spade 1.7.0
Michael Linderman
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/spade | | Last Changed Rev: 70052 / Revision: 74774 | | Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012) |
| 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 Leopard (10.5.8) / i386 | OK | OK | [ OK ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=spade.buildbin-libdir spade_1.7.0.tar.gz'
>>>>>>>
* installing *source* package 'spade' ...
checking for gcc... gcc -arch i386 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -arch i386 -std=gnu99 accepts -g... yes
checking for gcc -arch i386 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -arch i386 -std=gnu99 -E
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -arch i386 accepts -g... yes
checking how to run the C++ preprocessor... g++ -arch i386 -E
checking for gcc -arch i386 -std=gnu99 option to support OpenMP... -fopenmp
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking parallel/algorithm usability... no
checking parallel/algorithm presence... no
checking for parallel/algorithm... no
"Parallel STL not found using default"
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fopenmp -DPACKAGE_NAME=\"spade\" -DPACKAGE_TARNAME=\"spade\" -DPACKAGE_VERSION=\"0.20\" -DPACKAGE_STRING=\"spade\ 0.20\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -fPIC -g -O2 -Wall -fasm-blocks -c cluster.cc -o cluster.o
In file included from cluster.cc:26:
util.h:9:1: warning: "assert" redefined
In file included from /usr/include/c++/4.0.0/cassert:48,
from /usr/include/c++/4.0.0/debug/debug.h:272,
from /usr/include/c++/4.0.0/bits/stl_algobase.h:76,
from /usr/include/c++/4.0.0/algorithm:65,
from cluster.cc:8:
/usr/include/assert.h:56:1: warning: this is the location of the previous definition
cluster.cc: In function 'void<unnamed>::cluster(const <unnamed>::Data_t*, size_t, size_t, size_t, <unnamed>::Idx_t*)':
cluster.cc:253: warning: comparison between signed and unsigned integer expressions
cluster.cc:253: warning: iteration variable 'i' is unsigned
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fopenmp -DPACKAGE_NAME=\"spade\" -DPACKAGE_TARNAME=\"spade\" -DPACKAGE_VERSION=\"0.20\" -DPACKAGE_STRING=\"spade\ 0.20\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -fPIC -g -O2 -Wall -fasm-blocks -c downsample.cc -o downsample.o
In file included from downsample.cc:15:
util.h:9:1: warning: "assert" redefined
In file included from /usr/include/c++/4.0.0/cassert:48,
from /usr/include/c++/4.0.0/debug/debug.h:272,
from /usr/include/c++/4.0.0/bits/stl_algobase.h:76,
from /usr/include/c++/4.0.0/algorithm:65,
from downsample.cc:7:
/usr/include/assert.h:56:1: warning: this is the location of the previous definition
downsample.cc: In function '<unnamed>::Dist_t<unnamed>::compute_median_min_dist(<unnamed>::Data_t*, size_t, size_t, size_t)':
downsample.cc:44: warning: iteration variable 'i' is unsigned
downsample.cc: In function 'void<unnamed>::count_neighbors(<unnamed>::Data_t*, size_t, size_t, <unnamed>::Dist_t, <unnamed>::Dist_t, <unnamed>::Count_t*)':
downsample.cc:74: warning: iteration variable 'i' is unsigned
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fopenmp -DPACKAGE_NAME=\"spade\" -DPACKAGE_TARNAME=\"spade\" -DPACKAGE_VERSION=\"0.20\" -DPACKAGE_STRING=\"spade\ 0.20\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -fPIC -g -O2 -Wall -fasm-blocks -c spade.cc -o spade.o
spade.cc: In function 'void R_init_spade(DllInfo*)':
spade.cc:8: warning: unused variable '_CallFun'
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fopenmp -DPACKAGE_NAME=\"spade\" -DPACKAGE_TARNAME=\"spade\" -DPACKAGE_VERSION=\"0.20\" -DPACKAGE_STRING=\"spade\ 0.20\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -fPIC -g -O2 -Wall -fasm-blocks -c upsample.cc -o upsample.o
In file included from upsample.cc:13:
util.h:9:1: warning: "assert" redefined
In file included from /usr/include/c++/4.0.0/cassert:48,
from /usr/include/c++/4.0.0/debug/debug.h:272,
from /usr/include/c++/4.0.0/bits/stl_algobase.h:76,
from /usr/include/c++/4.0.0/algorithm:65,
from upsample.cc:7:
/usr/include/assert.h:56:1: warning: this is the location of the previous definition
upsample.cc: In function 'void<unnamed>::assign_cluster(const <unnamed>::Data_t*, const <unnamed>::Data_t*, <unnamed>::Idx_t*, size_t, size_t, size_t, <unnamed>::Idx_t*)':
upsample.cc:35: warning: iteration variable 'i' is unsigned
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o spade.so cluster.o downsample.o spade.o upsample.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/spade.buildbin-libdir/spade/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'SPADE.Rnw'
** testing if installed package can be loaded
* DONE (spade)
>>>>>>>
>>>>>>> FIXING LINKS FOR spade.buildbin-libdir/spade/libs/i386/spade.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" "spade.buildbin-libdir/spade/libs/i386/spade.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "spade.buildbin-libdir/spade/libs/i386/spade.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" "spade.buildbin-libdir/spade/libs/i386/spade.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "spade.buildbin-libdir/spade/libs/i386/spade.so"
>>>>>>>
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=spade.buildbin-libdir --libs-only spade_1.7.0.tar.gz'
>>>>>>>
* installing *source* package 'spade' ...
checking for gcc... gcc -arch x86_64 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -arch x86_64 -std=gnu99 accepts -g... yes
checking for gcc -arch x86_64 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -arch x86_64 -std=gnu99 -E
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -arch x86_64 accepts -g... yes
checking how to run the C++ preprocessor... g++ -arch x86_64 -E
checking for gcc -arch x86_64 -std=gnu99 option to support OpenMP... -fopenmp
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking parallel/algorithm usability... no
checking parallel/algorithm presence... no
checking for parallel/algorithm... no
"Parallel STL not found using default"
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - x86_64
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -fopenmp -DPACKAGE_NAME=\"spade\" -DPACKAGE_TARNAME=\"spade\" -DPACKAGE_VERSION=\"0.20\" -DPACKAGE_STRING=\"spade\ 0.20\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -fPIC -g -O2 -Wall -fasm-blocks -c cluster.cc -o cluster.o
In file included from cluster.cc:26:
util.h:9:1: warning: "assert" redefined
In file included from /usr/include/c++/4.0.0/cassert:48,
from /usr/include/c++/4.0.0/debug/debug.h:272,
from /usr/include/c++/4.0.0/bits/stl_algobase.h:76,
from /usr/include/c++/4.0.0/algorithm:65,
from cluster.cc:8:
/usr/include/assert.h:56:1: warning: this is the location of the previous definition
cluster.cc: In function 'void<unnamed>::cluster(const <unnamed>::Data_t*, size_t, size_t, size_t, <unnamed>::Idx_t*)':
cluster.cc:253: warning: comparison between signed and unsigned integer expressions
cluster.cc:253: warning: iteration variable 'i' is unsigned
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -fopenmp -DPACKAGE_NAME=\"spade\" -DPACKAGE_TARNAME=\"spade\" -DPACKAGE_VERSION=\"0.20\" -DPACKAGE_STRING=\"spade\ 0.20\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -fPIC -g -O2 -Wall -fasm-blocks -c downsample.cc -o downsample.o
In file included from downsample.cc:15:
util.h:9:1: warning: "assert" redefined
In file included from /usr/include/c++/4.0.0/cassert:48,
from /usr/include/c++/4.0.0/debug/debug.h:272,
from /usr/include/c++/4.0.0/bits/stl_algobase.h:76,
from /usr/include/c++/4.0.0/algorithm:65,
from downsample.cc:7:
/usr/include/assert.h:56:1: warning: this is the location of the previous definition
downsample.cc: In function '<unnamed>::Dist_t<unnamed>::compute_median_min_dist(<unnamed>::Data_t*, size_t, size_t, size_t)':
downsample.cc:44: warning: iteration variable 'i' is unsigned
downsample.cc: In function 'void<unnamed>::count_neighbors(<unnamed>::Data_t*, size_t, size_t, <unnamed>::Dist_t, <unnamed>::Dist_t, <unnamed>::Count_t*)':
downsample.cc:74: warning: iteration variable 'i' is unsigned
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -fopenmp -DPACKAGE_NAME=\"spade\" -DPACKAGE_TARNAME=\"spade\" -DPACKAGE_VERSION=\"0.20\" -DPACKAGE_STRING=\"spade\ 0.20\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -fPIC -g -O2 -Wall -fasm-blocks -c spade.cc -o spade.o
spade.cc: In function 'void R_init_spade(DllInfo*)':
spade.cc:8: warning: unused variable '_CallFun'
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -fopenmp -DPACKAGE_NAME=\"spade\" -DPACKAGE_TARNAME=\"spade\" -DPACKAGE_VERSION=\"0.20\" -DPACKAGE_STRING=\"spade\ 0.20\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -fPIC -g -O2 -Wall -fasm-blocks -c upsample.cc -o upsample.o
In file included from upsample.cc:13:
util.h:9:1: warning: "assert" redefined
In file included from /usr/include/c++/4.0.0/cassert:48,
from /usr/include/c++/4.0.0/debug/debug.h:272,
from /usr/include/c++/4.0.0/bits/stl_algobase.h:76,
from /usr/include/c++/4.0.0/algorithm:65,
from upsample.cc:7:
/usr/include/assert.h:56:1: warning: this is the location of the previous definition
upsample.cc: In function 'void<unnamed>::assign_cluster(const <unnamed>::Data_t*, const <unnamed>::Data_t*, <unnamed>::Idx_t*, size_t, size_t, size_t, <unnamed>::Idx_t*)':
upsample.cc:35: warning: iteration variable 'i' is unsigned
g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o spade.so cluster.o downsample.o spade.o upsample.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/spade.buildbin-libdir/spade/libs/x86_64
* DONE (spade)
>>>>>>>
>>>>>>> FIXING LINKS FOR spade.buildbin-libdir/spade/libs/x86_64/spade.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" "spade.buildbin-libdir/spade/libs/x86_64/spade.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "spade.buildbin-libdir/spade/libs/x86_64/spade.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" "spade.buildbin-libdir/spade/libs/x86_64/spade.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "spade.buildbin-libdir/spade/libs/x86_64/spade.so"