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Package 177/671HostnameOS / ArchBUILDCHECKBUILD BIN
DESeq2 1.0.9
Michael Love
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/DESeq2
Last Changed Rev: 75874 / Revision: 76155
Last Changed Date: 2013-04-22 08:32:34 -0700 (Mon, 22 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: DESeq2
Version: 1.0.9
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DESeq2_1.0.9.tar.gz
StartedAt: 2013-05-01 04:30:20 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 04:34:48 -0700 (Wed, 01 May 2013)
EllapsedTime: 267.8 seconds
RetCode: 0
Status:  OK 
CheckDir: DESeq2.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/DESeq2.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 'DESeq2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DESeq2' version '1.0.9'
* 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 'DESeq2' can be installed ... [33s/39s] 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 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 ... [45s/47s] 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

DESeq2.Rcheck/00install.out:

* installing *source* package 'DESeq2' ...
** 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" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c DESeq2.cpp -o DESeq2.o
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
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 DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
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 DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
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 DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
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 DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
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 DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
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 DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
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 DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
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 DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
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 DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:443:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:2967:42: warning: operand of ? changes signedness: 'sword' (aka 'int') to 'const uword' (aka 'const unsigned int') [-Wsign-conversion]
  const uword row_offset = (in_id < 0) ? -in_id : 0;
              ˜˜˜˜˜˜˜˜˜˜                 ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:2968:43: warning: operand of ? changes signedness: 'const sword' (aka 'const int') to 'const uword' (aka 'const unsigned int') [-Wsign-conversion]
  const uword col_offset = (in_id > 0) ?  in_id : 0;
              ˜˜˜˜˜˜˜˜˜˜                  ^˜˜˜˜
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:448:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/subview_meat.hpp:2228:42: warning: operand of ? changes signedness: 'sword' (aka 'int') to 'const uword' (aka 'const unsigned int') [-Wsign-conversion]
  const uword row_offset = (in_id < 0) ? -in_id : 0;
              ˜˜˜˜˜˜˜˜˜˜                 ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/subview_meat.hpp:2229:43: warning: operand of ? changes signedness: 'const sword' (aka 'const int') to 'const uword' (aka 'const unsigned int') [-Wsign-conversion]
  const uword col_offset = (in_id > 0) ?  in_id : 0;
              ˜˜˜˜˜˜˜˜˜˜                  ^˜˜˜˜
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:458:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/SpMat_iterators_meat.hpp:393:19: warning: implicit conversion changes signedness: 'int' to 'uword' (aka 'unsigned int') [-Wsign-conversion]
  uword cur_pos = -1;
        ˜˜˜˜˜˜˜   ^˜
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:462:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/SpSubview_iterators_meat.hpp:581:19: warning: implicit conversion changes signedness: 'int' to 'uword' (aka 'unsigned int') [-Wsign-conversion]
  uword cur_pos = -1;
        ˜˜˜˜˜˜˜   ^˜
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:30:
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 DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:30:
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 DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:30:
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 DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:30:
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 DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:30:
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 DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:30:
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 DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:30:
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 ) ;
               ˜˜˜˜˜          ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:31:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloWrap.h:115:43: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
            VECTOR res(::Rcpp::Dimension( n_rows , n_cols )) ;
                       ˜˜                 ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloWrap.h:115:52: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
            VECTOR res(::Rcpp::Dimension( n_rows , n_cols )) ;
                       ˜˜                          ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloWrap.h:131:43: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
            VECTOR res(::Rcpp::Dimension( n_rows , n_cols )) ;
                       ˜˜                 ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloWrap.h:131:52: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
            VECTOR res(::Rcpp::Dimension( n_rows , n_cols )) ;
                       ˜˜                          ^˜˜˜˜˜
DESeq2.cpp:149:17: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
  a = log_alpha(i);
      ˜˜˜˜˜˜˜˜˜ ^
DESeq2.cpp:153:67: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
  lp = log_posterior(a, yrow, mu_hat_row, x, log_alpha_prior_mean(i), log_alpha_prior_sigmasq, use_prior);
                                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
DESeq2.cpp:154:69: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
  dlp = dlog_posterior(a, yrow, mu_hat_row, x, log_alpha_prior_mean(i), log_alpha_prior_sigmasq, use_prior);
                                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
DESeq2.cpp:156:14: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
  initial_lp(i) = lp;
  ˜˜˜˜˜˜˜˜˜˜ ^
DESeq2.cpp:157:15: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
  initial_dlp(i) = dlp;
  ˜˜˜˜˜˜˜˜˜˜˜ ^
DESeq2.cpp:158:15: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
  last_change(i) = -1.0;
  ˜˜˜˜˜˜˜˜˜˜˜ ^
DESeq2.cpp:161:10: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
    iter(i)++;
    ˜˜˜˜ ^
DESeq2.cpp:172:97: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
    theta_kappa = -1.0 * log_posterior(a + kappa*dlp, yrow, mu_hat_row, x, log_alpha_prior_mean(i), log_alpha_prior_sigmasq, use_prior);
                                                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
DESeq2.cpp:178:19: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
      iter_accept(i)++;
      ˜˜˜˜˜˜˜˜˜˜˜ ^
DESeq2.cpp:180:74: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
      lpnew = log_posterior(a, yrow, mu_hat_row, x, log_alpha_prior_mean(i), log_alpha_prior_sigmasq, use_prior);
                                                    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
DESeq2.cpp:193:73: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
      dlp = dlog_posterior(a, yrow, mu_hat_row, x, log_alpha_prior_mean(i), log_alpha_prior_sigmasq, use_prior);
                                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
DESeq2.cpp:200:23: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
      if (iter_accept(i) % 5 == 0) {
          ˜˜˜˜˜˜˜˜˜˜˜ ^
DESeq2.cpp:207:11: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
  last_lp(i) = lp;
  ˜˜˜˜˜˜˜ ^
DESeq2.cpp:208:12: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
  last_dlp(i) = dlp;
  ˜˜˜˜˜˜˜˜ ^
DESeq2.cpp:209:13: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
  last_d2lp(i) = d2log_posterior(a, yrow, mu_hat_row, x, log_alpha_prior_mean(i), log_alpha_prior_sigmasq, use_prior);
  ˜˜˜˜˜˜˜˜˜ ^
DESeq2.cpp:209:79: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
  last_d2lp(i) = d2log_posterior(a, yrow, mu_hat_row, x, log_alpha_prior_mean(i), log_alpha_prior_sigmasq, use_prior);
                                                         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
DESeq2.cpp:210:13: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
  log_alpha(i) = a;
  ˜˜˜˜˜˜˜˜˜ ^
DESeq2.cpp:212:15: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
  last_change(i) = change;
  ˜˜˜˜˜˜˜˜˜˜˜ ^
DESeq2.cpp:233:13: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
int y_n = y.n_rows;
    ˜˜˜   ˜˜^˜˜˜˜˜
DESeq2.cpp:250:18: warning: implicit conversion changes signedness: 'int' to 'uword' (aka 'unsigned int') [-Wsign-conversion]
  nfrow = nf.row(i).t();
          ˜˜     ^
DESeq2.cpp:251:16: warning: implicit conversion changes signedness: 'int' to 'uword' (aka 'unsigned int') [-Wsign-conversion]
  yrow = y.row(i).t();
         ˜     ^
DESeq2.cpp:252:27: warning: implicit conversion changes signedness: 'int' to 'uword' (aka 'unsigned int') [-Wsign-conversion]
  beta_hat = beta_mat.row(i).t();
             ˜˜˜˜˜˜˜˜     ^
DESeq2.cpp:254:10: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
    iter(i)++;
    ˜˜˜˜ ^
DESeq2.cpp:256:47: warning: implicit conversion changes signedness: 'int' to 'uword' (aka 'unsigned int') [-Wsign-conversion]
    w = arma::diagmat(mu_hat/(1.0 + alpha_hat[i] * mu_hat));
                                    ˜˜˜˜˜˜˜˜˜ ^
DESeq2.cpp:272:19: warning: implicit conversion changes signedness: 'int' to 'uword' (aka 'unsigned int') [-Wsign-conversion]
  last_change.row(i) = change.t();
  ˜˜˜˜˜˜˜˜˜˜˜     ^
DESeq2.cpp:273:16: warning: implicit conversion changes signedness: 'int' to 'uword' (aka 'unsigned int') [-Wsign-conversion]
  beta_mat.row(i) = beta_hat.t();
  ˜˜˜˜˜˜˜˜     ^
DESeq2.cpp:274:20: warning: implicit conversion changes signedness: 'int' to 'uword' (aka 'unsigned int') [-Wsign-conversion]
  beta_var_mat.row(i) = arma::diagvec((x.t() * w * x + ridge).i() * x.t() * w * x * (x.t() * w * x + ridge).i()).t();
  ˜˜˜˜˜˜˜˜˜˜˜˜     ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
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 DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
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 DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
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 DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
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 DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:112:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/as.h:26:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/Exporter.h:63:27: warning: implicit conversion changes signedness: 'R_len_t' (aka 'int') to 'uword' (aka 'unsigned int') [-Wsign-conversion]
                T result( ::Rf_length(object) ) ;
                  ˜˜˜˜˜˜  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/as.h:83:29: note: in instantiation of member function 'Rcpp::traits::IndexingExporter<arma::Col<double>, double>::get' requested here
            return exporter.get() ;
                            ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/as.h:126:16: note: in instantiation of function template specialization 'Rcpp::internal::as<arma::Col<double> >' requested here
        return internal::as<T>( m_sexp, typename traits::r_type_traits<T>::r_category() ) ;
               ^
DESeq2.cpp:31:31: note: in instantiation of function template specialization 'Rcpp::as<arma::Col<double> >' requested here
  arma::mat w = arma::diagmat(Rcpp::as<arma::vec>(w_diag));
                              ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:110:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/export.h:108:9: warning: implicit conversion changes signedness: 'R_len_t' (aka 'int') to 'uword' (aka 'unsigned int') [-Wsign-conversion]
                                res[i] =  start[i] ;
                                ˜˜˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/export.h:128:4: note: in instantiation of function template specialization 'Rcpp::internal::export_indexing__impl<arma::Col<double>, double>' requested here
                        export_indexing__impl<T,value_type>(
                        ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/export.h:146:4: note: in instantiation of function template specialization 'Rcpp::internal::export_indexing__dispatch<arma::Col<double>, double>' requested here
                        export_indexing__dispatch<T,value_type>( 
                        ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/Exporter.h:64:17: note: in instantiation of function template specialization 'Rcpp::internal::export_indexing<arma::Col<double>, double>' requested here
                ::Rcpp::internal::export_indexing<T,value_type>( object, result ) ;
                ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/as.h:83:29: note: in instantiation of member function 'Rcpp::traits::IndexingExporter<arma::Col<double>, double>::get' requested here
            return exporter.get() ;
                            ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/as.h:126:16: note: in instantiation of function template specialization 'Rcpp::internal::as<arma::Col<double> >' requested here
        return internal::as<T>( m_sexp, typename traits::r_type_traits<T>::r_category() ) ;
               ^
DESeq2.cpp:31:31: note: in instantiation of function template specialization 'Rcpp::as<arma::Col<double> >' requested here
  arma::mat w = arma::diagmat(Rcpp::as<arma::vec>(w_diag));
                              ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:429:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemv.hpp:464:41: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int  m           = A.n_rows;
                        ˜             ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemv.hpp:539:5: note: in instantiation of function template specialization 'arma::gemv<true, false, false>::apply_blas_type<double>' requested here
    gemv<do_trans_A, use_alpha, use_beta>::apply_blas_type(y,A,x,alpha,beta);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:506:9: note: in instantiation of member function 'arma::gemv<true, false, false>::apply' requested here
        gemv<true,         false, false>::apply(out.memptr(), B, A.memptr());
        ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:674:5: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false>' requested here
    glue_times::apply<eT, do_trans_A, do_trans_B, use_alpha>(tmp, A,   B, alpha);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:169:3: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false, false>' requested here
  glue_times::apply
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:234:3: note: in instantiation of function template specialization 'arma::glue_times_redirect<3>::apply<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::Mat<double> >' requested here
  glue_times_redirect<N_mat>::apply(out, X);
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:3918:14: note: in instantiation of function template specialization 'arma::glue_times::apply<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double> >' requested here
  glue_type::apply(*this, X);
             ^
DESeq2.cpp:32:17: note: in instantiation of function template specialization 'arma::Mat<double>::Mat<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>' requested here
  arma::mat b = x.t() * w * x;
                ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:429:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemv.hpp:465:41: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int  n           = A.n_cols;
                        ˜             ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemv.hpp:464:41: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int  m           = A.n_rows;
                        ˜             ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemv.hpp:539:5: note: in instantiation of function template specialization 'arma::gemv<false, false, false>::apply_blas_type<double>' requested here
    gemv<do_trans_A, use_alpha, use_beta>::apply_blas_type(y,A,x,alpha,beta);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:511:9: note: in instantiation of member function 'arma::gemv<false, false, false>::apply' requested here
        gemv<false,        false, false>::apply(out.memptr(), A, B.memptr());
        ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:674:5: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false>' requested here
    glue_times::apply<eT, do_trans_A, do_trans_B, use_alpha>(tmp, A,   B, alpha);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:169:3: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false, false>' requested here
  glue_times::apply
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:234:3: note: in instantiation of function template specialization 'arma::glue_times_redirect<3>::apply<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::Mat<double> >' requested here
  glue_times_redirect<N_mat>::apply(out, X);
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:3918:14: note: in instantiation of function template specialization 'arma::glue_times::apply<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double> >' requested here
  glue_type::apply(*this, X);
             ^
DESeq2.cpp:32:17: note: in instantiation of function template specialization 'arma::Mat<double>::Mat<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>' requested here
  arma::mat b = x.t() * w * x;
                ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:429:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemv.hpp:465:41: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int  n           = A.n_cols;
                        ˜             ˜˜^˜˜˜˜˜
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:430:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:403:32: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int m   = C.n_rows;
                       ˜     ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:485:5: note: in instantiation of function template specialization 'arma::gemm<false, false, false, false>::apply_blas_type<double>' requested here
    gemm<do_trans_A, do_trans_B, use_alpha, use_beta>::apply_blas_type(C,A,B,alpha,beta);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:515:9: note: in instantiation of member function 'arma::gemm<false, false, false, false>::apply' requested here
        gemm<false, false, false, false>::apply(out, A, B);
        ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:674:5: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false>' requested here
    glue_times::apply<eT, do_trans_A, do_trans_B, use_alpha>(tmp, A,   B, alpha);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:169:3: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false, false>' requested here
  glue_times::apply
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:234:3: note: in instantiation of function template specialization 'arma::glue_times_redirect<3>::apply<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::Mat<double> >' requested here
  glue_times_redirect<N_mat>::apply(out, X);
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:3918:14: note: in instantiation of function template specialization 'arma::glue_times::apply<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double> >' requested here
  glue_type::apply(*this, X);
             ^
DESeq2.cpp:32:17: note: in instantiation of function template specialization 'arma::Mat<double>::Mat<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>' requested here
  arma::mat b = x.t() * w * x;
                ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:430:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:404:32: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int n   = C.n_cols;
                       ˜     ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:405:47: warning: operand of ? changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int k   = (do_trans_A) ? A.n_rows : A.n_cols;
                       ˜                    ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:405:58: warning: operand of ? changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int k   = (do_trans_A) ? A.n_rows : A.n_cols;
                       ˜                               ˜˜^˜˜˜˜˜
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:429:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemv.hpp:464:41: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int  m           = A.n_rows;
                        ˜             ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemv.hpp:539:5: note: in instantiation of function template specialization 'arma::gemv<true, true, false>::apply_blas_type<double>' requested here
    gemv<do_trans_A, use_alpha, use_beta>::apply_blas_type(y,A,x,alpha,beta);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:523:9: note: in instantiation of member function 'arma::gemv<true, true, false>::apply' requested here
        gemv<true,         true, false>::apply(out.memptr(), B, A.memptr(), alpha);
        ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:674:5: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false>' requested here
    glue_times::apply<eT, do_trans_A, do_trans_B, use_alpha>(tmp, A,   B, alpha);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:169:3: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false, false>' requested here
  glue_times::apply
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:234:3: note: in instantiation of function template specialization 'arma::glue_times_redirect<3>::apply<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::Mat<double> >' requested here
  glue_times_redirect<N_mat>::apply(out, X);
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:3918:14: note: in instantiation of function template specialization 'arma::glue_times::apply<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double> >' requested here
  glue_type::apply(*this, X);
             ^
DESeq2.cpp:32:17: note: in instantiation of function template specialization 'arma::Mat<double>::Mat<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>' requested here
  arma::mat b = x.t() * w * x;
                ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:429:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemv.hpp:465:41: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int  n           = A.n_cols;
                        ˜             ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemv.hpp:464:41: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int  m           = A.n_rows;
                        ˜             ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemv.hpp:539:5: note: in instantiation of function template specialization 'arma::gemv<false, true, false>::apply_blas_type<double>' requested here
    gemv<do_trans_A, use_alpha, use_beta>::apply_blas_type(y,A,x,alpha,beta);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:528:9: note: in instantiation of member function 'arma::gemv<false, true, false>::apply' requested here
        gemv<false,        true, false>::apply(out.memptr(), A, B.memptr(), alpha);
        ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:674:5: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false>' requested here
    glue_times::apply<eT, do_trans_A, do_trans_B, use_alpha>(tmp, A,   B, alpha);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:169:3: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false, false>' requested here
  glue_times::apply
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:234:3: note: in instantiation of function template specialization 'arma::glue_times_redirect<3>::apply<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::Mat<double> >' requested here
  glue_times_redirect<N_mat>::apply(out, X);
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:3918:14: note: in instantiation of function template specialization 'arma::glue_times::apply<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double> >' requested here
  glue_type::apply(*this, X);
             ^
DESeq2.cpp:32:17: note: in instantiation of function template specialization 'arma::Mat<double>::Mat<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>' requested here
  arma::mat b = x.t() * w * x;
                ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:429:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemv.hpp:465:41: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int  n           = A.n_cols;
                        ˜             ˜˜^˜˜˜˜˜
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:430:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:403:32: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int m   = C.n_rows;
                       ˜     ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:485:5: note: in instantiation of function template specialization 'arma::gemm<false, false, true, false>::apply_blas_type<double>' requested here
    gemm<do_trans_A, do_trans_B, use_alpha, use_beta>::apply_blas_type(C,A,B,alpha,beta);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:532:9: note: in instantiation of member function 'arma::gemm<false, false, true, false>::apply' requested here
        gemm<false, false, true, false>::apply(out, A, B, alpha);
        ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:674:5: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false>' requested here
    glue_times::apply<eT, do_trans_A, do_trans_B, use_alpha>(tmp, A,   B, alpha);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:169:3: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false, false>' requested here
  glue_times::apply
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:234:3: note: in instantiation of function template specialization 'arma::glue_times_redirect<3>::apply<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::Mat<double> >' requested here
  glue_times_redirect<N_mat>::apply(out, X);
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:3918:14: note: in instantiation of function template specialization 'arma::glue_times::apply<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double> >' requested here
  glue_type::apply(*this, X);
             ^
DESeq2.cpp:32:17: note: in instantiation of function template specialization 'arma::Mat<double>::Mat<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>' requested here
  arma::mat b = x.t() * w * x;
                ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:430:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:404:32: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int n   = C.n_cols;
                       ˜     ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:405:47: warning: operand of ? changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int k   = (do_trans_A) ? A.n_rows : A.n_cols;
                       ˜                    ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:405:58: warning: operand of ? changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int k   = (do_trans_A) ? A.n_rows : A.n_cols;
                       ˜                               ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:403:32: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int m   = C.n_rows;
                       ˜     ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:485:5: note: in instantiation of function template specialization 'arma::gemm<true, false, false, false>::apply_blas_type<double>' requested here
    gemm<do_trans_A, do_trans_B, use_alpha, use_beta>::apply_blas_type(C,A,B,alpha,beta);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:549:9: note: in instantiation of member function 'arma::gemm<true, false, false, false>::apply' requested here
        gemm<true, false, false, false>::apply(out, A, B);
        ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:674:5: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false>' requested here
    glue_times::apply<eT, do_trans_A, do_trans_B, use_alpha>(tmp, A,   B, alpha);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:169:3: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false, false>' requested here
  glue_times::apply
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:234:3: note: in instantiation of function template specialization 'arma::glue_times_redirect<3>::apply<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::Mat<double> >' requested here
  glue_times_redirect<N_mat>::apply(out, X);
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:3918:14: note: in instantiation of function template specialization 'arma::glue_times::apply<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double> >' requested here
  glue_type::apply(*this, X);
             ^
DESeq2.cpp:32:17: note: in instantiation of function template specialization 'arma::Mat<double>::Mat<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>' requested here
  arma::mat b = x.t() * w * x;
                ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:430:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:404:32: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int n   = C.n_cols;
                       ˜     ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:405:47: warning: operand of ? changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int k   = (do_trans_A) ? A.n_rows : A.n_cols;
                       ˜                    ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:405:58: warning: operand of ? changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int k   = (do_trans_A) ? A.n_rows : A.n_cols;
                       ˜                               ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:403:32: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int m   = C.n_rows;
                       ˜     ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:485:5: note: in instantiation of function template specialization 'arma::gemm<true, false, true, false>::apply_blas_type<double>' requested here
    gemm<do_trans_A, do_trans_B, use_alpha, use_beta>::apply_blas_type(C,A,B,alpha,beta);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:566:9: note: in instantiation of member function 'arma::gemm<true, false, true, false>::apply' requested here
        gemm<true, false, true, false>::apply(out, A, B, alpha);
        ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:674:5: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false>' requested here
    glue_times::apply<eT, do_trans_A, do_trans_B, use_alpha>(tmp, A,   B, alpha);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:169:3: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false, false>' requested here
  glue_times::apply
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:234:3: note: in instantiation of function template specialization 'arma::glue_times_redirect<3>::apply<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::Mat<double> >' requested here
  glue_times_redirect<N_mat>::apply(out, X);
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:3918:14: note: in instantiation of function template specialization 'arma::glue_times::apply<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double> >' requested here
  glue_type::apply(*this, X);
             ^
DESeq2.cpp:32:17: note: in instantiation of function template specialization 'arma::Mat<double>::Mat<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>' requested here
  arma::mat b = x.t() * w * x;
                ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:430:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:404:32: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int n   = C.n_cols;
                       ˜     ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:405:47: warning: operand of ? changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int k   = (do_trans_A) ? A.n_rows : A.n_cols;
                       ˜                    ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:405:58: warning: operand of ? changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int k   = (do_trans_A) ? A.n_rows : A.n_cols;
                       ˜                               ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:403:32: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int m   = C.n_rows;
                       ˜     ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:485:5: note: in instantiation of function template specialization 'arma::gemm<false, true, false, false>::apply_blas_type<double>' requested here
    gemm<do_trans_A, do_trans_B, use_alpha, use_beta>::apply_blas_type(C,A,B,alpha,beta);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:583:9: note: in instantiation of member function 'arma::gemm<false, true, false, false>::apply' requested here
        gemm<false, true, false, false>::apply(out, A, B);
        ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:674:5: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false>' requested here
    glue_times::apply<eT, do_trans_A, do_trans_B, use_alpha>(tmp, A,   B, alpha);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:169:3: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false, false>' requested here
  glue_times::apply
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:234:3: note: in instantiation of function template specialization 'arma::glue_times_redirect<3>::apply<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::Mat<double> >' requested here
  glue_times_redirect<N_mat>::apply(out, X);
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:3918:14: note: in instantiation of function template specialization 'arma::glue_times::apply<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double> >' requested here
  glue_type::apply(*this, X);
             ^
DESeq2.cpp:32:17: note: in instantiation of function template specialization 'arma::Mat<double>::Mat<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>' requested here
  arma::mat b = x.t() * w * x;
                ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:430:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:404:32: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int n   = C.n_cols;
                       ˜     ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:405:47: warning: operand of ? changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int k   = (do_trans_A) ? A.n_rows : A.n_cols;
                       ˜                    ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:405:58: warning: operand of ? changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int k   = (do_trans_A) ? A.n_rows : A.n_cols;
                       ˜                               ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:403:32: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int m   = C.n_rows;
                       ˜     ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:485:5: note: in instantiation of function template specialization 'arma::gemm<false, true, true, false>::apply_blas_type<double>' requested here
    gemm<do_trans_A, do_trans_B, use_alpha, use_beta>::apply_blas_type(C,A,B,alpha,beta);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:600:9: note: in instantiation of member function 'arma::gemm<false, true, true, false>::apply' requested here
        gemm<false, true, true, false>::apply(out, A, B, alpha);
        ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:674:5: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false>' requested here
    glue_times::apply<eT, do_trans_A, do_trans_B, use_alpha>(tmp, A,   B, alpha);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:169:3: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false, false>' requested here
  glue_times::apply
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:234:3: note: in instantiation of function template specialization 'arma::glue_times_redirect<3>::apply<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::Mat<double> >' requested here
  glue_times_redirect<N_mat>::apply(out, X);
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:3918:14: note: in instantiation of function template specialization 'arma::glue_times::apply<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double> >' requested here
  glue_type::apply(*this, X);
             ^
DESeq2.cpp:32:17: note: in instantiation of function template specialization 'arma::Mat<double>::Mat<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>' requested here
  arma::mat b = x.t() * w * x;
                ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:430:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:404:32: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int n   = C.n_cols;
                       ˜     ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:405:47: warning: operand of ? changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int k   = (do_trans_A) ? A.n_rows : A.n_cols;
                       ˜                    ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:405:58: warning: operand of ? changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int k   = (do_trans_A) ? A.n_rows : A.n_cols;
                       ˜                               ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:403:32: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int m   = C.n_rows;
                       ˜     ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:485:5: note: in instantiation of function template specialization 'arma::gemm<true, true, false, false>::apply_blas_type<double>' requested here
    gemm<do_trans_A, do_trans_B, use_alpha, use_beta>::apply_blas_type(C,A,B,alpha,beta);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:617:9: note: in instantiation of member function 'arma::gemm<true, true, false, false>::apply' requested here
        gemm<true, true, false, false>::apply(out, A, B);
        ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:674:5: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false>' requested here
    glue_times::apply<eT, do_trans_A, do_trans_B, use_alpha>(tmp, A,   B, alpha);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:169:3: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false, false>' requested here
  glue_times::apply
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:234:3: note: in instantiation of function template specialization 'arma::glue_times_redirect<3>::apply<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::Mat<double> >' requested here
  glue_times_redirect<N_mat>::apply(out, X);
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:3918:14: note: in instantiation of function template specialization 'arma::glue_times::apply<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double> >' requested here
  glue_type::apply(*this, X);
             ^
DESeq2.cpp:32:17: note: in instantiation of function template specialization 'arma::Mat<double>::Mat<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>' requested here
  arma::mat b = x.t() * w * x;
                ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:430:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:404:32: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int n   = C.n_cols;
                       ˜     ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:405:47: warning: operand of ? changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int k   = (do_trans_A) ? A.n_rows : A.n_cols;
                       ˜                    ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:405:58: warning: operand of ? changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int k   = (do_trans_A) ? A.n_rows : A.n_cols;
                       ˜                               ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:403:32: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int m   = C.n_rows;
                       ˜     ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:485:5: note: in instantiation of function template specialization 'arma::gemm<true, true, true, false>::apply_blas_type<double>' requested here
    gemm<do_trans_A, do_trans_B, use_alpha, use_beta>::apply_blas_type(C,A,B,alpha,beta);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:634:9: note: in instantiation of member function 'arma::gemm<true, true, true, false>::apply' requested here
        gemm<true, true, true, false>::apply(out, A, B, alpha);
        ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:674:5: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false>' requested here
    glue_times::apply<eT, do_trans_A, do_trans_B, use_alpha>(tmp, A,   B, alpha);
    ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:169:3: note: in instantiation of function template specialization 'arma::glue_times::apply<double, true, false, false, false>' requested here
  glue_times::apply
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/glue_times_meat.hpp:234:3: note: in instantiation of function template specialization 'arma::glue_times_redirect<3>::apply<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::Mat<double> >' requested here
  glue_times_redirect<N_mat>::apply(out, X);
  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:3918:14: note: in instantiation of function template specialization 'arma::glue_times::apply<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double> >' requested here
  glue_type::apply(*this, X);
             ^
DESeq2.cpp:32:17: note: in instantiation of function template specialization 'arma::Mat<double>::Mat<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>' requested here
  arma::mat b = x.t() * w * x;
                ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:430:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:404:32: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int n   = C.n_cols;
                       ˜     ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:405:47: warning: operand of ? changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int k   = (do_trans_A) ? A.n_rows : A.n_cols;
                       ˜                    ˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/gemm.hpp:405:58: warning: operand of ? changes signedness: 'const uword' (aka 'const unsigned int') to 'const blas_int' (aka 'const int') [-Wsign-conversion]
        const blas_int k   = (do_trans_A) ? A.n_rows : A.n_cols;
                       ˜                               ˜˜^˜˜˜˜˜
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:439:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/auxlib_meat.hpp:374:30: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'blas_int' (aka 'int') [-Wsign-conversion]
    blas_int n_rows    = out.n_rows;
             ˜˜˜˜˜˜      ˜˜˜˜^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/auxlib_meat.hpp:71:14: note: in instantiation of function template specialization 'arma::auxlib::inv_inplace_lapack<double>' requested here
    status = auxlib::inv_inplace_lapack(out);
             ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/op_inv_meat.hpp:54:39: note: in instantiation of function template specialization 'arma::auxlib::inv<double>' requested here
    const bool status = (mode == 0) ? auxlib::inv(out, X.m) : auxlib::inv(out, X.m, true);
                                      ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:3532:12: note: in instantiation of function template specialization 'arma::op_inv::apply<arma::Mat<double> >' requested here
  op_type::apply(*this, X);
           ^
DESeq2.cpp:84:19: note: in instantiation of function template specialization 'arma::Mat<double>::Mat<arma::Mat<double>, arma::op_inv>' requested here
  arma::mat b_i = b.i();
                  ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:439:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/auxlib_meat.hpp:375:30: warning: implicit conversion changes signedness: 'const uword' (aka 'const unsigned int') to 'blas_int' (aka 'int') [-Wsign-conversion]
    blas_int n_cols    = out.n_cols;
             ˜˜˜˜˜˜      ˜˜˜˜^˜˜˜˜˜
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:112:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/as.h:26:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/Exporter.h:85:27: warning: implicit conversion changes signedness: 'int' to 'uword' (aka 'unsigned int') [-Wsign-conversion]
                T result( dims_[0], dims_[1] ) ;
                  ˜˜˜˜˜˜  ^˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/as.h:83:29: note: in instantiation of member function 'Rcpp::traits::MatrixExporter<arma::Mat<double>, double>::get' requested here
            return exporter.get() ;
                            ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/as.h:126:16: note: in instantiation of function template specialization 'Rcpp::internal::as<arma::Mat<double> >' requested here
        return internal::as<T>( m_sexp, typename traits::r_type_traits<T>::r_category() ) ;
               ^
DESeq2.cpp:119:15: note: in instantiation of function template specialization 'Rcpp::as<arma::Mat<double> >' requested here
arma::mat x = Rcpp::as<arma::mat>(xSEXP);
              ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:112:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/as.h:26:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/Exporter.h:85:37: warning: implicit conversion changes signedness: 'int' to 'uword' (aka 'unsigned int') [-Wsign-conversion]
                T result( dims_[0], dims_[1] ) ;
                  ˜˜˜˜˜˜            ^˜˜˜˜˜˜˜
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:110:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/export.h:108:9: warning: implicit conversion changes signedness: 'R_len_t' (aka 'int') to 'uword' (aka 'unsigned int') [-Wsign-conversion]
                                res[i] =  start[i] ;
                                ˜˜˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/export.h:128:4: note: in instantiation of function template specialization 'Rcpp::internal::export_indexing__impl<arma::Mat<double>, double>' requested here
                        export_indexing__impl<T,value_type>(
                        ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/export.h:146:4: note: in instantiation of function template specialization 'Rcpp::internal::export_indexing__dispatch<arma::Mat<double>, double>' requested here
                        export_indexing__dispatch<T,value_type>( 
                        ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/Exporter.h:86:17: note: in instantiation of function template specialization 'Rcpp::internal::export_indexing<arma::Mat<double>, double>' requested here
                ::Rcpp::internal::export_indexing<T,value_type>( object, result ) ;
                ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/as.h:83:29: note: in instantiation of member function 'Rcpp::traits::MatrixExporter<arma::Mat<double>, double>::get' requested here
            return exporter.get() ;
                            ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/as.h:126:16: note: in instantiation of function template specialization 'Rcpp::internal::as<arma::Mat<double> >' requested here
        return internal::as<T>( m_sexp, typename traits::r_type_traits<T>::r_category() ) ;
               ^
DESeq2.cpp:119:15: note: in instantiation of function template specialization 'Rcpp::as<arma::Mat<double> >' requested here
arma::mat x = Rcpp::as<arma::mat>(xSEXP);
              ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:34:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/Promise.h:26:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/Vector.h:54:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:261:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        return cache.ref( offset(i) ) ;
               ˜˜˜˜˜      ^˜˜˜˜˜˜˜˜
DESeq2.cpp:149:16: note: in instantiation of member function 'Rcpp::Vector<14>::operator()' requested here
  a = log_alpha(i);
               ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:34:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/Promise.h:26:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/Vector.h:54:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:261:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        return cache.ref( offset(i) ) ;
               ˜˜˜˜˜      ^˜˜˜˜˜˜˜˜
DESeq2.cpp:161:9: note: in instantiation of member function 'Rcpp::Vector<13>::operator()' requested here
    iter(i)++;
        ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
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:116:16: warning: implicit conversion changes signedness: 'typename iterator_traits<const double *>::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:166:9: note: in instantiation of function template specialization 'Rcpp::internal::primitive_range_wrap__impl__nocast<const double *, double>' requested here
        return primitive_range_wrap__impl__nocast<InputIterator,T>( first, last, typename std::iterator_traits<InputIterator>::iterator_category() ) ;
               ^
/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<const double *, double>' 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<const double *, double>' 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<const double *, double>' 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:903:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap<const double *>' requested here
        return internal::range_wrap( first, last ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloWrap.h:31:26: note: in instantiation of function template specialization 'Rcpp::wrap<const double *>' requested here
            ::Rcpp::RObject x = ::Rcpp::wrap( object.memptr() , object.memptr() + object.n_elem ) ;
                                ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloWrap.h:45:9: note: in instantiation of function template specialization 'Rcpp::RcppArmadillo::arma_wrap<arma::Col<double> >' requested here
        return RcppArmadillo::arma_wrap( data, Dimension( data.n_elem, 1) ) ;
               ^
DESeq2.cpp:260:19: note: in instantiation of function template specialization 'Rcpp::wrap<double>' requested here
    beta_hat_nv = wrap(beta_hat);
                  ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
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:118:43: 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 DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
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:121:26: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        int __trip_count = size >> 2 ;
            ˜˜˜˜˜˜˜˜˜˜˜˜   ˜˜˜˜˜^˜˜˜
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:30:
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:30:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/operators/operators.h:27:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/operators/Comparator_With_One_Value.h:56:45: warning: implicit conversion turns floating-point number into integer: 'const STORAGE' (aka 'const double') to 'int' [-Wconversion]
        inline int rhs_is_na(int i) const { return rhs ; }
                                            ˜˜˜˜˜˜ ^˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/operators/Comparator_With_One_Value.h:39:33: note: in instantiation of member function 'Rcpp::sugar::Comparator_With_One_Value<14, Rcpp::sugar::greater<14>, true, Rcpp::sugar::Vectorized<fabs, true, Rcpp::Vector<14> > >::rhs_is_na' requested here
                                &Comparator_With_One_Value::rhs_is_na :
                                                            ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/operators/logical_operators__Vector__primitive.h:82:9: note: in instantiation of member function 'Rcpp::sugar::Comparator_With_One_Value<14, Rcpp::sugar::greater<14>, true, Rcpp::sugar::Vectorized<fabs, true, Rcpp::Vector<14> > >::Comparator_With_One_Value' requested here
        return Rcpp::sugar::Comparator_With_One_Value<
               ^
DESeq2.cpp:264:38: note: in instantiation of function template specialization 'operator><14, true, Rcpp::sugar::Vectorized<fabs, true, Rcpp::Vector<14> > >' requested here
    too_large = abs(beta_hat_new_nv) > large;
                                     ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:30:
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:30:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/operators/operators.h:27:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/operators/Comparator_With_One_Value.h:59:42: warning: implicit conversion turns floating-point number into integer: 'STORAGE' (aka 'double') to 'int' [-Wconversion]
                return Rcpp::traits::is_na<RTYPE>(x) ? x : op( x, rhs ) ;
                ˜˜˜˜˜˜                                 ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/operators/Comparator_With_One_Value.h:40:33: note: in instantiation of member function 'Rcpp::sugar::Comparator_With_One_Value<14, Rcpp::sugar::greater<14>, true, Rcpp::sugar::Vectorized<fabs, true, Rcpp::Vector<14> > >::rhs_is_not_na' requested here
                                &Comparator_With_One_Value::rhs_is_not_na ;
                                                            ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/operators/logical_operators__Vector__primitive.h:82:9: note: in instantiation of member function 'Rcpp::sugar::Comparator_With_One_Value<14, Rcpp::sugar::greater<14>, true, Rcpp::sugar::Vectorized<fabs, true, Rcpp::Vector<14> > >::Comparator_With_One_Value' requested here
        return Rcpp::sugar::Comparator_With_One_Value<
               ^
DESeq2.cpp:264:38: note: in instantiation of function template specialization 'operator><14, true, Rcpp::sugar::Vectorized<fabs, true, Rcpp::Vector<14> > >' requested here
    too_large = abs(beta_hat_new_nv) > large;
                                     ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
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:483:16: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        size_t size = object.size() ;
               ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:508:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_unknown_iterable__logical<Rcpp::sugar::Comparator_With_One_Value<14, Rcpp::sugar::greater<14>, true, Rcpp::sugar::Vectorized<fabs, true, Rcpp::Vector<14> > > >' requested here
        return wrap_dispatch_unknown_iterable__logical( object, 
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:614:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_unknown_iterable__matrix_interface<Rcpp::sugar::Comparator_With_One_Value<14, Rcpp::sugar::greater<14>, true, Rcpp::sugar::Vectorized<fabs, true, Rcpp::Vector<14> > > >' requested here
        return wrap_dispatch_unknown_iterable__matrix_interface( object, 
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:691:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_unknown_iterable<Rcpp::sugar::Comparator_With_One_Value<14, Rcpp::sugar::greater<14>, true, Rcpp::sugar::Vectorized<fabs, true, Rcpp::Vector<14> > > >' requested here
        return wrap_dispatch_unknown_iterable( object, typename ::Rcpp::traits::has_iterator<T>::type() ) ;
               ^
/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<Rcpp::sugar::Comparator_With_One_Value<14, Rcpp::sugar::greater<14>, true, Rcpp::sugar::Vectorized<fabs, true, Rcpp::Vector<14> > > >' 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<Rcpp::sugar::Comparator_With_One_Value<14, Rcpp::sugar::greater<14>, true, Rcpp::sugar::Vectorized<fabs, true, Rcpp::Vector<14> > > >' 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: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        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<Rcpp::sugar::Comparator_With_One_Value<14, Rcpp::sugar::greater<14>, true, Rcpp::sugar::Vectorized<fabs, true, Rcpp::Vector<14> > > >' 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/api/meat/Vector.h:178:38: note: in instantiation of function template specialization 'Rcpp::wrap<Rcpp::sugar::Comparator_With_One_Value<14, Rcpp::sugar::greater<14>, true, Rcpp::sugar::Vectorized<fabs, true, Rcpp::Vector<14> > > >' requested here
            set_sexp( r_cast<RTYPE>( wrap(x) ) ); 
                                     ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/Vector.h:186:9: note: in instantiation of function template specialization 'Rcpp::Vector<10>::assign_sugar_expression<Rcpp::sugar::Comparator_With_One_Value<14, Rcpp::sugar::greater<14>, true, Rcpp::sugar::Vectorized<fabs, true, Rcpp::Vector<14> > > >' requested here
        assign_sugar_expression( x.get_ref() ) ;
        ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/Vector.h:165:9: note: in instantiation of function template specialization 'Rcpp::Vector<10>::assign_object<Rcpp::sugar::Comparator_With_One_Value<14, Rcpp::sugar::greater<14>, true, Rcpp::sugar::Vectorized<fabs, true, Rcpp::Vector<14> > > >' requested here
        assign_object( x, typename traits::is_sugar_expression<T>::type() ) ;
        ^
DESeq2.cpp:264:15: note: in instantiation of function template specialization 'Rcpp::Vector<10>::operator=<Rcpp::sugar::Comparator_With_One_Value<14, Rcpp::sugar::greater<14>, true, Rcpp::sugar::Vectorized<fabs, true, Rcpp::Vector<14> > > >' requested here
    too_large = abs(beta_hat_new_nv) > large;
              ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
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 DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:30:
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:30:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/operators/operators.h:27:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/operators/Comparator_With_One_Value.h:56:45: warning: implicit conversion turns floating-point number into integer: 'const STORAGE' (aka 'const double') to 'int' [-Wconversion]
        inline int rhs_is_na(int i) const { return rhs ; }
                                            ˜˜˜˜˜˜ ^˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/operators/Comparator_With_One_Value.h:39:33: note: in instantiation of member function 'Rcpp::sugar::Comparator_With_One_Value<14, Rcpp::sugar::less<14>, true, Rcpp::Vector<14> >::rhs_is_na' requested here
                                &Comparator_With_One_Value::rhs_is_na :
                                                            ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/operators/logical_operators__Vector__primitive.h:38:9: note: in instantiation of member function 'Rcpp::sugar::Comparator_With_One_Value<14, Rcpp::sugar::less<14>, true, Rcpp::Vector<14> >::Comparator_With_One_Value' requested here
        return Rcpp::sugar::Comparator_With_One_Value<
               ^
DESeq2.cpp:268:43: note: in instantiation of function template specialization 'operator<<14, true, Rcpp::Vector<14> >' requested here
    } else if (all(too_large | (change_nv < tol)).is_true()) {
                                          ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:30:
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:30:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/operators/operators.h:27:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/operators/Comparator_With_One_Value.h:59:42: warning: implicit conversion turns floating-point number into integer: 'STORAGE' (aka 'double') to 'int' [-Wconversion]
                return Rcpp::traits::is_na<RTYPE>(x) ? x : op( x, rhs ) ;
                ˜˜˜˜˜˜                                 ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/operators/Comparator_With_One_Value.h:40:33: note: in instantiation of member function 'Rcpp::sugar::Comparator_With_One_Value<14, Rcpp::sugar::less<14>, true, Rcpp::Vector<14> >::rhs_is_not_na' requested here
                                &Comparator_With_One_Value::rhs_is_not_na ;
                                                            ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/operators/logical_operators__Vector__primitive.h:38:9: note: in instantiation of member function 'Rcpp::sugar::Comparator_With_One_Value<14, Rcpp::sugar::less<14>, true, Rcpp::Vector<14> >::Comparator_With_One_Value' requested here
        return Rcpp::sugar::Comparator_With_One_Value<
               ^
DESeq2.cpp:268:43: note: in instantiation of function template specialization 'operator<<14, true, Rcpp::Vector<14> >' requested here
    } else if (all(too_large | (change_nv < tol)).is_true()) {
                                          ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:356:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/fn_diagvec.hpp:21:59: warning: operand of ? changes signedness: 'sword' (aka 'int') to 'uword' (aka 'unsigned int') [-Wsign-conversion]
  return Op<T1, op_diagvec>(X.get_ref(), ((diag_id < 0) ? -diag_id : diag_id), ((diag_id < 0) ? 1 : 0) );
         ˜˜                                               ^˜˜˜˜˜˜˜
DESeq2.cpp:274:25: note: in instantiation of function template specialization 'arma::diagvec<arma::Glue<arma::Glue<arma::Glue<arma::Glue<arma::Op<arma::eGlue<arma::Glue<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::eglue_plus>, arma::op_inv>, arma::Op<arma::Mat<double>, arma::op_htrans>, arma::glue_times>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>, arma::Op<arma::eGlue<arma::Glue<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::eglue_plus>, arma::op_inv>, arma::glue_times> >' requested here
  beta_var_mat.row(i) = arma::diagvec((x.t() * w * x + ridge).i() * x.t() * w * x * (x.t() * w * x + ridge).i()).t();
                        ^
In file included from DESeq2.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo:356:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include/armadillo_bits/fn_diagvec.hpp:21:70: warning: operand of ? changes signedness: 'const sword' (aka 'const int') to 'uword' (aka 'unsigned int') [-Wsign-conversion]
  return Op<T1, op_diagvec>(X.get_ref(), ((diag_id < 0) ? -diag_id : diag_id), ((diag_id < 0) ? 1 : 0) );
         ˜˜                                                          ^˜˜˜˜˜˜
127 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 DESeq2.so DESeq2.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/DESeq2.Rcheck/DESeq2/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DESeq2)

DESeq2.Rcheck/DESeq2-Ex.timings:

nameusersystemelapsed
DESeq3.5820.0903.745
DESeqDataSet0.1080.0040.118
counts0.1540.0100.199
design0.1560.0050.373
dispersionFunction1.8000.0322.173
dispersions2.0490.0362.363
estimateDispersions1.7190.0121.732
estimateDispersionsGeneEst1.8170.0161.871
estimateSizeFactors0.1620.0040.172
estimateSizeFactorsForMatrix0.1400.0020.147
makeExampleDESeqDataSet0.1450.0090.188
nbinomLRT2.5640.0242.614
nbinomWaldTest2.4300.0212.530
normalizationFactors2.8040.0252.871
plotDispEsts2.2800.0262.336
plotMA2.7850.0202.845
plotPCA1.8530.0151.969
results2.8700.0072.880
rlogTransformation3.2650.0223.303
sizeFactors0.1840.0030.189
varianceStabilizingTransformation1.6150.0171.645