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BUILD report for rTANDEM on celaya2

This page was generated on 2020-01-16 13:36:08 -0500 (Thu, 16 Jan 2020).

Package 1482/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rTANDEM 1.27.0
Frederic Fournier
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/rTANDEM
Branch: master
Last Commit: e769e6a
Last Changed Date: 2019-10-29 13:36:28 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  ERROR [ ERROR ] skipped  skipped 

Summary

Package: rTANDEM
Version: 1.27.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data rTANDEM
StartedAt: 2020-01-15 21:00:03 -0500 (Wed, 15 Jan 2020)
EndedAt: 2020-01-15 21:05:43 -0500 (Wed, 15 Jan 2020)
EllapsedTime: 339.9 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data rTANDEM
###
##############################################################################
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* checking for file ‘rTANDEM/DESCRIPTION’ ... OK
* preparing ‘rTANDEM’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘rTANDEM’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c PTMTreeSearch.cpp -o PTMTreeSearch.o
In file included from PTMTreeSearch.cpp:14:
In file included from ./PTMTreeSearch.h:16:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
In file included from PTMTreeSearch.cpp:16:
In file included from ./mscore.h:146:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pOut;
                ^
                      []
./mmotif.h:295:16: note: allocated with 'new[]' here
                char *pOut = new char[256];
                             ^
PTMTreeSearch.cpp:382:12: warning: unused variable 'dMaxExpect' [-Wunused-variable]
    double dMaxExpect = atof(strValue.c_str());
           ^
PTMTreeSearch.cpp:402:54: warning: array subscript is of type 'char' [-Wchar-subscripts]
          for (unsigned int k = 1; k < m_vmodModificationsDB[itAa->m_cRes].size(); k++){
                                                            ^~~~~~~~~~~~~
PTMTreeSearch.cpp:403:21: warning: array subscript is of type 'char' [-Wchar-subscripts]
            if (floor((mods[itAa->m_cRes][k])*10000) == iModSize){
                           ^~~~~~~~~~~~~
PTMTreeSearch.cpp:405:24: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_vmodModificationsDB[itAa->m_cRes][k].m_uiCount++;
                                     ^~~~~~~~~~~~~
PTMTreeSearch.cpp:406:28: warning: array subscript is of type 'char' [-Wchar-subscripts]
                if (m_vmodModificationsDB[itAa->m_cRes][k].m_dTarget < itAa->m_fPval-1.0)
                                         ^~~~~~~~~~~~~
PTMTreeSearch.cpp:407:26: warning: array subscript is of type 'char' [-Wchar-subscripts]
                  m_vmodModificationsDB[itAa->m_cRes][k].m_dTarget = itAa->m_fPval-1.0;
                                       ^~~~~~~~~~~~~
PTMTreeSearch.cpp:408:28: warning: array subscript is of type 'char' [-Wchar-subscripts]
                if (m_vmodModificationsDB[itAa->m_cRes][k].m_dTargetEval > expect)
                                         ^~~~~~~~~~~~~
PTMTreeSearch.cpp:409:26: warning: array subscript is of type 'char' [-Wchar-subscripts]
                  m_vmodModificationsDB[itAa->m_cRes][k].m_dTargetEval = expect;
                                       ^~~~~~~~~~~~~
PTMTreeSearch.cpp:54:10: warning: unused variable 'tActiveNow' [-Wunused-variable]
  size_t tActiveNow = 0;
         ^
PTMTreeSearch.cpp:380:10: warning: unused variable 'dMaxExpect' [-Wunused-variable]
  double dMaxExpect = 0.1;
         ^
PTMTreeSearch.cpp:751:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
          m_vmodModificationsDB[resid].push_back(mod);
                               ^~~~~~
PTMTreeSearch.cpp:875:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_vmodModificationsDB[resid].push_back(mod);
                             ^~~~~~
PTMTreeSearch.cpp:1018:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_vmodModificationsDB[resid].push_back(mod);
                             ^~~~~~
PTMTreeSearch.cpp:1170:28: warning: array subscript is of type 'char' [-Wchar-subscripts]
      m_vmodModificationsDB[resid].push_back(mod);
                           ^~~~~~
PTMTreeSearch.cpp:1156:10: warning: unused variable 'pos' [-Wunused-variable]
  size_t pos = 0;
         ^
23 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c PTMTreeSearchScore.cpp -o PTMTreeSearchScore.o
In file included from PTMTreeSearchScore.cpp:13:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
In file included from PTMTreeSearchScore.cpp:14:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pOut;
                ^
                      []
./mmotif.h:295:16: note: allocated with 'new[]' here
                char *pOut = new char[256];
                             ^
In file included from PTMTreeSearchScore.cpp:20:
./stack_ptmtreesearch.h:88:24: error: no template named 'stack'
        bool operator==(const stack<_Ty, _Container>& _Left,
                              ^
./stack_ptmtreesearch.h:89:9: error: no template named 'stack'
                const stack<_Ty, _Container>& _Right)
                      ^
./stack_ptmtreesearch.h:96:24: error: no template named 'stack'
        bool operator!=(const stack<_Ty, _Container>& _Left,
                              ^
./stack_ptmtreesearch.h:97:9: error: no template named 'stack'
                const stack<_Ty, _Container>& _Right)
                      ^
./stack_ptmtreesearch.h:104:23: error: no template named 'stack'
        bool operator<(const stack<_Ty, _Container>& _Left,
                             ^
./stack_ptmtreesearch.h:105:9: error: no template named 'stack'
                const stack<_Ty, _Container>& _Right)
                      ^
./stack_ptmtreesearch.h:112:23: error: no template named 'stack'
        bool operator>(const stack<_Ty, _Container>& _Left,
                             ^
./stack_ptmtreesearch.h:113:9: error: no template named 'stack'
                const stack<_Ty, _Container>& _Right)
                      ^
./stack_ptmtreesearch.h:120:24: error: no template named 'stack'
        bool operator<=(const stack<_Ty, _Container>& _Left,
                              ^
./stack_ptmtreesearch.h:121:9: error: no template named 'stack'
                const stack<_Ty, _Container>& _Right)
                      ^
./stack_ptmtreesearch.h:128:24: error: no template named 'stack'
        bool operator>=(const stack<_Ty, _Container>& _Left,
                              ^
./stack_ptmtreesearch.h:129:9: error: no template named 'stack'
                const stack<_Ty, _Container>& _Right)
                      ^
PTMTreeSearchScore.cpp:329:3: error: reference to 'stack' is ambiguous
                stack <PTMState, vector<PTMState> > PTMStateDeque;
                ^
./stack_ptmtreesearch.h:21:8: note: candidate found by name lookup is 'stack'
        class stack
              ^
/usr/local/clang8/bin/../include/c++/v1/stack:113:28: note: candidate found by name lookup is 'std::__1::stack'
class _LIBCPP_TEMPLATE_VIS stack
                           ^
PTMTreeSearchScore.cpp:339:3: error: use of undeclared identifier 'PTMStateDeque'
                PTMStateDeque.push(root);
                ^
PTMTreeSearchScore.cpp:345:11: error: use of undeclared identifier 'PTMStateDeque'
                while (!PTMStateDeque.empty()){
                        ^
PTMTreeSearchScore.cpp:347:12: error: use of undeclared identifier 'PTMStateDeque'
                        state = PTMStateDeque.access_top();
                                ^
PTMTreeSearchScore.cpp:356:6: error: use of undeclared identifier 'PTMStateDeque'
                                        PTMStateDeque.pop();
                                        ^
PTMTreeSearchScore.cpp:363:5: error: use of undeclared identifier 'PTMStateDeque'
                                PTMStateDeque.pop();
                                ^
PTMTreeSearchScore.cpp:369:19: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        dPTM = m_pdMods[m_pSeq[uiLevel]][uiModIt];
                                       ^~~~~~~~~~~~~~~~
PTMTreeSearchScore.cpp:373:31: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){ //this was the last modification, so delete this state
                                                          ^~~~~~~~~~~~~~~~
PTMTreeSearchScore.cpp:375:6: error: use of undeclared identifier 'PTMStateDeque'
                                        PTMStateDeque.pop();
                                        ^
PTMTreeSearchScore.cpp:528:31: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){
                                                          ^~~~~~~~~~~~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
11 warnings and 20 errors generated.
make: *** [PTMTreeSearchScore.o] Error 1
ERROR: compilation failed for package ‘rTANDEM’
* removing ‘/private/tmp/Rtmp2ZR2Ei/Rinst1182a64aa2c39/rTANDEM’
      -----------------------------------
ERROR: package installation failed