BayesPeak 1.12.0
Jonathan Cairns
| 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/BayesPeak | | 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=BayesPeak.buildbin-libdir BayesPeak_1.12.0.tar.gz'
>>>>>>>
* installing *source* package 'BayesPeak' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c bayespeak.c -o bayespeak.o
In file included from bayespeak.c:9:
./bayespeak_gsl.h:40:22: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
long int h = s / q1;
˜ ˜˜^˜˜˜
./bayespeak_gsl.h:41:38: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
long int t = a1 * (s - h * q1) - h * r1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
./bayespeak_gsl.h:41:32: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
long int t = a1 * (s - h * q1) - h * r1;
˜ ˜˜^˜˜˜
./bayespeak_gsl.h:41:42: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
long int t = a1 * (s - h * q1) - h * r1;
˜ ˜˜^˜˜˜
./bayespeak_gsl.h:44:11: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
s = t;
˜ ^
./bayespeak_gsl.h:49:22: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
long int h = s / q1;
˜ ˜˜^˜˜˜
./bayespeak_gsl.h:50:38: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
long int t = a1 * (s - h * q1) - h * r1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
./bayespeak_gsl.h:50:32: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
long int t = a1 * (s - h * q1) - h * r1;
˜ ˜˜^˜˜˜
./bayespeak_gsl.h:50:42: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
long int t = a1 * (s - h * q1) - h * r1;
˜ ˜˜^˜˜˜
./bayespeak_gsl.h:53:11: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
s = t;
˜ ^
./bayespeak_gsl.h:74:19: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
long int h1 = x / q1;
˜˜ ˜˜^˜˜˜
./bayespeak_gsl.h:75:36: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
long int t1 = a1 * (x - h1 * q1) - h1 * r1;
˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./bayespeak_gsl.h:75:30: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
long int t1 = a1 * (x - h1 * q1) - h1 * r1;
˜ ˜˜˜^˜˜˜
./bayespeak_gsl.h:75:41: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
long int t1 = a1 * (x - h1 * q1) - h1 * r1;
˜ ˜˜˜^˜˜˜
./bayespeak_gsl.h:77:19: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
long int h2 = y / q2;
˜˜ ˜˜^˜˜˜
./bayespeak_gsl.h:78:36: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
long int t2 = a2 * (y - h2 * q2) - h2 * r2;
˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
./bayespeak_gsl.h:78:30: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
long int t2 = a2 * (y - h2 * q2) - h2 * r2;
˜ ˜˜˜^˜˜˜
./bayespeak_gsl.h:78:41: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
long int t2 = a2 * (y - h2 * q2) - h2 * r2;
˜ ˜˜˜^˜˜˜
./bayespeak_gsl.h:86:14: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
state->x = t1;
˜ ^˜
./bayespeak_gsl.h:87:14: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
state->y = t2;
˜ ^˜
./bayespeak_gsl.h:91:40: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
long int delta = state->shuffle[j] - t2;
˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./bayespeak_gsl.h:91:42: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
long int delta = state->shuffle[j] - t2;
˜ ^˜
./bayespeak_gsl.h:94:16: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
state->n = delta;
˜ ^˜˜˜˜
./bayespeak_gsl.h:95:25: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
state->shuffle[j] = t1;
˜ ^˜
bayespeak.c:38:12: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
return (1 - gsl_cdf_ugaussian_Q (x));
˜˜˜˜˜˜ ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
bayespeak.c:43:9: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
return logfact(n);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
bayespeak.c:155:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
stateZ = (int*) R_alloc(N, sizeof(int));
˜˜˜˜˜˜˜ ^
bayespeak.c:156:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
scorepos = (double*) R_alloc(N, sizeof(double));
˜˜˜˜˜˜˜ ^
bayespeak.c:157:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
scoreneg = (double*) R_alloc(N, sizeof(double));
˜˜˜˜˜˜˜ ^
bayespeak.c:158:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
probX = (double*) R_alloc(N, sizeof(double));
˜˜˜˜˜˜˜ ^
bayespeak.c:173:16: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
int burnin = ceil(iters/2); //, na = ceil(iters*11/20), nstar = ceil(iters*3/4);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
bayespeak.c:238:48: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double *gamma_pow = (double*) R_alloc((*w_max + 2), sizeof(double));
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜˜
bayespeak.c:248:51: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double *gammanew_pow = (double*) R_alloc((*w_max + 2), sizeof(double));
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜˜
bayespeak.c:256:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
probZ = (double**) R_alloc(N, sizeof(double*));
˜˜˜˜˜˜˜ ^
bayespeak.c:267:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
Y[i] = (double*) R_alloc(N, sizeof(double));
˜˜˜˜˜˜˜ ^
bayespeak.c:268:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
cdfZ[i] = (double*) R_alloc(N, sizeof(double));
˜˜˜˜˜˜˜ ^
bayespeak.c:269:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
P2[i] = (double*) R_alloc(N, sizeof(double));
˜˜˜˜˜˜˜ ^
bayespeak.c:540:21: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
c0 = normald(-a0/sd0);
˜˜˜˜˜˜˜ ˜˜˜^˜˜˜
bayespeak.c:541:21: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
c1 = normald(-a1/sd1);
˜˜˜˜˜˜˜ ˜˜˜^˜˜˜
bayespeak.c:542:24: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
c2 = normald(-gamma/sd2);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜˜
bayespeak.c:543:23: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
cc0 = normald(-aa0/sd0);
˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜
bayespeak.c:544:23: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
cc1 = normald(-aa1/sd1);
˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜
bayespeak.c:545:28: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
cc2 = normald(-gammanew/sd2);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜
43 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 BayesPeak.so bayespeak.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/BayesPeak.buildbin-libdir/BayesPeak/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BayesPeak)
>>>>>>>
>>>>>>> FIXING LINKS FOR BayesPeak.buildbin-libdir/BayesPeak/libs//BayesPeak.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" "BayesPeak.buildbin-libdir/BayesPeak/libs//BayesPeak.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "BayesPeak.buildbin-libdir/BayesPeak/libs//BayesPeak.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" "BayesPeak.buildbin-libdir/BayesPeak/libs//BayesPeak.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "BayesPeak.buildbin-libdir/BayesPeak/libs//BayesPeak.so"