Package: Rdisop

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Rdisop_1.20.0.tar.gz

StartedAt: 2013-05-01 09:59:47 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 10:00:48 -0700 (Wed, 01 May 2013)

EllapsedTime: 61.1 seconds

RetCode: 0

Status:  OK

CheckDir: Rdisop.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Rdisop.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 'Rdisop/DESCRIPTION' ... OK
* this is package 'Rdisop' version '1.20.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'Rdisop' can be installed ... [26s/28s] 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 ... NOTE
File '/Users/biocbuild/bbs-2.12-bioc/meat/Rdisop.Rcheck/Rdisop/libs/Rdisop.so':
  Found '__ZSt4cout', possibly from 'std::cout' (C++)
    Object: 'imslib/src/ims/distributionprobabilityscorer.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'Makefile'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [1s/1s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'doRUnit.R' [2s/2s]
 [3s/3s] 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

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

* installing *source* package 'Rdisop' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c disop.cpp -o disop.o
In file included from disop.cpp:18:
In file included from ./imslib/src/ims/alphabet.h:8:
./imslib/src/ims/element.h:169:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                      if (isotopes.getAbundance(i) > 0.5) { 
                          ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:175:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        return isotopes.getMass(i);
                               ˜˜˜˜˜˜˜˜         ^
./imslib/src/ims/element.h:177:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                      if (isotopes.getAbundance(i) > maxval) {
                          ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:178:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        maxval = isotopes.getAbundance(i);
                                 ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:183:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    return isotopes.getMass(maxindex);
                           ˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜˜
In file included from disop.cpp:26:
./imslib/src/ims/decomp/realmassdecomposer.h:55:20: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                typedef unsigned long long number_of_decompositions_type;
                                 ^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:130:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        switch (size - i){                          
                     ˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:190:44: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP x = PROTECT( Rf_allocVector( VECSXP, size ) );
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:209:44: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP x = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:237:48: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP names = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:245:26: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
                SET_STRING_ELT( names, i, Rf_mkChar(buf.c_str()) ) ;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:266:48: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP names = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:274:26: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
                SET_STRING_ELT( names, i, Rf_mkChar(buf.c_str()) ) ;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:311:44: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP x = PROTECT( Rf_allocVector( VECSXP, size ) );
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:312:48: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP names = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:319:22: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
                SET_VECTOR_ELT( x, i, element ) ;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜     ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:320:26: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
                SET_STRING_ELT( names, i, Rf_mkChar(buf.c_str()) ) ; 
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:343:44: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP x = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:344:48: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP names = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:484:44: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP x = PROTECT( Rf_allocVector( LGLSXP, size ) );
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:29:
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 disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:29:
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 disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:29:
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 disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:29:
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 disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:29:
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 disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:29:
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 disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:29:
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 ) ;
               ˜˜˜˜˜          ^
disop.cpp:76:4: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
          + 0.5 * (static_cast<int>(molecule.getElementAbundance("N"))
          ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
disop.cpp:106:8: warning: unused variable 'parityeven' [-Wunused-variable]
  bool parityeven = !parityodd;
       ^
disop.cpp:308:39: warning: implicit conversion changes signedness: 'distribution_t::size_type' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                                                        candidate_abundances.begin() + size, 
                                                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜
disop.cpp:313:37: warning: implicit conversion changes signedness: 'distribution_t::size_type' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                                        candidate_abundances.begin() + size,            // end of source range
                                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜
disop.cpp:181:6: warning: unused variable 'number_molecules_shown' [-Wunused-variable]
        int number_molecules_shown = 100;
            ^
disop.cpp:219:32: warning: implicit conversion loses integer precision: 'peaks_container::size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                abundances_sum += abundances(i);
                                  ˜˜˜˜˜˜˜˜˜˜ ^
disop.cpp:222:14: warning: implicit conversion loses integer precision: 'peaks_container::size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                abundances(i) /= abundances_sum;
                ˜˜˜˜˜˜˜˜˜˜ ^
disop.cpp:230:36: warning: implicit conversion loses integer precision: 'masses_container::size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                peaklist_masses.push_back(masses(mi));
                                          ˜˜˜˜˜˜ ^˜
disop.cpp:231:44: warning: implicit conversion loses integer precision: 'masses_container::size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                peaklist_abundances.push_back(abundances(mi));
                                              ˜˜˜˜˜˜˜˜˜˜ ^˜
disop.cpp:380:36: warning: implicit conversion loses integer precision: 'masses_container::size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                peaklist_masses.push_back(masses(mi));
                                          ˜˜˜˜˜˜ ^˜
disop.cpp:381:44: warning: implicit conversion loses integer precision: 'masses_container::size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                peaklist_abundances.push_back(abundances(mi));
                                              ˜˜˜˜˜˜˜˜˜˜ ^˜
disop.cpp:396:32: warning: implicit conversion loses integer precision: 'peaks_container::size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                abundances_sum += abundances(i);
                                  ˜˜˜˜˜˜˜˜˜˜ ^
disop.cpp:399:14: warning: implicit conversion loses integer precision: 'peaks_container::size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                abundances(i) /= abundances_sum;
                ˜˜˜˜˜˜˜˜˜˜ ^
disop.cpp:404:32: warning: implicit conversion loses integer precision: 'masses_container::size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                mess_masses.push_back(masses(mi));
                                      ˜˜˜˜˜˜ ^˜
disop.cpp:405:40: warning: implicit conversion loses integer precision: 'masses_container::size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                mess_abundances.push_back(abundances(mi));
                                          ˜˜˜˜˜˜˜˜˜˜ ^˜
disop.cpp:652:16: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                charge(i) = z;
                ˜˜˜˜˜˜ ^
disop.cpp:669:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    REAL(tmp_isotopes)[0 + 2*j] = masses[j];
                                                  ˜˜˜˜˜˜ ^
disop.cpp:670:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    REAL(tmp_isotopes)[1 + 2*j] = intensities[j];
                                                  ˜˜˜˜˜˜˜˜˜˜˜ ^
disop.cpp:714:25: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        distribution_t::SIZE = maxisotopes;
                             ˜ ^˜˜˜˜˜˜˜˜˜˜
disop.cpp:819:26: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  distribution_t::SIZE = maxisotopes;
                       ˜ ^˜˜˜˜˜˜˜˜˜˜
disop.cpp:825:59: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
    const char *symbol = CHAR(Rf_asChar(getListElement(l, "name")));
                                                          ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:395:25: note: expanded from macro 'CHAR'
#define CHAR(x)         R_CHAR(x)
                               ^
disop.cpp:827:80: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
    nominal_mass_type nominalmass = (nominal_mass_type) REAL(getListElement(l, "mass"))[0];
                                                                               ^
disop.cpp:829:38: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
    SEXP isotope = getListElement(l, "isotope");        
                                     ^
disop.cpp:831:57: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
    int numisotopes = Rf_length(getListElement(isotope, "mass"));
                                                        ^
disop.cpp:832:49: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
    double *mass = REAL(getListElement(isotope, "mass"));       
                                                ^
disop.cpp:833:54: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
    double *abundance = REAL(getListElement(isotope, "abundance"));     
                                                     ^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:104:16: warning: implicit conversion changes signedness: 'typename iterator_traits<__normal_iterator<const Date *, vector<Date, allocator<Date> > > >::difference_type' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        size_t size = std::distance( first, last ) ;
               ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:178:9: note: in instantiation of function template specialization 'Rcpp::internal::primitive_range_wrap__impl<__gnu_cxx::__normal_iterator<const Rcpp::Date *, std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >, Rcpp::Date>' requested here
        return primitive_range_wrap__impl<InputIterator,T>( first, last, typename ::Rcpp::traits::r_sexptype_needscast<T>() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:364:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap_dispatch___impl<__gnu_cxx::__normal_iterator<const Rcpp::Date *, std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >, Rcpp::Date>' requested here
        return range_wrap_dispatch___impl<InputIterator,T>( first, last, typename ::Rcpp::traits::r_type_traits<T>::r_category() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:374:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap_dispatch<__gnu_cxx::__normal_iterator<const Rcpp::Date *, std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >, Rcpp::Date>' requested here
        return range_wrap_dispatch<InputIterator,typename traits::remove_reference<typename std::iterator_traits<InputIterator>::value_type>::type >( first, last ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:493:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap<__gnu_cxx::__normal_iterator<const Rcpp::Date *, std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > > >' requested here
        return range_wrap( object.begin(), object.end() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:501:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_range_sugar_expression<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
        return wrap_range_sugar_expression( object, typename Rcpp::traits::is_sugar_expression<T>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:508:9: note: (skipping 3 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        return wrap_dispatch_unknown_iterable__logical( object, 
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:723:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_unknown<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
        return wrap_dispatch_unknown( object, typename ::Rcpp::traits::is_convertible<T,SEXP>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:740:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_eigen<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
        return wrap_dispatch_eigen( object, typename traits::is_eigen_base<T>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:760:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_unknown_importable<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
        return wrap_dispatch_unknown_importable( object, typename ::Rcpp::traits::is_importer<T>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:863:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
        return internal::wrap_dispatch( object, typename ::Rcpp::traits::wrap_type_traits<T>::wrap_category() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/DateVector.h:54:47: note: in instantiation of function template specialization 'Rcpp::wrap<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
        inline operator SEXP() const { return wrap( v ) ; } 
                                              ^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:106:43: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP x = PROTECT( Rf_allocVector( RTYPE, size ) );
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:104:16: warning: implicit conversion changes signedness: 'typename iterator_traits<__normal_iterator<const Datetime *, vector<Datetime, allocator<Datetime> > > >::difference_type' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        size_t size = std::distance( first, last ) ;
               ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:178:9: note: in instantiation of function template specialization 'Rcpp::internal::primitive_range_wrap__impl<__gnu_cxx::__normal_iterator<const Rcpp::Datetime *, std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >, Rcpp::Datetime>' requested here
        return primitive_range_wrap__impl<InputIterator,T>( first, last, typename ::Rcpp::traits::r_sexptype_needscast<T>() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:364:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap_dispatch___impl<__gnu_cxx::__normal_iterator<const Rcpp::Datetime *, std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >, Rcpp::Datetime>' requested here
        return range_wrap_dispatch___impl<InputIterator,T>( first, last, typename ::Rcpp::traits::r_type_traits<T>::r_category() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:374:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap_dispatch<__gnu_cxx::__normal_iterator<const Rcpp::Datetime *, std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >, Rcpp::Datetime>' requested here
        return range_wrap_dispatch<InputIterator,typename traits::remove_reference<typename std::iterator_traits<InputIterator>::value_type>::type >( first, last ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:493:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap<__gnu_cxx::__normal_iterator<const Rcpp::Datetime *, std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > > >' requested here
        return range_wrap( object.begin(), object.end() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:501:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_range_sugar_expression<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
        return wrap_range_sugar_expression( object, typename Rcpp::traits::is_sugar_expression<T>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:508:9: note: (skipping 3 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        return wrap_dispatch_unknown_iterable__logical( object, 
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:723:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_unknown<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
        return wrap_dispatch_unknown( object, typename ::Rcpp::traits::is_convertible<T,SEXP>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:740:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_eigen<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
        return wrap_dispatch_eigen( object, typename traits::is_eigen_base<T>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:760:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_unknown_importable<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
        return wrap_dispatch_unknown_importable( object, typename ::Rcpp::traits::is_importer<T>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:863:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
        return internal::wrap_dispatch( object, typename ::Rcpp::traits::wrap_type_traits<T>::wrap_category() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/DatetimeVector.h:54:47: note: in instantiation of function template specialization 'Rcpp::wrap<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
        inline operator SEXP() const { return wrap( v ) ; } 
                                              ^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:106:43: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP x = PROTECT( Rf_allocVector( RTYPE, size ) );
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:81:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/meat.h:29:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/Matrix.h:38:28: warning: implicit conversion changes signedness: 'const int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
        VECTOR( Dimension( nrows_, ncols ) ), 
                ˜˜˜˜˜˜˜˜˜  ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppMatrix__backward.h:34:61: note: in instantiation of member function 'Rcpp::Matrix<13>::Matrix' requested here
                Rcpp::Matrix< Rcpp::traits::r_sexptype_traits<T>::rtype > mat( nx, ny ) ;
                                                                          ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppMatrix__backward.h:44:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap__old__rcppmatrix<int>' requested here
        return internal::wrap__old__rcppmatrix( x ); 
               ^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:81:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/meat.h:29:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/Matrix.h:38:36: warning: implicit conversion changes signedness: 'const int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
        VECTOR( Dimension( nrows_, ncols ) ), 
                ˜˜˜˜˜˜˜˜˜          ^˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/Matrix.h:38:28: warning: implicit conversion changes signedness: 'const int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
        VECTOR( Dimension( nrows_, ncols ) ), 
                ˜˜˜˜˜˜˜˜˜  ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppMatrix__backward.h:34:61: note: in instantiation of member function 'Rcpp::Matrix<14>::Matrix' requested here
                Rcpp::Matrix< Rcpp::traits::r_sexptype_traits<T>::rtype > mat( nx, ny ) ;
                                                                          ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppMatrix__backward.h:48:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap__old__rcppmatrix<double>' requested here
        return internal::wrap__old__rcppmatrix( x ); 
               ^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:81:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/meat.h:29:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/Matrix.h:38:36: warning: implicit conversion changes signedness: 'const int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
        VECTOR( Dimension( nrows_, ncols ) ), 
                ˜˜˜˜˜˜˜˜˜          ^˜˜˜˜
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:28:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/classic.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppResultSet.h:39:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppVector.h:66:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    v = (T *) R_alloc(len, sizeof(T));
              ˜˜˜˜˜˜˜ ^˜˜
disop.cpp:172:30: note: in instantiation of member function 'RcppVector<double>::RcppVector' requested here
        RcppVector<double> masses = RcppVector<double>(v_masses);
                                    ^
In file included from disop.cpp:26:
In file included from ./imslib/src/ims/decomp/realmassdecomposer.h:7:
./imslib/src/ims/decomp/integermassdecomposer.h:494:9: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'decomposition_value_type' (aka 'unsigned int') [-Wshorten-64-to-32]
        return getAllDecompositions(mass).size();
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/c++/4.2.1/memory:258:21: note: in instantiation of member function 'ims::IntegerMassDecomposer<unsigned long, unsigned int>::getNumberOfDecompositions' requested here
      ˜auto_ptr() { delete _M_ptr; }
                    ^
./imslib/src/ims/decomp/realmassdecomposer.h:33:7: note: in instantiation of member function 'std::auto_ptr<ims::IntegerMassDecomposer<unsigned long, unsigned int> >::˜auto_ptr' requested here
class RealMassDecomposer {
      ^
disop.cpp:637:49: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP isotopes = PROTECT(Rf_allocVector(VECSXP, scores.size()));
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
disop.cpp:342:9: note: in instantiation of function template specialization 'rlistScores<double>' requested here
          rl = rlistScores(scores, Rf_asInteger(z));
               ^
disop.cpp:649:9: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                score(i) = it->first;
                ˜˜˜˜˜ ^
disop.cpp:651:19: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                exactmass(i) = it->second.getMass();
                ˜˜˜˜˜˜˜˜˜ ^
disop.cpp:652:16: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                charge(i) = z;
                ˜˜˜˜˜˜ ^
disop.cpp:658:7: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                DBE(i) = getDBE(it->second, z);
                ˜˜˜ ^
disop.cpp:669:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    REAL(tmp_isotopes)[0 + 2*j] = masses[j];
                                                  ˜˜˜˜˜˜ ^
disop.cpp:670:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    REAL(tmp_isotopes)[1 + 2*j] = intensities[j];
                                                  ˜˜˜˜˜˜˜˜˜˜˜ ^
disop.cpp:628:27: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        RcppVector<double> score(scores.size());
                           ˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
disop.cpp:629:31: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        RcppVector<double> exactmass(scores.size());
                           ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
disop.cpp:630:25: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        RcppVector<int> charge(scores.size());
                        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
disop.cpp:635:25: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        RcppVector<double> DBE(scores.size());
                           ˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
disop.cpp:665:12: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                int ny = masses.size();
                    ˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:28:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/classic.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppResultSet.h:39:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppVector.h:80:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    v = (T *) R_alloc(len, sizeof(T));
              ˜˜˜˜˜˜˜ ^˜˜
disop.cpp:628:21: note: in instantiation of member function 'RcppVector<double>::RcppVector' requested here
        RcppVector<double> score(scores.size());
                           ^
disop.cpp:342:9: note: in instantiation of function template specialization 'rlistScores<double>' requested here
          rl = rlistScores(scores, Rf_asInteger(z));
               ^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:28:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/classic.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppResultSet.h:39:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppVector.h:80:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    v = (T *) R_alloc(len, sizeof(T));
              ˜˜˜˜˜˜˜ ^˜˜
disop.cpp:630:18: note: in instantiation of member function 'RcppVector<int>::RcppVector' requested here
        RcppVector<int> charge(scores.size());
                        ^
disop.cpp:342:9: note: in instantiation of function template specialization 'rlistScores<double>' requested here
          rl = rlistScores(scores, Rf_asInteger(z));
               ^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:208:16: warning: implicit conversion changes signedness: 'typename iterator_traits<__normal_iterator<const basic_string<char> *, vector<basic_string<char>, allocator<basic_string<char> > > > >::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:364:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap_dispatch___impl<__gnu_cxx::__normal_iterator<const std::basic_string<char> *, std::vector<std::basic_string<char>, std::allocator<std::basic_string<char> > > >, std::basic_string<char> >' 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 std::basic_string<char> *, std::vector<std::basic_string<char>, std::allocator<std::basic_string<char> > > >, std::basic_string<char> >' 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 std::basic_string<char> *, std::vector<std::basic_string<char>, std::allocator<std::basic_string<char> > > > >' 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<std::basic_string<char>, std::allocator<std::basic_string<char> > > >' 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: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_unknown_iterable__logical<std::vector<std::basic_string<char>, std::allocator<std::basic_string<char> > > >' 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: (skipping 5 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        return wrap_dispatch_unknown_iterable__matrix_interface( object, 
               ^
/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<std::basic_string<char>, std::allocator<std::basic_string<char> > > >' 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/RcppClassic/include/classic/RcppResultSet__backward.h:27:19: note: in instantiation of function template specialization 'Rcpp::wrap<std::vector<std::basic_string<char>, std::allocator<std::basic_string<char> > > >' requested here
        push_back( name, Rcpp::wrap(t) );
                         ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppResultSet.h:58:13: note: in instantiation of function template specialization 'RcppResultSet::add__impl<std::vector<std::basic_string<char>, std::allocator<std::basic_string<char> > > >' requested here
        return add__impl( name, object ) ;
               ^
disop.cpp:679:5: note: in instantiation of function template specialization 'RcppResultSet::add<std::vector<std::basic_string<char>, std::allocator<std::basic_string<char> > > >' requested here
        rs.add("formula", formula);
           ^
disop.cpp:342:9: note: in instantiation of function template specialization 'rlistScores<double>' requested here
          rl = rlistScores(scores, Rf_asInteger(z));
               ^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:209:44: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP x = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:212:22: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
                SET_STRING_ELT( x, i, make_charsexp(*first) ) ;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜     ^
/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:493:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap<const double *>' 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: (skipping 7 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        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:863:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch<RcppVector<double> >' 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/RcppClassic/include/classic/RcppResultSet__backward.h:27:19: note: in instantiation of function template specialization 'Rcpp::wrap<RcppVector<double> >' requested here
        push_back( name, Rcpp::wrap(t) );
                         ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppResultSet.h:58:13: note: in instantiation of function template specialization 'RcppResultSet::add__impl<RcppVector<double> >' requested here
        return add__impl( name, object ) ;
               ^
disop.cpp:680:5: note: in instantiation of function template specialization 'RcppResultSet::add<RcppVector<double> >' requested here
        rs.add("score", score);
           ^
disop.cpp:342:9: note: in instantiation of function template specialization 'rlistScores<double>' requested here
          rl = rlistScores(scores, Rf_asInteger(z));
               ^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h: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 disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:130:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        switch (size - i){                          
                     ˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:121:26: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        int __trip_count = size >> 2 ;
            ˜˜˜˜˜˜˜˜˜˜˜˜   ˜˜˜˜˜^˜˜˜
88 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
In file included from imslib/src/ims/element.cpp:6:
./imslib/src/ims/element.h:169:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                      if (isotopes.getAbundance(i) > 0.5) { 
                          ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:175:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        return isotopes.getMass(i);
                               ˜˜˜˜˜˜˜˜         ^
./imslib/src/ims/element.h:177:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                      if (isotopes.getAbundance(i) > maxval) {
                          ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:178:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        maxval = isotopes.getAbundance(i);
                                 ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:183:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    return isotopes.getMass(maxindex);
                           ˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜˜
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
In file included from imslib/src/ims/composedelement.cpp:8:
In file included from ./imslib/src/ims/composedelement.h:7:
./imslib/src/ims/element.h:169:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                      if (isotopes.getAbundance(i) > 0.5) { 
                          ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:175:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        return isotopes.getMass(i);
                               ˜˜˜˜˜˜˜˜         ^
./imslib/src/ims/element.h:177:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                      if (isotopes.getAbundance(i) > maxval) {
                          ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:178:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        maxval = isotopes.getAbundance(i);
                                 ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:183:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    return isotopes.getMass(maxindex);
                           ˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜˜
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
In file included from imslib/src/ims/alphabet.cpp:6:
In file included from ./imslib/src/ims/alphabet.h:8:
./imslib/src/ims/element.h:169:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                      if (isotopes.getAbundance(i) > 0.5) { 
                          ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:175:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        return isotopes.getMass(i);
                               ˜˜˜˜˜˜˜˜         ^
./imslib/src/ims/element.h:177:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                      if (isotopes.getAbundance(i) > maxval) {
                          ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:178:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        maxval = isotopes.getAbundance(i);
                                 ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:183:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    return isotopes.getMass(maxindex);
                           ˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜˜
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
In file included from imslib/src/ims/distributedalphabet.cpp:7:
In file included from ./imslib/src/ims/distributedalphabet.h:7:
In file included from ./imslib/src/ims/alphabet.h:8:
./imslib/src/ims/element.h:169:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                      if (isotopes.getAbundance(i) > 0.5) { 
                          ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:175:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        return isotopes.getMass(i);
                               ˜˜˜˜˜˜˜˜         ^
./imslib/src/ims/element.h:177:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                      if (isotopes.getAbundance(i) > maxval) {
                          ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:178:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        maxval = isotopes.getAbundance(i);
                                 ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:183:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    return isotopes.getMass(maxindex);
                           ˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜˜
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
imslib/src/ims/isotopespecies.cpp:85:37: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                updateCoefficients(1, indexes, 0, power, power, temp_container);
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                ^˜˜˜˜
imslib/src/ims/isotopespecies.cpp:85:44: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                updateCoefficients(1, indexes, 0, power, power, temp_container);
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                       ^˜˜˜˜
imslib/src/ims/isotopespecies.cpp:125:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        } else  if (coefficient >= indexes[i]+1) {
                                   ˜˜˜˜˜˜˜ ^
imslib/src/ims/isotopespecies.cpp:126:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                updateIndexes(i, indexes);
                ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
imslib/src/ims/isotopespecies.cpp:129:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                size_type mass = (coefficient >= indexes[i]+1) ? (indexes[i]+1): 1;
                                                 ˜˜˜˜˜˜˜ ^
imslib/src/ims/isotopespecies.cpp:129:61: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                size_type mass = (coefficient >= indexes[i]+1) ? (indexes[i]+1): 1;
                                                                  ˜˜˜˜˜˜˜ ^
imslib/src/ims/isotopespecies.cpp:129:63: warning: operand of ? changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                size_type mass = (coefficient >= indexes[i]+1) ? (indexes[i]+1): 1;
                          ˜˜˜˜                                    ˜˜˜˜˜˜˜˜˜˜^˜
imslib/src/ims/isotopespecies.cpp:130:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                for (size_type j = indexes[i]+2; static_cast<int>(j) <= coefficient; ++j) {
                               ˜   ˜˜˜˜˜˜˜˜˜˜^˜
imslib/src/ims/isotopespecies.cpp:130:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                for (size_type j = indexes[i]+2; static_cast<int>(j) <= coefficient; ++j) {
                                   ˜˜˜˜˜˜˜ ^
imslib/src/ims/isotopespecies.cpp:132:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        mass /= (j - indexes[i]);
                                   ˜ ^˜˜˜˜˜˜˜˜˜
imslib/src/ims/isotopespecies.cpp:132:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        mass /= (j - indexes[i]);
                                     ˜˜˜˜˜˜˜ ^
imslib/src/ims/isotopespecies.cpp:136:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        (coefficient - indexes[i]) * isotopes[0].mass + indexes[i] * isotopes[i+1].mass,
                                       ˜˜˜˜˜˜˜ ^
imslib/src/ims/isotopespecies.cpp:136:60: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        (coefficient - indexes[i]) * isotopes[0].mass + indexes[i] * isotopes[i+1].mass,
                                                                        ˜˜˜˜˜˜˜ ^
imslib/src/ims/isotopespecies.cpp:136:75: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        (coefficient - indexes[i]) * isotopes[0].mass + indexes[i] * isotopes[i+1].mass,
                                                                                     ˜˜˜˜˜˜˜˜ ˜^˜
imslib/src/ims/isotopespecies.cpp:137:81: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                         mass * std::pow(isotopes[0].abundance, static_cast<int>(coefficient-indexes[i])) * 
                                                                                             ˜˜˜˜˜˜˜ ^
imslib/src/ims/isotopespecies.cpp:138:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        std::pow(isotopes[i+1].abundance, static_cast<int>(indexes[i])));
                                                 ˜˜˜˜˜˜˜˜ ˜^˜
imslib/src/ims/isotopespecies.cpp:138:66: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        std::pow(isotopes[i+1].abundance, static_cast<int>(indexes[i])));
                                                                                           ˜˜˜˜˜˜˜ ^
imslib/src/ims/isotopespecies.cpp:141:63: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                updateCoefficients(i, indexes, counter, coefficient-indexes[i], coefficient, temp_container);
                                                                    ˜˜˜˜˜˜˜ ^
imslib/src/ims/isotopespecies.cpp:145:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                updateIndexes(i+1, indexes);
                ˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜^˜
imslib/src/ims/isotopespecies.cpp:149:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        (coefficient-1)*isotopes[0].mass + isotopes[i+2].mass,
                                                           ˜˜˜˜˜˜˜˜ ˜^˜
imslib/src/ims/isotopespecies.cpp:150:95: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        coefficient * std::pow(isotopes[0].abundance, static_cast<int>(coefficient)-1) * isotopes[i+2].abundance);
                                                                                                         ˜˜˜˜˜˜˜˜ ˜^˜
21 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/base/parser/keggligandcompoundsparser.cpp -o imslib/src/ims/base/parser/keggligandcompoundsparser.o
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:31: warning: '&&' within '||' [-Wlogical-op-parentheses]
        for (;  letter_pos < last_pos && 
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:31: note: place parentheses around the '&&' expression to silence this warning
        for (;  letter_pos < last_pos && 
                                      ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
imslib/src/ims/calib/matchmatrix.cpp:34:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                matrix[row].start=column;
                                 ˜^˜˜˜˜˜
imslib/src/ims/calib/matchmatrix.cpp:35:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                matrix[row].end=column;
                               ˜^˜˜˜˜˜
imslib/src/ims/calib/matchmatrix.cpp:94:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const key_type' (aka 'const int') [-Wshorten-64-to-32]
                        (*m)[row]=candidate;
                        ˜    ^˜˜
imslib/src/ims/calib/matchmatrix.cpp:121:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const key_type' (aka 'const int') [-Wshorten-64-to-32]
                        (*m)[row]=candidate;
                        ˜    ^˜˜
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./imslib/src/ims/calib/linearpointsetmatcher.h:246:27: warning: implicit conversion changes signedness: 'int' to 'std::size_t' (aka 'unsigned long') [-Wsign-conversion]
        MatchMatrix match_matrix(m);
                    ˜˜˜˜˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/calib/linearpointsetmatcher.h:256:21: warning: implicit conversion changes signedness: 'int' to 'std::size_t' (aka 'unsigned long') [-Wsign-conversion]
                        match_matrix.set(i,l);
                        ˜˜˜˜˜˜˜˜˜˜˜˜     ^
./imslib/src/ims/calib/linearpointsetmatcher.h:256:23: warning: implicit conversion changes signedness: 'int' to 'std::size_t' (aka 'unsigned long') [-Wsign-conversion]
                        match_matrix.set(i,l);
                        ˜˜˜˜˜˜˜˜˜˜˜˜       ^
./imslib/src/ims/calib/linearpointsetmatcher.h:259:22: warning: implicit conversion changes signedness: 'int' to 'std::size_t' (aka 'unsigned long') [-Wsign-conversion]
                                match_matrix.set(i,l);
                                ˜˜˜˜˜˜˜˜˜˜˜˜     ^
./imslib/src/ims/calib/linearpointsetmatcher.h:259:24: warning: implicit conversion changes signedness: 'int' to 'std::size_t' (aka 'unsigned long') [-Wsign-conversion]
                                match_matrix.set(i,l);
                                ˜˜˜˜˜˜˜˜˜˜˜˜       ^
./imslib/src/ims/calib/linearpointsetmatcher.h:269:26: warning: implicit conversion changes signedness: 'const int' to 'std::size_t' (aka 'unsigned long') [-Wsign-conversion]
                        match_matrix.unset(p->k,p->l);
                        ˜˜˜˜˜˜˜˜˜˜˜˜       ˜˜˜^
./imslib/src/ims/calib/linearpointsetmatcher.h:269:31: warning: implicit conversion changes signedness: 'const int' to 'std::size_t' (aka 'unsigned long') [-Wsign-conversion]
                        match_matrix.unset(p->k,p->l);
                        ˜˜˜˜˜˜˜˜˜˜˜˜            ˜˜˜^
./imslib/src/ims/calib/linearpointsetmatcher.h:275:24: warning: implicit conversion changes signedness: 'const int' to 'std::size_t' (aka 'unsigned long') [-Wsign-conversion]
                        match_matrix.set(p->k,p->l);
                        ˜˜˜˜˜˜˜˜˜˜˜˜     ˜˜˜^
./imslib/src/ims/calib/linearpointsetmatcher.h:275:29: warning: implicit conversion changes signedness: 'const int' to 'std::size_t' (aka 'unsigned long') [-Wsign-conversion]
                        match_matrix.set(p->k,p->l);
                        ˜˜˜˜˜˜˜˜˜˜˜˜          ˜˜˜^
imslib/src/ims/calib/linearpointsetmatcher.cpp:20:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
10 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o
In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:8:
./imslib/src/ims/decomp/realmassdecomposer.h:55:20: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
                typedef unsigned long long number_of_decompositions_type;
                                 ^
In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:9:
In file included from ./imslib/src/ims/decomp/decomputils.h:12:
In file included from ./imslib/src/ims/alphabet.h:8:
./imslib/src/ims/element.h:169:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                      if (isotopes.getAbundance(i) > 0.5) { 
                          ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:175:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        return isotopes.getMass(i);
                               ˜˜˜˜˜˜˜˜         ^
./imslib/src/ims/element.h:177:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                      if (isotopes.getAbundance(i) > maxval) {
                          ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:178:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        maxval = isotopes.getAbundance(i);
                                 ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:183:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    return isotopes.getMass(maxindex);
                           ˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜˜
In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:8:
In file included from ./imslib/src/ims/decomp/realmassdecomposer.h:7:
./imslib/src/ims/decomp/integermassdecomposer.h:222:72: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
        typename residues_table_row_type::iterator it = _ertable[1].begin() + it_inc;
                                                        ˜˜˜˜˜˜˜˜              ^˜˜˜˜˜
./imslib/src/ims/decomp/integermassdecomposer.h:192:2: note: in instantiation of member function 'ims::IntegerMassDecomposer<unsigned long, unsigned int>::fillExtendedResidueTable' requested here
        fillExtendedResidueTable(alphabet, lcms, mass_in_lcms, infty, witness_vector, ertable);
        ^
imslib/src/ims/decomp/realmassdecomposer.cpp:22:12: note: in instantiation of member function 'ims::IntegerMassDecomposer<unsigned long, unsigned int>::IntegerMassDecomposer' requested here
                                                        new integer_decomposer_type(weights));
                                                            ^
In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:8:
In file included from ./imslib/src/ims/decomp/realmassdecomposer.h:7:
./imslib/src/ims/decomp/integermassdecomposer.h:230:18: warning: implicit conversion changes signedness: 'typename __normal_iterator<unsigned long *, vector<unsigned long, allocator<unsigned long> > >::difference_type' (aka 'long') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                _witnessVector[it - _ertable[1].begin()] = std::make_pair(witness, counter);
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./imslib/src/ims/decomp/integermassdecomposer.h:231:9: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                it += it_inc;
                ˜˜    ^˜˜˜˜˜
./imslib/src/ims/decomp/integermassdecomposer.h:233:10: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
                        it -= _ertable[1].size();
                        ˜˜    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./imslib/src/ims/decomp/integermassdecomposer.h:494:9: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'decomposition_value_type' (aka 'unsigned int') [-Wshorten-64-to-32]
        return getAllDecompositions(mass).size();
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
imslib/src/ims/decomp/realmassdecomposer.cpp:22:12: note: in instantiation of member function 'ims::IntegerMassDecomposer<unsigned long, unsigned int>::getNumberOfDecompositions' requested here
                                                        new integer_decomposer_type(weights));
                                                            ^
11 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
In file included from imslib/src/ims/characteralphabet.cpp:3:
In file included from ./imslib/src/ims/characteralphabet.h:6:
In file included from imslib/src/ims/alphabet.h:8:
./imslib/src/ims/element.h:169:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                      if (isotopes.getAbundance(i) > 0.5) { 
                          ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:175:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        return isotopes.getMass(i);
                               ˜˜˜˜˜˜˜˜         ^
./imslib/src/ims/element.h:177:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                      if (isotopes.getAbundance(i) > maxval) {
                          ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:178:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        maxval = isotopes.getAbundance(i);
                                 ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:183:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    return isotopes.getMass(maxindex);
                           ˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜˜
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
In file included from imslib/src/ims/nitrogenrulefilter.cpp:5:
In file included from ./imslib/src/ims/nitrogenrulefilter.h:4:
In file included from ./imslib/src/ims/composedelement.h:7:
./imslib/src/ims/element.h:169:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                      if (isotopes.getAbundance(i) > 0.5) { 
                          ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:175:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        return isotopes.getMass(i);
                               ˜˜˜˜˜˜˜˜         ^
./imslib/src/ims/element.h:177:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                      if (isotopes.getAbundance(i) > maxval) {
                          ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:178:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        maxval = isotopes.getAbundance(i);
                                 ˜˜˜˜˜˜˜˜              ^
./imslib/src/ims/element.h:183:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                    return isotopes.getMass(maxindex);
                           ˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜˜
5 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 Rdisop.so disop.o imslib/src/ims/element.o imslib/src/ims/composedelement.o imslib/src/ims/isotopedistribution.o imslib/src/ims/alphabet.o imslib/src/ims/weights.o imslib/src/ims/distributedalphabet.o imslib/src/ims/transformation.o imslib/src/ims/isotopespecies.o imslib/src/ims/base/parser/alphabettextparser.o imslib/src/ims/base/parser/distributedalphabettextparser.o imslib/src/ims/base/parser/massestextparser.o imslib/src/ims/base/parser/moleculesequenceparser.o imslib/src/ims/base/parser/standardmoleculesequenceparser.o imslib/src/ims/base/parser/keggligandcompoundsparser.o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o imslib/src/ims/calib/linepairstabber.o imslib/src/ims/calib/matchmatrix.o imslib/src/ims/calib/linearpointsetmatcher.o imslib/src/ims/decomp/realmassdecomposer.o imslib/src/ims/utils/distribution.o imslib/src/ims/distributionprobabilityscorer.o imslib/src/ims/characteralphabet.o imslib/src/ims/nitrogenrulefilter.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/lib/libRcppClassic.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/Rdisop.Rcheck/Rdisop/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'Rdisop.Rnw' 
** testing if installed package can be loaded
* DONE (Rdisop)

name	user	system	elapsed
addMolecules	0.010	0.001	0.013
decomposeMass	0.081	0.011	0.109
getMolecule	0.009	0.001	0.010
initializeCHNOPS	0.01	0.00	0.01