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) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:36:08 -0500 (Thu, 16 Jan 2020).
| Package 1482/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rTANDEM 1.27.0 Frederic Fournier
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| 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 |
| Package: rTANDEM |
| Version: 1.27.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rTANDEM |
| StartedAt: 2020-01-15 18:31:18 -0500 (Wed, 15 Jan 2020) |
| EndedAt: 2020-01-15 18:31:50 -0500 (Wed, 15 Jan 2020) |
| EllapsedTime: 32.8 seconds |
| RetCode: 1 |
| Status: ERROR |
##############################################################################
##############################################################################
###
### 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++ -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 ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rTANDEM’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rTANDEM’