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INSTALL report for rTANDEM on merida1

This page was generated on 2021-02-27 12:15:49 -0500 (Sat, 27 Feb 2021).

To the developers/maintainers of the rTANDEM package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1589/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rTANDEM 1.30.0
Frederic Fournier
Snapshot Date: 2021-02-26 14:50:01 -0500 (Fri, 26 Feb 2021)
URL: https://git.bioconductor.org/packages/rTANDEM
Branch: RELEASE_3_12
Last Commit: 96455bf
Last Changed Date: 2020-10-27 10:48:41 -0500 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    ERROR  
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    NA  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    NA  
merida1macOS 10.14.6 Mojave / x86_64  ERROR    ERROR  skippedskipped

Summary

Package: rTANDEM
Version: 1.30.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rTANDEM
StartedAt: 2021-02-26 16:45:29 -0500 (Fri, 26 Feb 2021)
EndedAt: 2021-02-26 16:46:12 -0500 (Fri, 26 Feb 2021)
EllapsedTime: 42.9 seconds
RetCode: 1
Status:   ERROR  

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rTANDEM
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘rTANDEM’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -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:15:
In file included from ./mrefine.h:136:
In file included from ./mplugin.h:133:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
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:380:10: warning: unused variable 'dMaxExpect' [-Wunused-variable]
  double dMaxExpect = 0.1;
         ^
PTMTreeSearch.cpp:54:10: warning: unused variable 'tActiveNow' [-Wunused-variable]
  size_t tActiveNow = 0;
         ^
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;
         ^
24 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -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:
In file included from ./mhistogram.h:134:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
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
              ^
/Library/Developer/CommandLineTools/usr/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=]
12 warnings and 20 errors generated.
make: *** [PTMTreeSearchScore.o] Error 1
ERROR: compilation failed for package ‘rTANDEM’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rTANDEM’