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Package 83/671HostnameOS / ArchBUILDCHECKBUILD BIN
birta 1.4.0
Benedikt Zacher , 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/birta
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 [ WARNINGS ] OK 

Summary

Package: birta
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch birta_1.4.0.tar.gz
StartedAt: 2013-05-01 03:00:16 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 03:01:35 -0700 (Wed, 01 May 2013)
EllapsedTime: 79.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: birta.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/birta.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'birta/DESCRIPTION' ... OK
* this is package 'birta' version '1.4.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'birta' can be installed ... [7s/8s] WARNING
Found the following significant warnings:
  getStates.cpp:228:12: warning: variable 'nreps' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  getStates.cpp:259:13: warning: variable 'nreps' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  getStates.cpp:201:13: warning: variable 'nreps' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
See '/Users/biocbuild/bbs-2.12-bioc/meat/birta.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [12s/12s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/birta.Rcheck/00check.log'
for details.

birta.Rcheck/00install.out:

* installing *source* package 'birta' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c BayesNetwork.cpp -o BayesNetwork.o
BayesNetwork.cpp:108:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
          this->S[c] = (int *) malloc(sizeof(int)*A_cnt);
                                                 ˜^˜˜˜˜
BayesNetwork.cpp:109:64: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
          this->posterior_miRNA[c] = (double *) malloc(sizeof(double)*A_cnt);
                                                                     ˜^˜˜˜˜
BayesNetwork.cpp:122:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
          this->T[c] = (int *) malloc(sizeof(int)*T_cnt);
                                                 ˜^˜˜˜˜
BayesNetwork.cpp:123:61: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
          this->posterior_TF[c] = (double *) malloc(sizeof(double)*T_cnt);
                                                                  ˜^˜˜˜˜
BayesNetwork.cpp:139:47: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        this->miR_higher_in_condition = (int*)calloc(A_cnt, sizeof(int));
                                              ˜˜˜˜˜˜ ^˜˜˜˜
BayesNetwork.cpp:179:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        mean_c1 = mean_c1/(rep_cnt[1][0] * S2O[i].size());
                                           ^˜˜˜˜˜˜˜˜˜˜˜˜ ˜
BayesNetwork.cpp:180:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        mean_c2 = mean_c2/(rep_cnt[1][1] * S2O[i].size()) ;
                                           ^˜˜˜˜˜˜˜˜˜˜˜˜ ˜
BayesNetwork.cpp:230:48: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                this->posterior_omega_TF = (double**) calloc(T_cnt, sizeof(double*));
                                                      ˜˜˜˜˜˜ ^˜˜˜˜
BayesNetwork.cpp:233:51: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                this->posterior_omega_miRNA = (double**) calloc(A_cnt, sizeof(double*));
                                                         ˜˜˜˜˜˜ ^˜˜˜˜
BayesNetwork.cpp:503:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                T_npossible_swaps[condition] = T_npossible_swaps[condition] - T_possible_swaps[condition][switchid].size();
                                               ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
BayesNetwork.cpp:497:22: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                        int size_before = T_possible_swaps[condition][curr_tf].size();
                            ˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BayesNetwork.cpp:499:21: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                        int size_after = T_possible_swaps[condition][curr_tf].size();
                            ˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BayesNetwork.cpp:503:63: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                T_npossible_swaps[condition] = T_npossible_swaps[condition] - T_possible_swaps[condition][switchid].size();
                                             ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BayesNetwork.cpp:545:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                S_npossible_swaps = S_npossible_swaps - S_possible_swaps[switchid].size();
                                    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
BayesNetwork.cpp:539:22: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                        int size_before = S_possible_swaps[curr_tf].size();
                            ˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BayesNetwork.cpp:541:21: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                        int size_after = S_possible_swaps[curr_tf].size();
                            ˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BayesNetwork.cpp:545:41: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                S_npossible_swaps = S_npossible_swaps - S_possible_swaps[switchid].size();
                                  ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BayesNetwork.cpp:656:70: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        double *log_lik_trace = (double*)malloc(sizeof(double)*(niter+burnin+1));
                                                              ˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜
BayesNetwork.cpp:668:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                nactive_miRNAs = (int**)calloc(O_cnt, sizeof(int*));
                                        ˜˜˜˜˜˜ ^˜˜˜˜
BayesNetwork.cpp:672:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                nactive_TFs = (int**)calloc(O_cnt, sizeof(int*));
                                     ˜˜˜˜˜˜ ^˜˜˜˜
BayesNetwork.cpp:1066:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                                new_neighbourhood = old_neighbourhood - 2*T_possible_swaps[condition][switchid].size(); // remove #swaps, that are not possible any more
                                                                    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
BayesNetwork.cpp:1168:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                                new_neighbourhood = old_neighbourhood - 2*S_possible_swaps[switchid].size(); // remove #swaps, that are not possible any more
                                                                    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
BayesNetwork.cpp:715:46: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                                                                log_lik -= (pow(A[c][i][r] - get_mu0(i, c), 2)/pow(A_sigma[i], 2));
                                                                                             ˜˜˜˜˜˜˜ ^
BayesNetwork.cpp:717:46: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                                                                log_lik -= logNB(A[c][i][r], get_mu0(i, c), A_sigma[i]);
                                                                                             ˜˜˜˜˜˜˜ ^
BayesNetwork.cpp:724:45: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                                                        log_lik -= pow((A[c][i][r] + get_mu0(i, c)*n0)/(1+n0), 2) - (alpha+0.5) * log(0.5*n0*pow(get_mu0(i, c),2)+0.5*pow(A[c][i][r],2)+beta);
                                                                                     ˜˜˜˜˜˜˜ ^
BayesNetwork.cpp:724:105: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                                                        log_lik -= pow((A[c][i][r] + get_mu0(i, c)*n0)/(1+n0), 2) - (alpha+0.5) * log(0.5*n0*pow(get_mu0(i, c),2)+0.5*pow(A[c][i][r],2)+beta);
                                                                                                                                                 ˜˜˜˜˜˜˜ ^
BayesNetwork.cpp:759:50: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                                                                log_lik -= (pow(Otf[c][i][r] - get_mu0TF(i, c), 2)/pow(TF_sigma[i], 2));
                                                                                               ˜˜˜˜˜˜˜˜˜ ^
BayesNetwork.cpp:761:50: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                                                                log_lik -= logNB(Otf[c][i][r], get_mu0TF(i, c), TF_sigma[i]);
                                                                                               ˜˜˜˜˜˜˜˜˜ ^
BayesNetwork.cpp:768:49: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                                                        log_lik -= pow((Otf[c][i][r] + get_mu0TF(i, c)*n0)/(1+n0), 2) - (alphaTF+0.5) * log(0.5*n0*pow(get_mu0TF(i, c),2)+0.5*pow(Otf[c][i][r],2)+betaTF);
                                                                                       ˜˜˜˜˜˜˜˜˜ ^
BayesNetwork.cpp:768:113: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                                                        log_lik -= pow((Otf[c][i][r] + get_mu0TF(i, c)*n0)/(1+n0), 2) - (alphaTF+0.5) * log(0.5*n0*pow(get_mu0TF(i, c),2)+0.5*pow(Otf[c][i][r],2)+betaTF);
                                                                                                                                                       ˜˜˜˜˜˜˜˜˜ ^
BayesNetwork.cpp:814:21: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                int curr_size = S_possible_swaps[swapid1].size();
                                    ˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BayesNetwork.cpp:819:18: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                        curr_size = S_possible_swaps[swapid1].size();
                                                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BayesNetwork.cpp:919:21: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                int curr_size = T_possible_swaps[condition][swapid1].size();
                                    ˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BayesNetwork.cpp:924:18: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                        curr_size = T_possible_swaps[condition][swapid1].size();
                                                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BayesNetwork.cpp:1066:45: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                                                new_neighbourhood = old_neighbourhood - 2*T_possible_swaps[condition][switchid].size(); // remove #swaps, that are not possible any more
                                                                  ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BayesNetwork.cpp:1168:45: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                                                new_neighbourhood = old_neighbourhood - 2*S_possible_swaps[switchid].size(); // remove #swaps, that are not possible any more
                                                                  ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
36 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c BayesNetworkNC.cpp -o BayesNetworkNC.o
BayesNetworkNC.cpp:91:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
          this->S[c] = (int *) malloc(sizeof(int)*A_cnt);
                                                 ˜^˜˜˜˜
BayesNetworkNC.cpp:92:64: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
          this->posterior_miRNA[c] = (double *) malloc(sizeof(double)*A_cnt);
                                                                     ˜^˜˜˜˜
BayesNetworkNC.cpp:105:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
          this->T[c] = (int *) malloc(sizeof(int)*T_cnt);
                                                 ˜^˜˜˜˜
BayesNetworkNC.cpp:106:61: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
          this->posterior_TF[c] = (double *) malloc(sizeof(double)*T_cnt);
                                                                  ˜^˜˜˜˜
BayesNetworkNC.cpp:123:47: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        this->miR_higher_in_condition = (int*)calloc(A_cnt, sizeof(int));
                                              ˜˜˜˜˜˜ ^˜˜˜˜
BayesNetworkNC.cpp:163:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        mean_c1 = mean_c1/(rep_cnt[1][0] * S2O[i].size());
                                           ^˜˜˜˜˜˜˜˜˜˜˜˜ ˜
BayesNetworkNC.cpp:164:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        mean_c2 = mean_c2/(rep_cnt[1][1] * S2O[i].size()) ;
                                           ^˜˜˜˜˜˜˜˜˜˜˜˜ ˜
BayesNetworkNC.cpp:203:48: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                this->posterior_omega_TF = (double**) calloc(T_cnt, sizeof(double*));
                                                      ˜˜˜˜˜˜ ^˜˜˜˜
BayesNetworkNC.cpp:206:51: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                this->posterior_omega_miRNA = (double**) calloc(A_cnt, sizeof(double*));
                                                         ˜˜˜˜˜˜ ^˜˜˜˜
BayesNetworkNC.cpp:240:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                S_npossible_swaps = S_npossible_swaps - S_possible_swaps[switchid].size();
                                    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
BayesNetworkNC.cpp:234:22: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                        int size_before = S_possible_swaps[curr_tf].size();
                            ˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BayesNetworkNC.cpp:236:21: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                        int size_after = S_possible_swaps[curr_tf].size();
                            ˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BayesNetworkNC.cpp:240:41: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                S_npossible_swaps = S_npossible_swaps - S_possible_swaps[switchid].size();
                                  ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BayesNetworkNC.cpp:268:70: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        double *log_lik_trace = (double*)malloc(sizeof(double)*(niter+burnin+1));
                                                              ˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜
BayesNetworkNC.cpp:280:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                nactive_miRNAs = (int**)calloc(O_cnt, sizeof(int*));
                                        ˜˜˜˜˜˜ ^˜˜˜˜
BayesNetworkNC.cpp:284:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                nactive_TFs = (int**)calloc(O_cnt, sizeof(int*));
                                     ˜˜˜˜˜˜ ^˜˜˜˜
BayesNetworkNC.cpp:677:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                                new_neighbourhood = old_neighbourhood - 2*T_possible_swaps[condition][switchid].size(); // remove #swaps, that are not possible any more
                                                                    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
BayesNetworkNC.cpp:779:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                                new_neighbourhood = old_neighbourhood - 2*S_possible_swaps[switchid].size(); // remove #swaps, that are not possible any more
                                                                    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
BayesNetworkNC.cpp:329:46: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                                                                log_lik -= (pow(A[c][i][r] - get_mu0(i, c), 2)/pow(A_sigma[i], 2));
                                                                                             ˜˜˜˜˜˜˜ ^
BayesNetworkNC.cpp:331:46: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                                                                log_lik -= logNB(A[c][i][r], get_mu0(i, c), A_sigma[i]);
                                                                                             ˜˜˜˜˜˜˜ ^
BayesNetworkNC.cpp:338:45: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                                                        log_lik -= pow((A[c][i][r] + get_mu0(i, c)*n0)/(1+n0), 2) - (alpha+0.5) * log(0.5*n0*pow(get_mu0(i, c),2)+0.5*pow(A[c][i][r],2)+beta);
                                                                                     ˜˜˜˜˜˜˜ ^
BayesNetworkNC.cpp:338:105: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                                                        log_lik -= pow((A[c][i][r] + get_mu0(i, c)*n0)/(1+n0), 2) - (alpha+0.5) * log(0.5*n0*pow(get_mu0(i, c),2)+0.5*pow(A[c][i][r],2)+beta);
                                                                                                                                                 ˜˜˜˜˜˜˜ ^
BayesNetworkNC.cpp:373:50: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                                                                log_lik -= (pow(Otf[c][i][r] - get_mu0TF(i, c), 2)/pow(TF_sigma[i], 2));
                                                                                               ˜˜˜˜˜˜˜˜˜ ^
BayesNetworkNC.cpp:375:50: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                                                                log_lik -= logNB(Otf[c][i][r], get_mu0TF(i, c), TF_sigma[i]);
                                                                                               ˜˜˜˜˜˜˜˜˜ ^
BayesNetworkNC.cpp:382:49: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                                                        log_lik -= pow((Otf[c][i][r] + get_mu0TF(i, c)*n0)/(1+n0), 2) - (alphaTF+0.5) * log(0.5*n0*pow(get_mu0TF(i, c),2)+0.5*pow(Otf[c][i][r],2)+betaTF);
                                                                                       ˜˜˜˜˜˜˜˜˜ ^
BayesNetworkNC.cpp:382:113: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
                                                        log_lik -= pow((Otf[c][i][r] + get_mu0TF(i, c)*n0)/(1+n0), 2) - (alphaTF+0.5) * log(0.5*n0*pow(get_mu0TF(i, c),2)+0.5*pow(Otf[c][i][r],2)+betaTF);
                                                                                                                                                       ˜˜˜˜˜˜˜˜˜ ^
BayesNetworkNC.cpp:428:21: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                int curr_size = S_possible_swaps[swapid1].size();
                                    ˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BayesNetworkNC.cpp:433:18: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                        curr_size = S_possible_swaps[swapid1].size();
                                                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BayesNetworkNC.cpp:533:21: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                int curr_size = T_possible_swaps[condition][swapid1].size();
                                    ˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BayesNetworkNC.cpp:538:18: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                        curr_size = T_possible_swaps[condition][swapid1].size();
                                                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BayesNetworkNC.cpp:677:45: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                                                new_neighbourhood = old_neighbourhood - 2*T_possible_swaps[condition][switchid].size(); // remove #swaps, that are not possible any more
                                                                  ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BayesNetworkNC.cpp:779:45: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                                                new_neighbourhood = old_neighbourhood - 2*S_possible_swaps[switchid].size(); // remove #swaps, that are not possible any more
                                                                  ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
32 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c getStates.cpp -o getStates.o
getStates.cpp:73:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                init_S[c] = (int*) R_alloc(A_cnt, sizeof(int));
                                                   ˜˜˜˜˜˜˜ ^˜˜˜˜
getStates.cpp:84:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        alpha_i0 = (double *)malloc(sizeof(double)*A_cnt);
                                                                  ˜^˜˜˜˜
getStates.cpp:85:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        alpha_i = (double *) malloc(sizeof(double)*A_cnt);
                                                                  ˜^˜˜˜˜
getStates.cpp:91:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                double* b_j = (double*) R_alloc(O_cnt, sizeof(double));
                                        ˜˜˜˜˜˜˜ ^˜˜˜˜
getStates.cpp:121:44: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                double **omega_miRNA = (double **)calloc(A_cnt, sizeof(double*));
                                                  ˜˜˜˜˜˜ ^˜˜˜˜
getStates.cpp:124:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        omega_miRNA[i] = (double*)calloc(curr_size, sizeof(double));
                                                  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
getStates.cpp:130:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                 double **omega_TF = (double **)calloc(T_cnt, sizeof(double*));
                                                ˜˜˜˜˜˜ ^˜˜˜˜
getStates.cpp:133:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        omega_TF[i] = (double*)calloc(curr_size, sizeof(double));
                                               ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
getStates.cpp:139:50: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                char **MymRNAs = (char **)malloc(sizeof(char*)*O_cnt);
                                                              ˜^˜˜˜˜
getStates.cpp:143:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        MymRNAs[i] = (char *)malloc(sizeof(char)*(l+1));
                                                                ˜ ˜^˜
getStates.cpp:150:51: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                char **MymiRNAs = (char **)malloc(sizeof(char*)*A_cnt);
                                                               ˜^˜˜˜˜
getStates.cpp:154:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        MymiRNAs[i] = (char *)malloc(sizeof(char)*(l+1));
                                                                 ˜ ˜^˜
getStates.cpp:166:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                init_T[c] = (int*) R_alloc(T_cnt, sizeof(int));
                                                   ˜˜˜˜˜˜˜ ^˜˜˜˜
getStates.cpp:172:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                char **MyTFs = (char **)malloc(sizeof(char*)*T_cnt);
                                                            ˜^˜˜˜˜
getStates.cpp:176:45: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        MyTFs[i] = (char *)malloc(sizeof(char)*(l+1));
                                                              ˜ ˜^˜
getStates.cpp:195:45: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        A[c] = (double**) malloc(sizeof(double*)*A_cnt);
                                                                ˜^˜˜˜˜
getStates.cpp:204:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                A[c][i] = (double*) malloc(sizeof(double)*nreps);
                                                                         ˜^˜˜˜˜
getStates.cpp:222:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                O[c] = (double**) malloc(sizeof(double*)*O_cnt);
                                                        ˜^˜˜˜˜
getStates.cpp:231:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        O[c][i] = (double*) malloc(sizeof(double)*nreps);
                                                                 ˜^˜˜˜˜
getStates.cpp:253:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        Otf[c] = (double**) malloc(sizeof(double*)*nTFexpr);
                                                                  ˜^˜˜˜˜˜˜
getStates.cpp:262:49: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                Otf[c][i] = (double*) malloc(sizeof(double)*nreps);
                                                                           ˜^˜˜˜˜
getStates.cpp:276:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                alpha_i0TF = (double *)malloc(sizeof(double)*nTFexpr);
                                                            ˜^˜˜˜˜˜˜
getStates.cpp:277:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                alpha_iTF = (double *) malloc(sizeof(double)*nTFexpr);
                                                            ˜^˜˜˜˜˜˜
getStates.cpp:278:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                TF_sigma = (double *) malloc(sizeof(double)*nTFexpr);
                                                           ˜^˜˜˜˜˜˜
getStates.cpp:322:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                O_sigma = (double *) malloc(sizeof(double)*O_cnt);
                                                          ˜^˜˜˜˜
getStates.cpp:331:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                A_sigma = (double *) malloc(sizeof(double)*A_cnt);
                                                          ˜^˜˜˜˜
getStates.cpp:339:45: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                O_mu[c] = (double *)malloc(sizeof(double)*O_cnt);
                                                         ˜^˜˜˜˜
getStates.cpp:228:12: warning: variable 'nreps' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        else if(c == 1) {
                                ^˜˜˜˜˜
getStates.cpp:231:46: note: uninitialized use occurs here
                        O[c][i] = (double*) malloc(sizeof(double)*nreps);
                                                                  ^˜˜˜˜
getStates.cpp:228:9: note: remove the 'if' if its condition is always true
                        else if(c == 1) {
                             ^˜˜˜˜˜˜˜˜˜˜
getStates.cpp:224:13: note: initialize the variable 'nreps' to silence this warning
                        int nreps;
                                 ^
                                  = 0
getStates.cpp:259:13: warning: variable 'nreps' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                                else if(c == 1) {
                                        ^˜˜˜˜˜
getStates.cpp:262:49: note: uninitialized use occurs here
                                Otf[c][i] = (double*) malloc(sizeof(double)*nreps);
                                                                            ^˜˜˜˜
getStates.cpp:259:10: note: remove the 'if' if its condition is always true
                                else if(c == 1) {
                                     ^˜˜˜˜˜˜˜˜˜˜
getStates.cpp:255:14: note: initialize the variable 'nreps' to silence this warning
                                int nreps;
                                         ^
                                          = 0
getStates.cpp:201:13: warning: variable 'nreps' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                                else if(c == 1) {
                                        ^˜˜˜˜˜
getStates.cpp:204:47: note: uninitialized use occurs here
                                A[c][i] = (double*) malloc(sizeof(double)*nreps);
                                                                          ^˜˜˜˜
getStates.cpp:201:10: note: remove the 'if' if its condition is always true
                                else if(c == 1) {
                                     ^˜˜˜˜˜˜˜˜˜˜
getStates.cpp:197:14: note: initialize the variable 'nreps' to silence this warning
                                int nreps;
                                         ^
                                          = 0
30 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 birta.so BayesNetwork.o BayesNetworkNC.o getStates.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/birta.Rcheck/birta/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 (birta)

birta.Rcheck/birta-Ex.timings:

nameusersystemelapsed
birta.run4.0790.0674.213
get_potential_swaps0.0130.0020.015
limmaAnalysis0.1240.0140.143
plotConvergence4.2050.0604.330