aCGH 1.38.0
Peter Dimitrov
| 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/aCGH | | 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=aCGH.buildbin-libdir aCGH_1.38.0.tar.gz'
>>>>>>>
* installing *source* package 'aCGH' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -g3 -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c hmm.cpp -o hmm.o
hmm.cpp:27:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ll += exp(alpha[i][0] = yll[i][0] + pi[i]);
˜˜˜˜˜ ^
hmm.cpp:27:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ll += exp(alpha[i][0] = yll[i][0] + pi[i]);
˜˜˜ ^
hmm.cpp:28:8: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
beta[i][T - 1] = 0;
˜˜˜˜ ^
hmm.cpp:28:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
beta[i][T - 1] = 0;
˜˜˜˜ ˜˜^˜˜
hmm.cpp:30:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Rprintf("yll[%d][0] = %f\tpi[%d] = %f\n", i, yll[i][0], i, pi[i]);
˜˜˜ ^
hmm.cpp:37:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
alpha[i][0] -= sum_log_lik;
˜˜˜˜˜ ^
hmm.cpp:40:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
i, alpha[i][0], i, T - 1, beta[i][T - 1]);
˜˜˜˜˜ ^
hmm.cpp:40:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
i, alpha[i][0], i, T - 1, beta[i][T - 1]);
˜˜˜˜ ^
hmm.cpp:40:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
i, alpha[i][0], i, T - 1, beta[i][T - 1]);
˜˜˜˜ ˜˜^˜˜
hmm.cpp:42:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
filter[i] = exp(alpha[i][0]);
˜˜˜˜˜ ^
hmm.cpp:57:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
beta[i][t] = alpha[i][m] = 0;
˜˜˜˜ ^
hmm.cpp:57:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
beta[i][t] = alpha[i][m] = 0;
˜˜˜˜ ^
hmm.cpp:57:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
beta[i][t] = alpha[i][m] = 0;
˜˜˜˜˜ ^
hmm.cpp:57:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
beta[i][t] = alpha[i][m] = 0;
˜˜˜˜˜ ^
hmm.cpp:61:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
alpha[i][m] +=
˜˜˜˜˜ ^
hmm.cpp:61:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
alpha[i][m] +=
˜˜˜˜˜ ^
hmm.cpp:62:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
exp(yll[i][m] + alpha[j][m - 1] + tpm[j][i]);
˜˜˜ ^
hmm.cpp:62:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
exp(yll[i][m] + alpha[j][m - 1] + tpm[j][i]);
˜˜˜ ^
hmm.cpp:62:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
exp(yll[i][m] + alpha[j][m - 1] + tpm[j][i]);
˜˜˜˜˜ ^
hmm.cpp:62:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
exp(yll[i][m] + alpha[j][m - 1] + tpm[j][i]);
˜˜˜˜˜ ˜˜^˜˜
hmm.cpp:62:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
exp(yll[i][m] + alpha[j][m - 1] + tpm[j][i]);
˜˜˜ ^
hmm.cpp:62:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
exp(yll[i][m] + alpha[j][m - 1] + tpm[j][i]);
˜˜˜ ^
hmm.cpp:63:10: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
beta[i][t] +=
˜˜˜˜ ^
hmm.cpp:63:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
beta[i][t] +=
˜˜˜˜ ^
hmm.cpp:64:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
exp(yll[i][t + 1] + beta[j][t + 1] + tpm[i][j]);
˜˜˜ ^
hmm.cpp:64:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
exp(yll[i][t + 1] + beta[j][t + 1] + tpm[i][j]);
˜˜˜ ˜˜^˜˜
hmm.cpp:64:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
exp(yll[i][t + 1] + beta[j][t + 1] + tpm[i][j]);
˜˜˜˜ ^
hmm.cpp:64:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
exp(yll[i][t + 1] + beta[j][t + 1] + tpm[i][j]);
˜˜˜˜ ˜˜^˜˜
hmm.cpp:64:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
exp(yll[i][t + 1] + beta[j][t + 1] + tpm[i][j]);
˜˜˜ ^
hmm.cpp:64:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
exp(yll[i][t + 1] + beta[j][t + 1] + tpm[i][j]);
˜˜˜ ^
hmm.cpp:67:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
avf += alpha[i][m], avb += beta[i][t];
˜˜˜˜˜ ^
hmm.cpp:67:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
avf += alpha[i][m], avb += beta[i][t];
˜˜˜˜˜ ^
hmm.cpp:67:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
avf += alpha[i][m], avb += beta[i][t];
˜˜˜˜ ^
hmm.cpp:67:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
avf += alpha[i][m], avb += beta[i][t];
˜˜˜˜ ^
hmm.cpp:74:10: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
alpha[i][m] = log(alpha[i][m]) - avf;
˜˜˜˜˜ ^
hmm.cpp:74:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
alpha[i][m] = log(alpha[i][m]) - avf;
˜˜˜˜˜ ^
hmm.cpp:74:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
alpha[i][m] = log(alpha[i][m]) - avf;
˜˜˜˜˜ ^
hmm.cpp:74:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
alpha[i][m] = log(alpha[i][m]) - avf;
˜˜˜˜˜ ^
hmm.cpp:75:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
beta[i][t] = log(beta[i][t]) - avb;
˜˜˜˜ ^
hmm.cpp:75:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
beta[i][t] = log(beta[i][t]) - avb;
˜˜˜˜ ^
hmm.cpp:75:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
beta[i][t] = log(beta[i][t]) - avb;
˜˜˜˜ ^
hmm.cpp:75:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
beta[i][t] = log(beta[i][t]) - avb;
˜˜˜˜ ^
hmm.cpp:77:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
filter[offs + i] = exp(alpha[i][m]);
˜˜˜˜˜ ^
hmm.cpp:77:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
filter[offs + i] = exp(alpha[i][m]);
˜˜˜˜˜ ^
hmm.cpp:80:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
i, m, alpha[i][m], i, t, beta[i][t]);
˜˜˜˜˜ ^
hmm.cpp:80:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
i, m, alpha[i][m], i, t, beta[i][t]);
˜˜˜˜˜ ^
hmm.cpp:80:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
i, m, alpha[i][m], i, t, beta[i][t]);
˜˜˜˜ ^
hmm.cpp:80:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
i, m, alpha[i][m], i, t, beta[i][t]);
˜˜˜˜ ^
hmm.cpp:21:10: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int T = yll[0].size(), k = yll.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
hmm.cpp:21:29: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int T = yll[0].size(), k = yll.size();
˜ ^˜˜˜˜˜˜˜˜˜
hmm.cpp:106:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector< vector<double> > log_lik_table(k, vector<double>(T));
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
hmm.cpp:106:59: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector< vector<double> > log_lik_table(k, vector<double>(T));
˜˜˜˜˜˜ ^
hmm.cpp:107:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector< vector<unsigned int> > ptrs(k, vector<unsigned int>(T));
˜˜˜˜ ^
hmm.cpp:107:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector< vector<unsigned int> > ptrs(k, vector<unsigned int>(T));
˜˜˜˜˜˜ ^
hmm.cpp:114:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> v(k);
˜ ^
hmm.cpp:117:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
log_lik_table[i][0] = yll[i][0] + pi[i];
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
hmm.cpp:117:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
log_lik_table[i][0] = yll[i][0] + pi[i];
˜˜˜ ^
hmm.cpp:128:7: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
v[j] = log_lik_table[j][m - 1] + tpm[j][i];
˜ ^
hmm.cpp:128:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
v[j] = log_lik_table[j][m - 1] + tpm[j][i];
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
hmm.cpp:128:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
v[j] = log_lik_table[j][m - 1] + tpm[j][i];
˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜^˜˜
hmm.cpp:128:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
v[j] = log_lik_table[j][m - 1] + tpm[j][i];
˜˜˜ ^
hmm.cpp:128:45: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
v[j] = log_lik_table[j][m - 1] + tpm[j][i];
˜˜˜ ^
hmm.cpp:129:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (v[j] > s)
˜ ^
hmm.cpp:130:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
s = v[j], best_ind = j;
˜ ^
hmm.cpp:133:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
log_lik_table[i][m] = yll[i][m] + v[ptrs[i][m] = best_ind];
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
hmm.cpp:133:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
log_lik_table[i][m] = yll[i][m] + v[ptrs[i][m] = best_ind];
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
hmm.cpp:133:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
log_lik_table[i][m] = yll[i][m] + v[ptrs[i][m] = best_ind];
˜˜˜ ^
hmm.cpp:133:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
log_lik_table[i][m] = yll[i][m] + v[ptrs[i][m] = best_ind];
˜˜˜ ^
hmm.cpp:133:45: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
log_lik_table[i][m] = yll[i][m] + v[ptrs[i][m] = best_ind];
˜˜˜˜ ^
hmm.cpp:133:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
log_lik_table[i][m] = yll[i][m] + v[ptrs[i][m] = best_ind];
˜˜˜˜ ^
hmm.cpp:133:53: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
log_lik_table[i][m] = yll[i][m] + v[ptrs[i][m] = best_ind];
˜ ^˜˜˜˜˜˜˜
hmm.cpp:140:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
double s = log_lik_table[0][T - 1];
˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜^˜˜
hmm.cpp:144:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (log_lik_table[i][T - 1] > s)
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
hmm.cpp:144:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (log_lik_table[i][T - 1] > s)
˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜^˜˜
hmm.cpp:145:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
s = log_lik_table[i][T - 1], states[T - 1] = i;
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
hmm.cpp:145:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
s = log_lik_table[i][T - 1], states[T - 1] = i;
˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜^˜˜
hmm.cpp:148:15: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
states[m] = ptrs[states[m + 1]][m + 1];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
hmm.cpp:148:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
states[m] = ptrs[states[m + 1]][m + 1];
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
hmm.cpp:148:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
states[m] = ptrs[states[m + 1]][m + 1];
˜˜˜˜ ˜˜^˜˜
hmm.cpp:150:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return log_lik_table[states[T - 1]][T - 1];
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
hmm.cpp:150:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return log_lik_table[states[T - 1]][T - 1];
˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜^˜˜
hmm.cpp:105:10: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int T = yll[0].size(), k = yll.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
hmm.cpp:105:29: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int T = yll[0].size(), k = yll.size();
˜ ^˜˜˜˜˜˜˜˜˜
hmm.cpp:167:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector< vector<double> > tpm(k, vector<double>(k)),
˜˜˜ ^
hmm.cpp:167:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector< vector<double> > tpm(k, vector<double>(k)),
˜˜˜˜˜˜ ^
hmm.cpp:168:8: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
yll(k, vector<double>(T)), alpha(k, vector<double>(T)),
˜˜˜ ^
hmm.cpp:168:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
yll(k, vector<double>(T)), alpha(k, vector<double>(T)),
˜˜˜˜˜˜ ^
hmm.cpp:168:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
yll(k, vector<double>(T)), alpha(k, vector<double>(T)),
˜˜˜˜˜ ^
hmm.cpp:168:55: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
yll(k, vector<double>(T)), alpha(k, vector<double>(T)),
˜˜˜˜˜˜ ^
hmm.cpp:169:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
beta(k, vector<double>(T)), gamma(k, vector<double>(T)),
˜˜˜˜ ^
hmm.cpp:169:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
beta(k, vector<double>(T)), gamma(k, vector<double>(T)),
˜˜˜˜˜˜ ^
hmm.cpp:169:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
beta(k, vector<double>(T)), gamma(k, vector<double>(T)),
˜˜˜˜˜ ^
hmm.cpp:169:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
beta(k, vector<double>(T)), gamma(k, vector<double>(T)),
˜˜˜˜˜˜ ^
hmm.cpp:170:8: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ksi(k, vector<double>(k));
˜˜˜ ^
hmm.cpp:170:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ksi(k, vector<double>(k));
˜˜˜˜˜˜ ^
hmm.cpp:171:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> old_pi(k), old_means(k);
˜˜˜˜˜˜ ^
hmm.cpp:171:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> old_pi(k), old_means(k);
˜˜˜˜˜˜˜˜˜ ^
hmm.cpp:175:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tpm[i][j] = log(TPM[offs + i]);
˜˜˜ ^
hmm.cpp:175:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tpm[i][j] = log(TPM[offs + i]);
˜˜˜ ^
hmm.cpp:191:10: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
yll[i][m] = -(M_LN_SQRT_2PI + 0.5 * x * x + log_sigma);
˜˜˜ ^
hmm.cpp:191:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
yll[i][m] = -(M_LN_SQRT_2PI + 0.5 * x * x + log_sigma);
˜˜˜ ^
hmm.cpp:212:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector< vector<double> > sum_ksi(k, vector<double>(k, 0));
˜˜˜˜˜˜˜ ^
hmm.cpp:222:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
avfb += exp(gamma[i][m] = alpha[i][m] + beta[i][m]);
˜˜˜˜˜ ^
hmm.cpp:222:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
avfb += exp(gamma[i][m] = alpha[i][m] + beta[i][m]);
˜˜˜˜˜ ^
hmm.cpp:222:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
avfb += exp(gamma[i][m] = alpha[i][m] + beta[i][m]);
˜˜˜˜˜ ^
hmm.cpp:222:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
avfb += exp(gamma[i][m] = alpha[i][m] + beta[i][m]);
˜˜˜˜˜ ^
hmm.cpp:222:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
avfb += exp(gamma[i][m] = alpha[i][m] + beta[i][m]);
˜˜˜˜ ^
hmm.cpp:222:54: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
avfb += exp(gamma[i][m] = alpha[i][m] + beta[i][m]);
˜˜˜˜ ^
hmm.cpp:226:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
exp(ksi[i][j] = alpha[i][m] + tpm[i][j] +
˜˜˜ ^
hmm.cpp:226:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
exp(ksi[i][j] = alpha[i][m] + tpm[i][j] +
˜˜˜ ^
hmm.cpp:226:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
exp(ksi[i][j] = alpha[i][m] + tpm[i][j] +
˜˜˜˜˜ ^
hmm.cpp:226:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
exp(ksi[i][j] = alpha[i][m] + tpm[i][j] +
˜˜˜˜˜ ^
hmm.cpp:226:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
exp(ksi[i][j] = alpha[i][m] + tpm[i][j] +
˜˜˜ ^
hmm.cpp:226:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
exp(ksi[i][j] = alpha[i][m] + tpm[i][j] +
˜˜˜ ^
hmm.cpp:227:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
yll[j][m + 1] + beta[j][m + 1]);
˜˜˜ ^
hmm.cpp:227:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
yll[j][m + 1] + beta[j][m + 1]);
˜˜˜ ˜˜^˜˜
hmm.cpp:227:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
yll[j][m + 1] + beta[j][m + 1]);
˜˜˜˜ ^
hmm.cpp:227:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
yll[j][m + 1] + beta[j][m + 1]);
˜˜˜˜ ˜˜^˜˜
hmm.cpp:234:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum_gamma[i] += (gamma[i][m] = exp(gamma[i][m] - avfb));
˜˜˜˜˜˜˜˜˜ ^
hmm.cpp:234:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum_gamma[i] += (gamma[i][m] = exp(gamma[i][m] - avfb));
˜˜˜˜˜ ^
hmm.cpp:234:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum_gamma[i] += (gamma[i][m] = exp(gamma[i][m] - avfb));
˜˜˜˜˜ ^
hmm.cpp:234:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum_gamma[i] += (gamma[i][m] = exp(gamma[i][m] - avfb));
˜˜˜˜˜ ^
hmm.cpp:234:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum_gamma[i] += (gamma[i][m] = exp(gamma[i][m] - avfb));
˜˜˜˜˜ ^
hmm.cpp:239:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum_ksi[i][j] += exp(ksi[i][j] - avksi);
˜˜˜˜˜˜˜ ^
hmm.cpp:239:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum_ksi[i][j] += exp(ksi[i][j] - avksi);
˜˜˜˜˜˜˜ ^
hmm.cpp:239:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum_ksi[i][j] += exp(ksi[i][j] - avksi);
˜˜˜ ^
hmm.cpp:239:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum_ksi[i][j] += exp(ksi[i][j] - avksi);
˜˜˜ ^
hmm.cpp:257:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
old_pi[i] = pi[i];
˜˜˜˜˜˜ ^
hmm.cpp:258:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
pi[i] = gamma[i][0];
˜˜˜˜˜ ^
hmm.cpp:268:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
double s = sum_ksi[i][0];
˜˜˜˜˜˜˜ ^
hmm.cpp:270:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
s += sum_ksi[i][j];
˜˜˜˜˜˜˜ ^
hmm.cpp:270:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
s += sum_ksi[i][j];
˜˜˜˜˜˜˜ ^
hmm.cpp:274:10: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tpm[i][j] = log(sum_ksi[i][j] / s);
˜˜˜ ^
hmm.cpp:274:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tpm[i][j] = log(sum_ksi[i][j] / s);
˜˜˜ ^
hmm.cpp:274:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tpm[i][j] = log(sum_ksi[i][j] / s);
˜˜˜˜˜˜˜ ^
hmm.cpp:274:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tpm[i][j] = log(sum_ksi[i][j] / s);
˜˜˜˜˜˜˜ ^
hmm.cpp:280:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
old_means[i] = means[i];
˜˜˜˜˜˜˜˜˜ ^
hmm.cpp:293:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
double x = _y[m] - old_means[i];
˜˜˜˜˜˜˜˜˜ ^
hmm.cpp:295:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
means[i] += gamma[i][m] * _y[m];
˜˜˜˜˜ ^
hmm.cpp:295:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
means[i] += gamma[i][m] * _y[m];
˜˜˜˜˜ ^
hmm.cpp:296:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum_sigma += gamma[i][m] * x * x;
˜˜˜˜˜ ^
hmm.cpp:296:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum_sigma += gamma[i][m] * x * x;
˜˜˜˜˜ ^
hmm.cpp:302:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
means[i] /= sum_gamma[i];
˜˜˜˜˜˜˜˜˜ ^
hmm.cpp:315:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
TPM[offs + i] = exp(tpm[i][j]);
˜˜˜ ^
hmm.cpp:315:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
TPM[offs + i] = exp(tpm[i][j]);
˜˜˜ ^
hmm.cpp:323:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
filter[offs + i] = gamma[i][m];
˜˜˜˜˜ ^
hmm.cpp:323:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
filter[offs + i] = gamma[i][m];
˜˜˜˜˜ ^
147 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 aCGH.so hmm.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/aCGH.buildbin-libdir/aCGH/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (aCGH)
>>>>>>>
>>>>>>> FIXING LINKS FOR aCGH.buildbin-libdir/aCGH/libs//aCGH.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" "aCGH.buildbin-libdir/aCGH/libs//aCGH.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "aCGH.buildbin-libdir/aCGH/libs//aCGH.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" "aCGH.buildbin-libdir/aCGH/libs//aCGH.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "aCGH.buildbin-libdir/aCGH/libs//aCGH.so"