜˜˜˜˜˜   ˜˜˜^˜
mcX2cloop.cpp:105:33: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                        newStat += diff * diff / E(i,k);
                                                                 ˜ ^
mcX2cloop.cpp:105:35: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
                                        newStat += diff * diff / E(i,k);
                                                                 ˜   ^
mcX2cloop.cpp:14:2: warning: unused label 'Rcpp' [-Wunused-label]
        Rcpp:NumericVector res(iB);
        ^˜˜˜˜
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:104:16: warning: implicit conversion changes signedness: 'typename iterator_traits<__normal_iterator<const Date *, vector<Date, allocator<Date> > > >::difference_type' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        size_t size = std::distance( first, last ) ;
               ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:178:9: note: in instantiation of function template specialization 'Rcpp::internal::primitive_range_wrap__impl<__gnu_cxx::__normal_iterator<const Rcpp::Date *, std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >, Rcpp::Date>' requested here
        return primitive_range_wrap__impl<InputIterator,T>( first, last, typename ::Rcpp::traits::r_sexptype_needscast<T>() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:364:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap_dispatch___impl<__gnu_cxx::__normal_iterator<const Rcpp::Date *, std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >, Rcpp::Date>' requested here
        return range_wrap_dispatch___impl<InputIterator,T>( first, last, typename ::Rcpp::traits::r_type_traits<T>::r_category() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:374:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap_dispatch<__gnu_cxx::__normal_iterator<const Rcpp::Date *, std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >, Rcpp::Date>' requested here
        return range_wrap_dispatch<InputIterator,typename traits::remove_reference<typename std::iterator_traits<InputIterator>::value_type>::type >( first, last ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:493:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap<__gnu_cxx::__normal_iterator<const Rcpp::Date *, std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > > >' requested here
        return range_wrap( object.begin(), object.end() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:501:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_range_sugar_expression<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
        return wrap_range_sugar_expression( object, typename Rcpp::traits::is_sugar_expression<T>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:508:9: note: (skipping 3 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        return wrap_dispatch_unknown_iterable__logical( object, 
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:723:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_unknown<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
        return wrap_dispatch_unknown( object, typename ::Rcpp::traits::is_convertible<T,SEXP>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:740:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_eigen<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
        return wrap_dispatch_eigen( object, typename traits::is_eigen_base<T>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:760:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_unknown_importable<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
        return wrap_dispatch_unknown_importable( object, typename ::Rcpp::traits::is_importer<T>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:863:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
        return internal::wrap_dispatch( object, typename ::Rcpp::traits::wrap_type_traits<T>::wrap_category() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/DateVector.h:54:47: note: in instantiation of function template specialization 'Rcpp::wrap<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
        inline operator SEXP() const { return wrap( v ) ; } 
                                              ^
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:106:43: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP x = PROTECT( Rf_allocVector( RTYPE, size ) );
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:104:16: warning: implicit conversion changes signedness: 'typename iterator_traits<__normal_iterator<const Datetime *, vector<Datetime, allocator<Datetime> > > >::difference_type' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        size_t size = std::distance( first, last ) ;
               ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:178:9: note: in instantiation of function template specialization 'Rcpp::internal::primitive_range_wrap__impl<__gnu_cxx::__normal_iterator<const Rcpp::Datetime *, std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >, Rcpp::Datetime>' requested here
        return primitive_range_wrap__impl<InputIterator,T>( first, last, typename ::Rcpp::traits::r_sexptype_needscast<T>() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:364:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap_dispatch___impl<__gnu_cxx::__normal_iterator<const Rcpp::Datetime *, std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >, Rcpp::Datetime>' requested here
        return range_wrap_dispatch___impl<InputIterator,T>( first, last, typename ::Rcpp::traits::r_type_traits<T>::r_category() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:374:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap_dispatch<__gnu_cxx::__normal_iterator<const Rcpp::Datetime *, std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >, Rcpp::Datetime>' requested here
        return range_wrap_dispatch<InputIterator,typename traits::remove_reference<typename std::iterator_traits<InputIterator>::value_type>::type >( first, last ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:493:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap<__gnu_cxx::__normal_iterator<const Rcpp::Datetime *, std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > > >' requested here
        return range_wrap( object.begin(), object.end() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:501:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_range_sugar_expression<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
        return wrap_range_sugar_expression( object, typename Rcpp::traits::is_sugar_expression<T>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:508:9: note: (skipping 3 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        return wrap_dispatch_unknown_iterable__logical( object, 
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:723:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_unknown<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
        return wrap_dispatch_unknown( object, typename ::Rcpp::traits::is_convertible<T,SEXP>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:740:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_eigen<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
        return wrap_dispatch_eigen( object, typename traits::is_eigen_base<T>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:760:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_unknown_importable<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
        return wrap_dispatch_unknown_importable( object, typename ::Rcpp::traits::is_importer<T>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:863:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
        return internal::wrap_dispatch( object, typename ::Rcpp::traits::wrap_type_traits<T>::wrap_category() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/DatetimeVector.h:54:47: note: in instantiation of function template specialization 'Rcpp::wrap<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
        inline operator SEXP() const { return wrap( v ) ; } 
                                              ^
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:106:43: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP x = PROTECT( Rf_allocVector( RTYPE, size ) );
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:81:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/meat.h:29:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/Matrix.h:38:28: warning: implicit conversion changes signedness: 'const int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
        VECTOR( Dimension( nrows_, ncols ) ), 
                ˜˜˜˜˜˜˜˜˜  ^˜˜˜˜˜
mcX2cloop.cpp:26:22: note: in instantiation of member function 'Rcpp::Matrix<14>::Matrix' requested here
        Rcpp::NumericMatrix E(iNumTable,4); // table of expected values (rows are different tables)
                            ^
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:81:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/meat.h:29:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/Matrix.h:38:36: warning: implicit conversion changes signedness: 'const int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
        VECTOR( Dimension( nrows_, ncols ) ), 
                ˜˜˜˜˜˜˜˜˜          ^˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/Matrix.h:98:75: warning: implicit conversion loses integer precision: 'const size_t' (aka 'const unsigned long') to 'int' [-Wshorten-64-to-32]
        return static_cast< Vector<RTYPE>* >( this )->operator[]( offset( i, j ) ) ;
                                                                  ˜˜˜˜˜˜  ^
mcX2cloop.cpp:29:39: note: in instantiation of member function 'Rcpp::Matrix<14>::operator()' requested here
                Rprintf("rowS: %f,%f,%f,%f\\n", rowS(0,0), rowS(1,0), rowS(0,1), rowS(1,1));
                                                    ^
In file included from mcX2cloop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:81:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/meat.h:29:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/Matrix.h:98:78: warning: implicit conversion loses integer precision: 'const size_t' (aka 'const unsigned long') to 'int' [-Wshorten-64-to-32]
        return static_cast< Vector<RTYPE>* >( this )->operator[]( offset( i, j ) ) ;
                                                                  ˜˜˜˜˜˜     ^
96 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 ddgraph.so mcX2cloop.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/ddgraph.Rcheck/ddgraph/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 (ddgraph)

name	user	system	elapsed
biased-dot-bn-dot-fit	0.028	0.004	0.040
biased-dot-graph	0.011	0.001	0.012
calcDependence	10.254	0.120	10.699
ciTest-comma-DDDataSet-dash-method	0.064	0.003	0.067
combinationsTest	0.041	0.004	0.045
convertPvalueToColorIndex	0.009	0.000	0.009
convertToFactor	0.019	0.001	0.021
estimateNetworkDistribution	0.178	0.002	0.188
formulaFalseNeg	0.011	0.001	0.011
independent-dot-contributions-dot-formula-dot-mul	0.015	0.001	0.016
independent-dot-contributions-dot-formula	0.013	0.001	0.014
is-dot-binary	0.014	0.001	0.016
logseq	0.007	0.002	0.015
makeDDDataSet	0.010	0.002	0.012
mapEnrichmentToColorsDual	0.009	0.002	0.011
mcMITest	0.022	0.002	0.024
mcX2Test	0.038	0.002	0.044
mcX2TestB50k	0.775	0.019	0.803
mesoBin	0.011	0.005	0.015
mesoCont	0.012	0.003	0.016
ncpc	3.926	0.046	3.984
ncpcResampling	0.013	0.001	0.014
plot-comma-DDGraph-comma-missing-dash-method	0.022	0.007	0.030
plotBNLearn	0.670	0.017	0.709
plotPCalg	27.835	0.245	28.499
prob-dot-distr-dot-norm	0.006	0.004	0.009
prob-dot-distr-dot-unif	0.006	0.001	0.007
random-dot-bn-dot-fit	0.013	0.003	0.018
readFurlongData	0.047	0.026	0.075
recalculateSVMparams	0.008	0.001	0.011
toDDDataSet-comma-FurlongDataSet-dash-method	0.308	0.005	0.319
toyExample	0.142	0.004	0.147