nem 2.36.0
Holger Froehlich
| 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/nem | | 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=nem.buildbin-libdir nem_2.36.0.tar.gz'
>>>>>>>
* installing *source* package 'nem' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c MCMC.c -o MCMC.o
MCMC.c:44:58: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
p -= inv_nu*abs(net[s][k]-prior[s][k]);
˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
MCMC.c:72:66: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
if(Psi[p][s] != 0 && abs(Psi[p][s]) <= t){ // p is a parent
˜˜˜ ^˜˜˜˜˜˜˜˜
MCMC.c:74:79: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
parent_perturb_prob = perturb_prob[p][t-1];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
MCMC.c:360:11: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
srand(seed);
˜˜˜˜˜ ^˜˜˜
MCMC.c:363:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double** matrix = (double**) R_alloc(nsgenes, sizeof(double*)); // for DIC calculation
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
MCMC.c:365:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double** M = (double**) R_alloc(nsgenes, sizeof(double*)); // for variance calculation
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
MCMC.c:367:44: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double** var_mean = (double**) R_alloc(nsgenes, sizeof(double*));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
MCMC.c:368:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double** newNet = (double**) R_alloc(nsgenes, sizeof(double*));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
MCMC.c:375:50: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double*** perturb_prob = (double***) R_alloc(nsgenes, sizeof(double**));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
MCMC.c:377:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
matrix[i] = (double*) R_alloc (nsgenes, sizeof(double)); // for DIC calculation
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
MCMC.c:379:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
M[i] = (double*)R_alloc(nsgenes, sizeof(double)); // for variance calculation
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
MCMC.c:381:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
var_mean[i] = (double*) R_alloc(nsgenes, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
MCMC.c:382:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
newNet[i] = (double*) R_alloc (nsgenes, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
MCMC.c:385:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
perturb_prob[i] = (double**) R_alloc(nsgenes, sizeof(double*));// R_alloc changed to R_alloc
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
MCMC.c:393:56: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
perturb_prob[i][j] = (double*) R_alloc(T , sizeof(double));// R_alloc changed to R_alloc
˜˜˜˜˜˜˜ ^
MCMC.c:399:49: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double* loglik0 = (double*) R_alloc(nsgenes + 1, sizeof(double));
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜
MCMC.c:359:35: warning: unused variable 'mutinf' [-Wunused-variable]
double loglikMean, loglikSum, mutinf, delta, logPrior_cur_scale;
^
MCMC.c:402:10: warning: unused variable 'stored' [-Wunused-variable]
long stored = 0;
^
MCMC.c:403:10: warning: unused variable 'stored2' [-Wunused-variable]
long stored2 = 0;
^
19 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c netlearn.c -o netlearn.o
netlearn.c:158:43: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double** tmp = (double**) R_alloc(nsgenes, sizeof(double*));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
netlearn.c:159:44: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double** tmp2 = (double**) R_alloc(nsgenes, sizeof(double*));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
netlearn.c:162:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp[i] = (double*) R_alloc(nsgenes, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
netlearn.c:163:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp2[i] = (double*) R_alloc(nsgenes, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
netlearn.c:177:47: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double*** perturb_prob = (double***) R_alloc(nsgenes, sizeof(double**));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
netlearn.c:179:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
perturb_prob[i] = (double**) R_alloc(nsgenes, sizeof(double*));// R_alloc changed to R_alloc
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
netlearn.c:181:43: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
perturb_prob[i][j] = (double*) R_alloc(T , sizeof(double));// R_alloc changed to R_alloc
˜˜˜˜˜˜˜ ^
netlearn.c:186:46: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double* loglik0 = (double*) R_alloc(nsgenes + 1, sizeof(double));
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜
netlearn.c:168:9: warning: unused variable 'lik_switch' [-Wunused-variable]
double lik_switch;
^
9 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c wrapper.c -o wrapper.o
wrapper.c:62:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double** Psi = (double**) R_alloc(nsgenes, sizeof(double*));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
wrapper.c:63:48: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double** perturb_prob = (double**) R_alloc(nsgenes, sizeof(double*));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
wrapper.c:66:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
Psi[s] = (double*) R_alloc(nsgenes, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
wrapper.c:68:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
perturb_prob[s] = (double*) R_alloc(nsgenes, sizeof(double));// calloc changed to R_alloc
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
wrapper.c:113:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double*** D = (double***) R_alloc(T, sizeof(double**));
˜˜˜˜˜˜˜ ^
wrapper.c:114:43: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double** initial = (double**) R_alloc(nsgenes, sizeof(double*));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
wrapper.c:115:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double** sdMat = (double**) R_alloc(nsgenes, sizeof(double*));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
wrapper.c:117:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double** mat = (double**) R_alloc(nsgenes, sizeof(double*));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
wrapper.c:118:64: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double* allLikelihoods = (double*) R_alloc(sample + burnin + 1, sizeof(double));
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
wrapper.c:122:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
networkPrior = (double**) R_alloc(nsgenes, sizeof(double*));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
wrapper.c:123:47: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double** Egene_prior = (double**) R_alloc(negenes, sizeof(double*));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
wrapper.c:127:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
D[t] = (double**) R_alloc(negenes, sizeof(double*));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
wrapper.c:129:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
D[t][i] = (double*) R_alloc(nsgenes, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
wrapper.c:130:56: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
Egene_prior[i] = (double*) R_alloc(nsgenes + 1, sizeof(double));
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜
wrapper.c:142:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
initial[s] = (double*) R_alloc(nsgenes, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
wrapper.c:143:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
networkPrior[s] = (double*) R_alloc(nsgenes, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
wrapper.c:145:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
sdMat[s] = (double*) R_alloc(nsgenes, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
wrapper.c:146:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mat[s] = (double*) R_alloc(nsgenes, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
18 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 nem.so MCMC.o netlearn.o wrapper.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/nem.buildbin-libdir/nem/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 (nem)
>>>>>>>
>>>>>>> FIXING LINKS FOR nem.buildbin-libdir/nem/libs//nem.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" "nem.buildbin-libdir/nem/libs//nem.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "nem.buildbin-libdir/nem/libs//nem.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" "nem.buildbin-libdir/nem/libs//nem.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "nem.buildbin-libdir/nem/libs//nem.so"