SMAP 1.24.0
Robin Andersson
| 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/SMAP | | 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=SMAP.buildbin-libdir SMAP_1.24.0.tar.gz'
>>>>>>>
* installing *source* package 'SMAP' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c gradient.c -o gradient.o
gradient.c:227:48: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
eta_change(&eta->Pi[i], &work_grad->Pi[i], sign(prod), e_change, e_same, e_min,
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rmath.h:335:15: note: expanded from macro 'sign'
#define sign Rf_sign
^
gradient.c:232:54: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
eta_change(&eta->A[i][j], &work_grad->A[i][j], sign(prod), e_change, e_same,
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rmath.h:335:15: note: expanded from macro 'sign'
#define sign Rf_sign
^
gradient.c:237:48: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
eta_change(&eta->mu[i], &work_grad->mu[i], sign(prod), e_change, e_same, e_min, e_max);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rmath.h:335:15: note: expanded from macro 'sign'
#define sign Rf_sign
^
gradient.c:240:54: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
eta_change(&eta->sigma[i], &work_grad->sigma[i], sign(prod), e_change, e_same,
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rmath.h:335:15: note: expanded from macro 'sign'
#define sign Rf_sign
^
gradient.c:247:10: warning: unused variable 'tmp' [-Wunused-variable]
double tmp;
^
gradient.c:302:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double **W_A = (double**) R_alloc(N, sizeof(double*));
˜˜˜˜˜˜˜ ^
gradient.c:312:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
W_A[i] = (double*) R_alloc(N, sizeof(double));
˜˜˜˜˜˜˜ ^
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c init.c -o init.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c overlap.c -o overlap.o
overlap.c:9:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp->ids = (int*) R_alloc(n, sizeof(int));
˜˜˜˜˜˜˜ ^
overlap.c:10:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp->olaps = (double*) R_alloc(n, sizeof(double));
˜˜˜˜˜˜˜ ^
overlap.c:47:45: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
o_struct **overlap = (o_struct**) R_alloc(t, sizeof(o_struct*));
˜˜˜˜˜˜˜ ^
overlap.c:64:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double *olap = (double*) R_alloc(i - prev_zero, sizeof(double));
˜˜˜˜˜˜˜ ˜˜^˜˜˜˜˜˜˜˜˜˜
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c prob.c -o prob.o
prob.c:9:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp->A = (double**) R_alloc(N, sizeof(double*));
˜˜˜˜˜˜˜ ^
prob.c:10:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp->Pi = (double*) R_alloc(N, sizeof(double));
˜˜˜˜˜˜˜ ^
prob.c:11:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp->mu = (double*) R_alloc(N, sizeof(double));
˜˜˜˜˜˜˜ ^
prob.c:12:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp->sigma = (double*) R_alloc(N, sizeof(double));
˜˜˜˜˜˜˜ ^
prob.c:15:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp->Z = (double**) R_alloc(N, sizeof(double*));
˜˜˜˜˜˜˜ ^
prob.c:16:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp->Y = (double*) R_alloc(N, sizeof(double));
˜˜˜˜˜˜˜ ^
prob.c:23:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp->A[i] = (double*) R_alloc(N, sizeof(double));
˜˜˜˜˜˜˜ ^
prob.c:26:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp->Z[i] = (double*) R_alloc(N, sizeof(double));
˜˜˜˜˜˜˜ ^
8 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c viterbi.c -o viterbi.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o SMAP.so gradient.o init.o overlap.o prob.o viterbi.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/SMAP.buildbin-libdir/SMAP/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'SMAP'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SMAP)
>>>>>>>
>>>>>>> FIXING LINKS FOR SMAP.buildbin-libdir/SMAP/libs//SMAP.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" "SMAP.buildbin-libdir/SMAP/libs//SMAP.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "SMAP.buildbin-libdir/SMAP/libs//SMAP.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" "SMAP.buildbin-libdir/SMAP/libs//SMAP.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "SMAP.buildbin-libdir/SMAP/libs//SMAP.so"