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Package 8/671HostnameOS / ArchBUILDCHECKBUILD BIN
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 ]

Summary

Package: aCGH
Version: 1.38.0
Command: rm -rf aCGH.buildbin-libdir && mkdir aCGH.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh aCGH_1.38.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R aCGH.buildbin-libdir
StartedAt: 2013-05-01 12:03:15 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 12:03:26 -0700 (Wed, 01 May 2013)
EllapsedTime: 10.5 seconds
RetCode: 0
Status:  OK 
PackageFile: aCGH_1.38.0.tgz
PackageFileSize: 2.231 MiB

Command output

>>>>>>> 
>>>>>>> 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"