XDE 2.14.0
Robert Scharpf
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/XDE | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | [ OK ] | |
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### Running command:
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### rm -rf XDE.buildbin-libdir && mkdir XDE.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh XDE_2.14.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R XDE.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=XDE.buildbin-libdir XDE_2.14.0.tar.gz'
>>>>>>>
* installing *source* package ‘XDE’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c Cholesky.cpp -o Cholesky.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c Matrix_v2.cpp -o Matrix_v2.o
In file included from Matrix_v2.cpp:1:
./Matrix_v2.h:4:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
^
Matrix_v2.cpp:244:7: warning: unused variable 'k' [-Wunused-variable]
int k = 1;
^
Matrix_v2.cpp:246:9: warning: unused variable 'j' [-Wunused-variable]
int i,j,r;
^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c Potential_v2.cpp -o Potential_v2.o
Potential_v2.cpp:374:34: warning: equality comparison result unused [-Wunused-comparison]
if (theGene[k][i] == 1) include == 1;
˜˜˜˜˜˜˜˜^˜˜˜
Potential_v2.cpp:374:34: note: use '=' to turn this equality comparison into an assignment
if (theGene[k][i] == 1) include == 1;
^˜
=
Potential_v2.cpp:876:14: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
if (omega0 = 0.0)
˜˜˜˜˜˜˜^˜˜˜˜
Potential_v2.cpp:876:14: note: place parentheses around the assignment to silence this warning
if (omega0 = 0.0)
^
( )
Potential_v2.cpp:876:14: note: use '==' to turn this assignment into an equality comparison
if (omega0 = 0.0)
^
==
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c Random_v2.cpp -o Random_v2.o
Random_v2.cpp:1847:10: warning: unused variable 'x' [-Wunused-variable]
double x,y,tt,sum;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c Rinterface_v2.cpp -o Rinterface_v2.o
In file included from Rinterface_v2.cpp:2:
In file included from ./Update_v2.h:8:
./Random.h:19:9: warning: 'PI' macro redefined
#define PI 3.14159265
^
/Library/Frameworks/R.framework/Resources/include/R_ext/Constants.h:32:9: note: previous definition is here
#define PI M_PI
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c Structure.cpp -o Structure.o
Structure.cpp:528:8: warning: unused variable 'c' [-Wunused-variable]
char c;
^
Structure.cpp:1642:8: warning: unused variable 'nRead' [-Wunused-variable]
int nRead = sscanf(var1,"%d",&value);
^
Structure.cpp:1668:12: warning: unused variable 'nRead' [-Wunused-variable]
int nRead = sscanf(var2,"%le",&value);
^
Structure.cpp:1579:12: warning: unused variable 'c' [-Wunused-variable]
char c;
^
Structure.cpp:1728:12: warning: unused variable 'c' [-Wunused-variable]
char c;
^
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c Update_v2.cpp -o Update_v2.o
Update_v2.cpp:3919:10: warning: unused variable 'pot' [-Wunused-variable]
double pot = - OmegaGibbs(df,D,oldClique,oldComponents,Q,G,Delta,
^
Update_v2.cpp:3973:10: warning: unused variable 'pot' [-Wunused-variable]
double pot = DeltaStarGibbs(oldClique,oldComponents,Q,G,S,newValues,
^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c Utility_v2.cpp -o Utility_v2.o
Utility_v2.cpp:221:12: warning: unused variable 'detPrior' [-Wunused-variable]
double detPrior = inverse(var,varInv);
^
Utility_v2.cpp:228:12: warning: unused variable 'detPosterior' [-Wunused-variable]
double detPosterior = 1.0 /inverse(varInv,var);
^
Utility_v2.cpp:303:9: warning: unused variable 's' [-Wunused-variable]
int s;
^
Utility_v2.cpp:328:12: warning: unused variable 'detPrior' [-Wunused-variable]
double detPrior = inverse(var,varInv);
^
Utility_v2.cpp:334:12: warning: unused variable 'detPosterior' [-Wunused-variable]
double detPosterior = 1.0 / inverse(varInv,var);
^
Utility_v2.cpp:764:6: warning: unused variable 'ngg' [-Wunused-variable]
int ngg = neighbour[gg].size();
^
Utility_v2.cpp:954:8: warning: unused variable 'ngg' [-Wunused-variable]
int ngg = neighbour[gg].size();
^
Utility_v2.cpp:1463:33: warning: unused variable 'itextra' [-Wunused-variable]
map<int,double>::iterator itextra = VinvSparse[k].end();
^
8 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c diffExpressed_main.cpp -o diffExpressed_main.o
In file included from diffExpressed_main.cpp:16:
./Random.h:19:9: warning: 'PI' macro redefined
#define PI 3.14159265
^
/Library/Frameworks/R.framework/Resources/include/R_ext/Constants.h:32:9: note: previous definition is here
#define PI M_PI
^
1 warning generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o XDE.so Cholesky.o Matrix_v2.o Potential_v2.o Random_v2.o Rinterface_v2.o Structure.o Update_v2.o Utility_v2.o diffExpressed_main.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/XDE.buildbin-libdir/XDE/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘pairs’ from package ‘graphics’ in package ‘XDE’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘XDE’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (XDE)
>>>>>>>
>>>>>>> FIXING LINKS FOR XDE.buildbin-libdir/XDE/libs//XDE.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgcc_s.1.dylib" "XDE.buildbin-libdir/XDE/libs//XDE.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.3.dylib" "XDE.buildbin-libdir/XDE/libs//XDE.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.5.2.dylib" "XDE.buildbin-libdir/XDE/libs//XDE.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.dylib" "XDE.buildbin-libdir/XDE/libs//XDE.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libquadmath.0.dylib" "XDE.buildbin-libdir/XDE/libs//XDE.so"