cn.farms 1.16.0
Andreas Mitterecker
| 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/cn.farms | | 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 cn.farms.buildbin-libdir && mkdir cn.farms.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh cn.farms_1.16.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R cn.farms.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=cn.farms.buildbin-libdir cn.farms_1.16.0.tar.gz'
>>>>>>>
* installing *source* package ‘cn.farms’ ...
** 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 R_init_cnfarms.c -o R_init_cnfarms.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 laplace.cpp -o laplace.o
laplace.cpp:275:10: warning: variable 'I1left' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if(argLeft >= 0.0 && argRight >= 0.0) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:364:36: note: uninitialized use occurs here
double I2left=(-leftMy/leftSigma)*I1left+I0left;
^˜˜˜˜˜
laplace.cpp:275:7: note: remove the 'if' if its condition is always true
else if(argLeft >= 0.0 && argRight >= 0.0) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:275:10: warning: variable 'I1left' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized]
else if(argLeft >= 0.0 && argRight >= 0.0) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:364:36: note: uninitialized use occurs here
double I2left=(-leftMy/leftSigma)*I1left+I0left;
^˜˜˜˜˜
laplace.cpp:275:10: note: remove the '&&' if its condition is always true
else if(argLeft >= 0.0 && argRight >= 0.0) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:198:15: note: initialize the variable 'I1left' to silence this warning
double I1left;
^
= 0.0
laplace.cpp:275:10: warning: variable 'I1right' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if(argLeft >= 0.0 && argRight >= 0.0) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:365:39: note: uninitialized use occurs here
double I2right=(-rightMy/rightSigma)*I1right+I0right;
^˜˜˜˜˜˜
laplace.cpp:275:7: note: remove the 'if' if its condition is always true
else if(argLeft >= 0.0 && argRight >= 0.0) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:275:10: warning: variable 'I1right' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized]
else if(argLeft >= 0.0 && argRight >= 0.0) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:365:39: note: uninitialized use occurs here
double I2right=(-rightMy/rightSigma)*I1right+I0right;
^˜˜˜˜˜˜
laplace.cpp:275:10: note: remove the '&&' if its condition is always true
else if(argLeft >= 0.0 && argRight >= 0.0) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
laplace.cpp:199:16: note: initialize the variable 'I1right' to silence this warning
double I1right;
^
= 0.0
laplace.cpp:442:6: warning: unused variable 'method' [-Wunused-variable]
int method=0;
^
laplace.cpp:23:11: warning: unused variable 'steps' [-Wunused-const-variable]
const int steps=30;
^
laplace.cpp:26:14: warning: unused variable 'integrationFailureFactor' [-Wunused-const-variable]
const double integrationFailureFactor=5.0;
^
laplace.cpp:27:14: warning: unused variable 'sigmaFactor' [-Wunused-const-variable]
const double sigmaFactor=0.1;
^
laplace.cpp:30:14: warning: unused variable 'Pi' [-Wunused-const-variable]
const double Pi=M_PI;
^
laplace.cpp:31:14: warning: unused variable 'E' [-Wunused-const-variable]
const double E=M_E;
^
laplace.cpp:34:14: warning: unused variable 'sqrt3' [-Wunused-const-variable]
const double sqrt3=1.7320508075688772935274463415058723669428052538104;
^
laplace.cpp:35:14: warning: unused variable 'sqrt2Pi' [-Wunused-const-variable]
const double sqrt2Pi=2.5066282746310005024157652848110452530069867406099;
^
12 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 sparse_farms.c -o sparse_farms.o
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 cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/cn.farms.buildbin-libdir/cn.farms/libs
** R
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** 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 (cn.farms)
>>>>>>>
>>>>>>> FIXING LINKS FOR cn.farms.buildbin-libdir/cn.farms/libs//cn.farms.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" "cn.farms.buildbin-libdir/cn.farms/libs//cn.farms.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.3.dylib" "cn.farms.buildbin-libdir/cn.farms/libs//cn.farms.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" "cn.farms.buildbin-libdir/cn.farms/libs//cn.farms.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.dylib" "cn.farms.buildbin-libdir/cn.farms/libs//cn.farms.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libquadmath.0.dylib" "cn.farms.buildbin-libdir/cn.farms/libs//cn.farms.so"