https://gcc.gnu.org/bugzilla/show_bug.cgi?id=60871
--- Comment #21 from Neil Kindlon <neil.kindlon at jax dot org> ---
Hi,
I regret to report that I encountered what appears to be a similar error in
gcc version 7.1.0. This is my first bug report here, so please correct me if
this information is not helpful or incomplete.
system type:
LSB Version:
:base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID: CentOS
Description: CentOS release 6.5 (Final)
Release: 6.5
Codename: Final
Linux version 2.6.32-696.18.7.el6.x86_64 (mockbu...@c1bl.rdu2.centos.org) (gcc
version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) ) #1 SMP Thu Jan 4 17:31:22 UTC
2018
gcc build options:
$ ./configure --prefix=/opt/compsci/gcc/7.1.0 --disable-multilib
Error:
$ make install
/projects/kindln/share/utils/jax-egtk/bio-pp/bpp-phyl/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp:
In constructor
‘bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(const
bpp::GeneticCode*, bpp::NucleotideSubstitutionModel*, const string&, bool)’:
/projects/kindln/share/utils/jax-egtk/bio-pp/bpp-phyl/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp:47:1:
internal compiler error: in possible_polymorphic_call_targets, at
ipa-devirt.c:1557
AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(
^
0x869deb possible_polymorphic_call_targets(tree_node*, long,
ipa_polymorphic_call_context, bool*, void**, int*)
../../gcc/ipa-devirt.c:1557
0x83cf91 possible_polymorphic_call_targets
../../gcc/ipa-utils.h:142
0x83cf91 gimple_fold_call
../../gcc/gimple-fold.c:1127
0x83cf91 fold_stmt_1
../../gcc/gimple-fold.c:1302
0xab6d3a substitute_and_fold(tree_node* (*)(tree_node*), bool
(*)(gimple_stmt_iterator*), bool)
../../gcc/tree-ssa-propagate.c:1200
0xa58b88 fini_copy_prop
../../gcc/tree-ssa-copy.c:587
0xa58b88 execute_copy_prop
../../gcc/tree-ssa-copy.c:631
0xa58b88 execute
../../gcc/tree-ssa-copy.c:669
Please submit a full bug report,
with preprocessed source if appropriate.
Please include the complete backtrace with any bug report.
See <http://gcc.gnu.org/bugs.html> for instructions.
make[2]: ***
[src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o]
Error 1
make[1]: *** [src/CMakeFiles/bpp-phyl-shared.dir/all] Error 2
make: *** [all] Error 2
In my last comment I attached the .ii.bz2 temporary file generated while
attempting to compile this.
I was attempting to build the bpp-phyl library in Bio++, which requires first
building bpp-core.I'm sorry to just paste the github sites, but there were many
files, and I'm only just starting to look at the code base.
https://github.com/BioPP/bpp-core
https://github.com/BioPP/bpp-phyl
git clone g...@github.com:BioPP/bpp-core.git
git clone g...@github.com:BioPP/bpp-phyl.git
I followed the default instructions in each for cmake and make install, and got
the error above.
This was the constructor:
AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(
const GeneticCode* gCode,
NucleotideSubstitutionModel* pmod,
const std::string& prefix,
bool paramRates) :
AbstractParameterAliasable(prefix),
AbstractWordSubstitutionModel(gCode->getSourceAlphabet(), new
CanonicalStateMap(gCode->getSourceAlphabet(), false), prefix),
hasParametrizedRates_(paramRates),
gCode_(gCode)
{
enableEigenDecomposition(true);
size_t i;
for (i = 0; i < 3; i++)
{
VSubMod_.push_back(pmod);
VnestedPrefix_.push_back(pmod->getNamespace());
}
pmod->setNamespace(prefix + "123_" + VnestedPrefix_[0]);
pmod->enableEigenDecomposition(0);
addParameters_(pmod->getParameters());
Vrate_.resize(3);
for (i = 0; i < 3; i++)
{
Vrate_[i] = 1.0 / 3;
}
if (hasParametrizedRates_)
{
// relative rates
for (i = 0; i < 2; i++)
{
addParameter_(new Parameter(prefix + "relrate" + TextTools::toString(i +
1), 1.0 / static_cast<double>(3 - i), &Parameter::PROP_CONSTRAINT_EX));
}
}
}
I hope this is helpful. If not, please let me know what other information is
required.
Thanks,
Neil
