spade 1.8.0
Michael Linderman
| 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/spade | | 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=spade.buildbin-libdir spade_1.8.0.tar.gz'
>>>>>>>
* installing *source* package 'spade' ...
checking for gcc... clang
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 clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ accepts -g... yes
checking how to run the C++ preprocessor... clang++ -E
checking for clang option to support OpenMP... unsupported
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
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -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 -mtune=native -g -O2 -Wall -pedantic -Wconversion -c cluster.cc -o cluster.o
cluster.cc:225:29: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
size_t num_valid = c_end - c_beg;
˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜˜˜˜˜
cluster.cc:277:15: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
assgn[(*b - data) / dim] = cur_Id;
˜˜˜^˜˜˜˜˜ ˜
cluster.cc:301:39: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
PROTECT(assgn = allocVector(INTSXP, obs)); n_protected++;
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -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 -mtune=native -g -O2 -Wall -pedantic -Wconversion -c downsample.cc -o downsample.o
downsample.cc:119:42: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
PROTECT(densities = allocVector(INTSXP, obs));
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -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 -mtune=native -g -O2 -Wall -pedantic -Wconversion -c spade.cc -o spade.o
spade.cc:8:31: warning: unused variable '_CallFun' [-Wunused-variable]
static const R_CallMethodDef _CallFun[] = {
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -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 -mtune=native -g -O2 -Wall -pedantic -Wconversion -c upsample.cc -o upsample.o
upsample.cc:43:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'Idx_t' (aka 'int') [-Wshorten-64-to-32]
min_idx = j;
˜ ^
upsample.cc:67:39: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
PROTECT(assign = allocVector(INTSXP, obs)); ++n_protected;
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
2 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 spade.so cluster.o downsample.o spade.o upsample.o -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
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (spade)
>>>>>>>
>>>>>>> FIXING LINKS FOR spade.buildbin-libdir/spade/libs//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//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//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//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//spade.so"