mgsa 1.8.1
Sebastian Bauer
| 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/mgsa | | Last Changed Rev: 75543 / Revision: 76155 | | Last Changed Date: 2013-04-10 16:47:11 -0700 (Wed, 10 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=mgsa.buildbin-libdir mgsa_1.8.1.tar.gz'
>>>>>>>
* installing *source* package 'mgsa' ...
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c mgsa.c -o mgsa.o
mgsa.c:57:9: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma omp critical
^
mgsa.c:117:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (!(p->values = R_alloc(p->number_of_states,sizeof(p->values[0]))))
˜˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:213:34: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
sample->u.discrete_index = rnd * prior->number_of_states;
˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:268:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (!(sum->values = R_alloc(number_of_breaks,sizeof(sum->values[0]))))
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:270:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(sum->values,0,number_of_breaks * sizeof(sum->values[0]));
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
mgsa.c:270:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(sum->values,0,number_of_breaks * sizeof(sum->values[0]));
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
mgsa.c:271:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (!(sum->breaks = R_alloc(number_of_breaks,sizeof(sum->breaks[0]))))
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:323:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (!(sum->dmap = R_alloc(number_of_discrete_values,sizeof(sum->dmap[0]))))
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:376:68: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
if (!(new_sum->breaks = (double*)R_alloc(1,sizeof(sum->breaks[0])*num_of_discrete_values)))
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:376:69: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (!(new_sum->breaks = (double*)R_alloc(1,sizeof(sum->breaks[0])*num_of_discrete_values)))
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:378:61: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(new_sum->breaks,sum->breaks,sizeof(sum->breaks[0])*num_of_discrete_values);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
mgsa.c:378:61: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(new_sum->breaks,sum->breaks,sizeof(sum->breaks[0])*num_of_discrete_values);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
mgsa.c:383:65: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
if (!(new_sum->values = (int*)R_alloc(1,sizeof(sum->values[0])*num_of_discrete_values)))
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:383:66: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (!(new_sum->values = (int*)R_alloc(1,sizeof(sum->values[0])*num_of_discrete_values)))
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:385:61: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(new_sum->values,sum->values,sizeof(sum->values[0])*num_of_discrete_values);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
mgsa.c:385:61: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(new_sum->values,sum->values,sizeof(sum->values[0])*num_of_discrete_values);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
mgsa.c:390:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (!(new_sum->dmap = R_alloc(num_of_discrete_values,sizeof(sum->dmap[0]))))
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:392:55: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(new_sum->dmap,sum->dmap,sizeof(sum->dmap[0])*num_of_discrete_values);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
mgsa.c:392:55: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(new_sum->dmap,sum->dmap,sizeof(sum->dmap[0])*num_of_discrete_values);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
mgsa.c:414:49: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
slot = val * (sum->num_of_discrete_values -1) / (sum->pdsc->uniform_continous_upper - sum->pdsc->uniform_continous_lower);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:579:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (!(cn->sets_active = (int*)R_alloc(number_of_sets,sizeof(cn->sets_active[0]))))
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:581:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(cn->sets_active,0,number_of_sets * sizeof(cn->sets_active[0]));
^˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
mgsa.c:581:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(cn->sets_active,0,number_of_sets * sizeof(cn->sets_active[0]));
^˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
mgsa.c:582:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (!(cn->set_partition = (int*)R_alloc(number_of_sets,sizeof(cn->set_partition[0]))))
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:584:57: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (!(cn->position_of_set_in_partition = (int*)R_alloc(number_of_sets,sizeof(cn->position_of_set_in_partition[0]))))
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:593:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (!(cn->hidden_count = (int*)R_alloc(n,sizeof(cn->hidden_count[0]))))
˜˜˜˜˜˜˜ ^
mgsa.c:595:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(cn->hidden_count,0,n * sizeof(cn->hidden_count[0]));
^ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
mgsa.c:595:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(cn->hidden_count,0,n * sizeof(cn->hidden_count[0]));
^ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
mgsa.c:597:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (!(cn->observable = (int*)R_alloc(n,sizeof(cn->observable[0]))))
˜˜˜˜˜˜˜ ^
mgsa.c:599:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(cn->observable,0,n * sizeof(cn->observable[0]));
^ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
mgsa.c:599:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(cn->observable,0,n * sizeof(cn->observable[0]));
^ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
mgsa.c:603:50: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (!(cn->max_score_sets_active = (int*)R_alloc(number_of_sets,sizeof(cn->max_score_sets_active[0]))))
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:607:54: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (!(cn->sets_activity_count = (uint64_t *)R_alloc(number_of_sets,sizeof(cn->sets_activity_count[0]))))
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:609:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(cn->sets_activity_count,0,number_of_sets * sizeof(cn->sets_activity_count[0]));
^˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
mgsa.c:609:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(cn->sets_activity_count,0,number_of_sets * sizeof(cn->sets_activity_count[0]));
^˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
mgsa.c:863:28: warning: implicit conversion changes signedness: 'int' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
return cn->number_of_sets + cn->number_of_inactive_sets * (cn->number_of_sets - cn->number_of_inactive_sets);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:900:23: warning: implicit conversion turns floating-point number into integer: 'double' to 'uint32_t' (aka 'unsigned int') [-Wconversion]
uint32_t proposal = (double)(genrand(mt) * possibilities);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:905:26: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
cn->proposal_toggle = proposal;
˜ ^˜˜˜˜˜˜˜
mgsa.c:906:20: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
toggle_state(cn,proposal);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
mgsa.c:912:20: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
proposal -= cn->number_of_sets;
˜˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:914:43: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
active_term_pos = (int)(proposal / cn->number_of_inactive_sets) + cn->number_of_inactive_sets;
˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:915:45: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
inactive_term_pos = (int)(proposal % cn->number_of_inactive_sets);
˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:1141:49: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (!(res.marg_set_activity = (double*)R_alloc(number_of_sets,sizeof(res.marg_set_activity[0]))))
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:1247:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (!(no = (int*)R_alloc(lo,sizeof(no[0])))) /* R's garbage collection takes care of it */
˜˜˜˜˜˜˜ ^˜
mgsa.c:1264:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (!(lset = (int*)R_alloc(lsets,sizeof(lset[0]))))
˜˜˜˜˜˜˜ ^˜˜˜˜
mgsa.c:1266:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (!(nsets = (int**)R_alloc(lsets,sizeof(nsets[0]))))
˜˜˜˜˜˜˜ ^˜˜˜˜
mgsa.c:1277:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (!(nsets[i] = (int*)R_alloc(lset[i],sizeof(nsets[i][0]))))
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
mgsa.c:1301:17: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
nas = R_alloc(las,sizeof(nas[0]));
˜˜˜˜˜˜˜ ^˜˜
mgsa.c:1410:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (!(r = (struct result*)R_alloc(irestarts,sizeof(*r))))
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
mgsa.c:1432:9: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma omp parallel for
^
mgsa.c:1438:9: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma omp critical
^
mgsa.c:1440:25: warning: implicit conversion turns floating-point number into integer: 'double' to 'unsigned long' [-Wconversion]
seed = (unif_rand() * (double)(INT32_MAX));
˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
52 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 mgsa.so mgsa.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/mgsa.buildbin-libdir/mgsa/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'mgsa'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (mgsa)
>>>>>>>
>>>>>>> FIXING LINKS FOR mgsa.buildbin-libdir/mgsa/libs//mgsa.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" "mgsa.buildbin-libdir/mgsa/libs//mgsa.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "mgsa.buildbin-libdir/mgsa/libs//mgsa.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" "mgsa.buildbin-libdir/mgsa/libs//mgsa.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "mgsa.buildbin-libdir/mgsa/libs//mgsa.so"