[Debian-med-packaging] Bug#853375: disulfinder: ftbfs with GCC-7

Tue Jan 31 09:30:51 UTC 2017

Package: src:disulfinder
Version: 1.2.11-6
Severity: normal
Tags: sid buster
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-7

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-7/g++-7, but succeeds to build with gcc-6/g++-6. The
severity of this report may be raised before the buster release.
There is no need to fix this issue in time for the stretch release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc7-20170126/disulfinder_1.2.11-6_unstable_gcc7.log
The last lines of the build log are at the end of this report.

To build with GCC 7, either set CC=gcc-7 CXX=g++-7 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-7/porting_to.html

[...]
BRNN/RNNs/StructureSearch.h:980:7: warning: unused variable 'num_nodes' [-Wunused-variable]
   int num_nodes = _toNodes.size();
       ^~~~~~~~~
In file included from BRNN/rnn_util.cpp:5:0:
BRNN/RNNs/RecursiveNN.h: In instantiation of 'void RecursiveNN<HA_Function, OA_Function, EMP>::fPropagateInput(std::vector<Node*>&, const DPAG&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent; DPAG = boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> >]':
BRNN/RNNs/RecursiveNN.h:1356:18:   required from 'void RecursiveNN<HA_Function, OA_Function, EMP>::propagateStructuredInput(std::vector<Node*>&, const std::pair<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> >, boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> > >&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent]'
BRNN/rnn_util.cpp:99:47:   required from here
BRNN/RNNs/RecursiveNN.h:1390:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     require(_n == toNodes[t]->_encodedInput.size(), "Error in input dim!");
             ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/RecursiveNN.h:1415:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    out_i!=out_end && edge_id[*out_i] < _v; ++out_i) {
BRNN/RNNs/RecursiveNN.h:1418:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=_n + edge_id[*out_i]*_m; i<_n + _m*(edge_id[*out_i] + 1); i++) {
                                     ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/RecursiveNN.h:1384:12: warning: variable 'vertex_id' set but not used [-Wunused-but-set-variable]
   VertexId vertex_id = boost::get(boost::vertex_index, sdag);
            ^~~~~~~~~
BRNN/RNNs/RecursiveNN.h: In instantiation of 'void RecursiveNN<HA_Function, OA_Function, EMP>::bPropagateInput(std::vector<Node*>&, const DPAG&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent; DPAG = boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> >]':
BRNN/RNNs/RecursiveNN.h:1359:34:   required from 'void RecursiveNN<HA_Function, OA_Function, EMP>::propagateStructuredInput(std::vector<Node*>&, const std::pair<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> >, boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> > >&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent]'
BRNN/rnn_util.cpp:99:47:   required from here
BRNN/RNNs/RecursiveNN.h:1470:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int t=0; t<toNodes.size(); t++) {
                ~^~~~~~~~~~~~~~~
BRNN/RNNs/RecursiveNN.h:1471:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     require(_n == toNodes[t]->_encodedInput.size(), "Error!");
             ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/RecursiveNN.h:1492:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    out_i!=out_end && edge_id[*out_i] < _v; ++out_i) {
BRNN/RNNs/RecursiveNN.h:1495:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=_n + edge_id[*out_i]*_m; i<_n + _m*(edge_id[*out_i] + 1); i++) {
                                     ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/RecursiveNN.h:1465:12: warning: variable 'vertex_id' set but not used [-Wunused-but-set-variable]
   VertexId vertex_id = boost::get(boost::vertex_index, sdag);
            ^~~~~~~~~
In file included from BRNN/rnn_util.cpp:6:0:
BRNN/RNNs/StructureSearch.h: In instantiation of 'float StructureSearch::RNNMeasure(const DPAG&, RNN<T1, T2, T3>*, std::vector<Node*>&, std::vector<float>&) [with T1 = TanH; T2 = Sigmoid; T3 = MGradientDescent; RNN = RecursiveNN; DPAG = boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> >]':
BRNN/RNNs/StructureSearch.h:989:11:   required from 'std::vector<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> > > StructureSearch::ConnectivityPatternSearch(RNN<T1, T2, T3>*, const std::vector<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> > >&, std::vector<float>&) [with T1 = TanH; T2 = Sigmoid; T3 = MGradientDescent; RNN = RecursiveNN]'
BRNN/rnn_util.cpp:396:65:   required from here
BRNN/RNNs/StructureSearch.h:186:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0; i<toNodes.size(); i++) {
                  ~^~~~~~~~~~~~~~~
make[2]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src'
Makefile:24: recipe for target 'disulfinder' failed
make[1]: *** [disulfinder] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: make -j64 returned exit code 2
debian/rules:12: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2