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Package 257/671HostnameOS / ArchBUILDCHECKBUILD BIN
GeneNetworkBuilder 1.2.0
Jianhong Ou
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/GeneNetworkBuilder
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: GeneNetworkBuilder
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneNetworkBuilder_1.2.0.tar.gz
StartedAt: 2013-05-01 05:48:27 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 05:49:58 -0700 (Wed, 01 May 2013)
EllapsedTime: 91.1 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneNetworkBuilder.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GeneNetworkBuilder.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 'GeneNetworkBuilder/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneNetworkBuilder' version '1.2.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'GeneNetworkBuilder' can be installed ... [11s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [22s/22s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
polishNetwork 6.658  0.554   7.416
filterNetwork 4.826  0.320   5.292
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [3s/3s]
 [3s/3s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'RBGL'
* 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 was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/GeneNetworkBuilder.Rcheck/00check.log'
for details.

GeneNetworkBuilder.Rcheck/00install.out:

* installing *source* package 'GeneNetworkBuilder' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c geneTree.cpp -o geneTree.o
geneTree.cpp:113:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        int tolerance = checkFC((*n->chd)[i]) ? 0 : 1;
                                                ˜         ^
geneTree.cpp:114:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if ((*n->chd)[i]->miRNA && !miRNAcnt4Tol) tolerance = 0;
                            ˜         ^
geneTree.cpp:116:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if (tolerance < (*n->chd)[i]->tol) {
                                        ˜         ^
geneTree.cpp:117:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                (*n->chd)[i]->tol = tolerance;
                                ˜         ^
geneTree.cpp:118:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                ChangeTolerance((*n->chd)[i]);
                                                ˜         ^
geneTree.cpp:208:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                if(!find((*cur->chd)[i]->name,t)) {
                                         ˜           ^
geneTree.cpp:209:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        Q.push_back((*cur->chd)[i]);
                                                    ˜           ^
geneTree.cpp:276:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        if(!find((*cur->chd)[i]->name,t)) {
                                                 ˜           ^
geneTree.cpp:277:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                Q.push_back((*cur->chd)[i]);
                                                            ˜           ^
geneTree.cpp:278:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                t.push_back((*cur->chd)[i]);
                                                            ˜           ^
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/Rcpp/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c nodefilter.cpp -o nodefilter.o
In file included from nodefilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:130:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        switch (size - i){                          
                     ˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:190:44: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP x = PROTECT( Rf_allocVector( VECSXP, size ) );
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from nodefilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:209:44: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP x = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from nodefilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:237:48: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP names = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from nodefilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:245:26: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
                SET_STRING_ELT( names, i, Rf_mkChar(buf.c_str()) ) ;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:266:48: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP names = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from nodefilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:274:26: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
                SET_STRING_ELT( names, i, Rf_mkChar(buf.c_str()) ) ;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:311:44: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP x = PROTECT( Rf_allocVector( VECSXP, size ) );
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from nodefilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:312:48: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP names = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from nodefilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:319:22: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
                SET_VECTOR_ELT( x, i, element ) ;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜     ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:320:26: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
                SET_STRING_ELT( names, i, Rf_mkChar(buf.c_str()) ) ; 
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:343:44: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP x = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from nodefilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:344:48: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP names = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from nodefilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:484:44: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP x = PROTECT( Rf_allocVector( LGLSXP, size ) );
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from nodefilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:50:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/Language.h:173:76: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
        unary_call( Language call_, int index ) : call(call_), proxy(call_,index){}
                                                               ˜˜˜˜˜       ^˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/Language.h:190:91: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
        binary_call( Language call_, int index1, int index2 ) : call(call_), proxy1(call_,index1), proxy2(call_,index2){}
                                                                             ˜˜˜˜˜˜       ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/Language.h:190:113: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
        binary_call( Language call_, int index1, int index2 ) : call(call_), proxy1(call_,index1), proxy2(call_,index2){}
                                                                                                   ˜˜˜˜˜˜       ^˜˜˜˜˜
In file included from nodefilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:60:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/Datetime.h:40:40: warning: implicit conversion changes signedness: 'const unsigned int' to 'int' [-Wsign-conversion]
                int getMicroSeconds() const { return m_us; }
                                              ˜˜˜˜˜˜ ^˜˜˜
In file included from nodefilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:70:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:28:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/hash.h:27:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:197:16: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        return RCPP_HASH(value) ;
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:45:61: note: expanded from macro 'RCPP_HASH'
    #define RCPP_HASH(X) (3141592653U * ((unsigned int)(X)) >> (32 - k))
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:212:14: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      addr = RCPP_HASH(val_u.u[0] + val_u.u[1]);
           ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:45:61: note: expanded from macro 'RCPP_HASH'
    #define RCPP_HASH(X) (3141592653U * ((unsigned int)(X)) >> (32 - k))
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:221:18: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
          addr = RCPP_HASH((val & 0xffffffff) ^ (val >> 32));
               ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:45:61: note: expanded from macro 'RCPP_HASH'
    #define RCPP_HASH(X) (3141592653U * ((unsigned int)(X)) >> (32 - k))
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
In file included from nodefilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:70:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:28:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/hash.h:28:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/SelfHash.h:95:16: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        return RCPP_HASH(value) ;
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:45:61: note: expanded from macro 'RCPP_HASH'
    #define RCPP_HASH(X) (3141592653U * ((unsigned int)(X)) >> (32 - k))
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
In file included from nodefilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:70:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:28:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/hash.h:28:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/SelfHash.h:110:14: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      addr = RCPP_HASH(val_u.u[0] + val_u.u[1]);
           ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:45:61: note: expanded from macro 'RCPP_HASH'
    #define RCPP_HASH(X) (3141592653U * ((unsigned int)(X)) >> (32 - k))
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
In file included from nodefilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:70:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:28:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/hash.h:28:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/SelfHash.h:119:18: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
          addr = RCPP_HASH((val & 0xffffffff) ^ (val >> 32));
               ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:45:61: note: expanded from macro 'RCPP_HASH'
    #define RCPP_HASH(X) (3141592653U * ((unsigned int)(X)) >> (32 - k))
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
In file included from nodefilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:70:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/functions/functions.h:37:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/functions/seq_along.h:49:24: warning: implicit conversion loses integer precision: 'const size_t' (aka 'const unsigned long') to 'int' [-Wshorten-64-to-32]
        return sugar::SeqLen( n ) ;
               ˜˜˜˜˜          ^
nodefilter.cpp:78:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        if ((*(*nit)->par)[i]->tol == this_step_tolerance)
                                            ˜              ^
nodefilter.cpp:79:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                parents.push_back((*(*nit)->par)[i]->name);
                                                                  ˜              ^
nodefilter.cpp:81:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        parents.push_back((*(*nit)->par)[i]->name);
                                                          ˜              ^
nodefilter.cpp:87:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                        Rfrom[i] = parents[i];
                                                   ˜˜˜˜˜˜˜ ^
nodefilter.cpp:95:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                int next_step_tolerance = (fabs((*(*nit)->chd)[i]->logFC)>=lfc && (*(*nit)->chd)[i]->pval<=pv) ? 0 : 1;
                                                                                                ˜              ^
nodefilter.cpp:95:90: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                int next_step_tolerance = (fabs((*(*nit)->chd)[i]->logFC)>=lfc && (*(*nit)->chd)[i]->pval<=pv) ? 0 : 1;
                                                                                                                                  ˜              ^
nodefilter.cpp:96:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                if ((*(*nit)->chd)[i]->miRNA && !miRNAcntTol) next_step_tolerance = 0;
                                                                    ˜              ^
nodefilter.cpp:97:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                                                if ((*(*nit)->chd)[i]->tol == (*nit)->tol + next_step_tolerance) {
                                                                    ˜              ^
nodefilter.cpp:85:27: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'const int' [-Wshorten-64-to-32]
                                CharacterVector Rfrom(parents.size());
                                                ˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from nodefilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:104:16: warning: implicit conversion changes signedness: 'typename iterator_traits<__normal_iterator<const Date *, vector<Date, allocator<Date> > > >::difference_type' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        size_t size = std::distance( first, last ) ;
               ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:178:9: note: in instantiation of function template specialization 'Rcpp::internal::primitive_range_wrap__impl<__gnu_cxx::__normal_iterator<const Rcpp::Date *, std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >, Rcpp::Date>' requested here
        return primitive_range_wrap__impl<InputIterator,T>( first, last, typename ::Rcpp::traits::r_sexptype_needscast<T>() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:364:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap_dispatch___impl<__gnu_cxx::__normal_iterator<const Rcpp::Date *, std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >, Rcpp::Date>' requested here
        return range_wrap_dispatch___impl<InputIterator,T>( first, last, typename ::Rcpp::traits::r_type_traits<T>::r_category() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:374:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap_dispatch<__gnu_cxx::__normal_iterator<const Rcpp::Date *, std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >, Rcpp::Date>' requested here
        return range_wrap_dispatch<InputIterator,typename traits::remove_reference<typename std::iterator_traits<InputIterator>::value_type>::type >( first, last ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:493:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap<__gnu_cxx::__normal_iterator<const Rcpp::Date *, std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > > >' requested here
        return range_wrap( object.begin(), object.end() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:501:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_range_sugar_expression<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
        return wrap_range_sugar_expression( object, typename Rcpp::traits::is_sugar_expression<T>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:508:9: note: (skipping 3 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        return wrap_dispatch_unknown_iterable__logical( object, 
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:723:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_unknown<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
        return wrap_dispatch_unknown( object, typename ::Rcpp::traits::is_convertible<T,SEXP>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:740:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_eigen<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
        return wrap_dispatch_eigen( object, typename traits::is_eigen_base<T>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:760:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_unknown_importable<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
        return wrap_dispatch_unknown_importable( object, typename ::Rcpp::traits::is_importer<T>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:863:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
        return internal::wrap_dispatch( object, typename ::Rcpp::traits::wrap_type_traits<T>::wrap_category() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/DateVector.h:54:47: note: in instantiation of function template specialization 'Rcpp::wrap<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
        inline operator SEXP() const { return wrap( v ) ; } 
                                              ^
In file included from nodefilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:106:43: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP x = PROTECT( Rf_allocVector( RTYPE, size ) );
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
In file included from nodefilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:104:16: warning: implicit conversion changes signedness: 'typename iterator_traits<__normal_iterator<const Datetime *, vector<Datetime, allocator<Datetime> > > >::difference_type' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        size_t size = std::distance( first, last ) ;
               ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:178:9: note: in instantiation of function template specialization 'Rcpp::internal::primitive_range_wrap__impl<__gnu_cxx::__normal_iterator<const Rcpp::Datetime *, std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >, Rcpp::Datetime>' requested here
        return primitive_range_wrap__impl<InputIterator,T>( first, last, typename ::Rcpp::traits::r_sexptype_needscast<T>() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:364:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap_dispatch___impl<__gnu_cxx::__normal_iterator<const Rcpp::Datetime *, std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >, Rcpp::Datetime>' requested here
        return range_wrap_dispatch___impl<InputIterator,T>( first, last, typename ::Rcpp::traits::r_type_traits<T>::r_category() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:374:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap_dispatch<__gnu_cxx::__normal_iterator<const Rcpp::Datetime *, std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >, Rcpp::Datetime>' requested here
        return range_wrap_dispatch<InputIterator,typename traits::remove_reference<typename std::iterator_traits<InputIterator>::value_type>::type >( first, last ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:493:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap<__gnu_cxx::__normal_iterator<const Rcpp::Datetime *, std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > > >' requested here
        return range_wrap( object.begin(), object.end() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:501:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_range_sugar_expression<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
        return wrap_range_sugar_expression( object, typename Rcpp::traits::is_sugar_expression<T>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:508:9: note: (skipping 3 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        return wrap_dispatch_unknown_iterable__logical( object, 
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:723:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_unknown<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
        return wrap_dispatch_unknown( object, typename ::Rcpp::traits::is_convertible<T,SEXP>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:740:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_eigen<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
        return wrap_dispatch_eigen( object, typename traits::is_eigen_base<T>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:760:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_unknown_importable<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
        return wrap_dispatch_unknown_importable( object, typename ::Rcpp::traits::is_importer<T>::type() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:863:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
        return internal::wrap_dispatch( object, typename ::Rcpp::traits::wrap_type_traits<T>::wrap_category() ) ;
               ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/DatetimeVector.h:54:47: note: in instantiation of function template specialization 'Rcpp::wrap<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
        inline operator SEXP() const { return wrap( v ) ; } 
                                              ^
In file included from nodefilter.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:106:43: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        SEXP x = PROTECT( Rf_allocVector( RTYPE, size ) );
                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
38 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 GeneNetworkBuilder.so geneTree.o nodefilter.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/GeneNetworkBuilder.Rcheck/GeneNetworkBuilder/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GeneNetworkBuilder)

GeneNetworkBuilder.Rcheck/GeneNetworkBuilder-Ex.timings:

nameusersystemelapsed
buildNetwork1.3740.1071.528
ce.IDsMap1.1240.0571.211
ce.interactionmap0.0620.0210.086
ce.mapIDs0.6390.0320.692
ce.miRNA.map0.0120.0060.022
convertID1.1850.0451.329
example.data0.1960.0080.210
filterNetwork4.8260.3205.292
hs.IDsMap0.2950.0160.317
hs.interactionmap0.1230.0160.144
hs.mapIDs0.0790.0070.085
hs.miRNA.map0.0080.0060.014
polishNetwork6.6580.5547.416
uniqueExprsData0.7650.0960.886