Robert Scharpf
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/XDE |
| Branch: master |
| Last Commit: d4d2c8c |
| Last Changed Date: 2019-10-29 13:34:48 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:31:08 -0500 (Thu, 16 Jan 2020).
| Package 1806/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| XDE 2.33.0 Robert Scharpf
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | NA | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | [ OK ] |
| Package: XDE |
| Version: 2.33.0 |
| Command: rm -rf XDE.buildbin-libdir && mkdir XDE.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh XDE_2.33.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R XDE.buildbin-libdir |
| StartedAt: 2020-01-16 12:01:32 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 12:02:55 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 83.7 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: XDE_2.33.0.tgz |
| PackageFileSize: 2.114 MiB |
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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_2.33.0.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_2.33.0.tar.gz'
>>>>>>>
* installing *source* package ‘XDE’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Cholesky.cpp -o Cholesky.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -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:246:9: warning: unused variable 'j' [-Wunused-variable]
int i,j,r;
^
Matrix_v2.cpp:244:7: warning: unused variable 'k' [-Wunused-variable]
int k = 1;
^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -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;
^~
=
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -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 [-Wmacro-redefined]
#define PI 3.14159265
^
/Library/Frameworks/R.framework/Resources/include/R_ext/Constants.h:36:9: note: previous definition is here
#define PI M_PI
^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -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 [-Wmacro-redefined]
#define PI 3.14159265
^
/Library/Frameworks/R.framework/Resources/include/R_ext/Constants.h:36:9: note: previous definition is here
#define PI M_PI
^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o
clang++ -std=gnu++11 -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 registerDynamicSymbol.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/XDE.buildbin-libdir/00LOCK-XDE/00new/XDE/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* 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/4.0/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/4.0/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/4.0/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/4.0/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/4.0/Resources/lib/libquadmath.0.dylib" "XDE.buildbin-libdir/XDE/libs//XDE.so"