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 ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GeneNetworkBuilder.buildbin-libdir GeneNetworkBuilder_1.2.0.tar.gz'
>>>>>>>
* 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 -g -O2 -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 -g -O2 -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.buildbin-libdir/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)
>>>>>>>
>>>>>>> FIXING LINKS FOR GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs//GeneNetworkBuilder.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs//GeneNetworkBuilder.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs//GeneNetworkBuilder.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs//GeneNetworkBuilder.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs//GeneNetworkBuilder.so"