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Boost : |
Subject: Re: [boost] Genetics library - advice needed.
From: Paul A. Bristow (pbristow_at_[hidden])
Date: 2015-06-15 11:36:49
> -----Original Message-----
> From: Boost [mailto:boost-bounces_at_[hidden]] On Behalf Of Andy Thomason
> Sent: 04 June 2015 15:11
> To: boost_at_[hidden]
> Subject: [boost] Genetics library - advice needed.
Hi Andy
As promised, I have started to look at your proposed library.
The actual stuff looks excellent (though I am ignorant about the field of genetics), but there are a
lot of things needed to get it running under bjam/b2 and to generate the Quickbook docs.
I'll have a go at knocking it (mainly docs) into shape so you have a 'known-working' (if not
'known-good'!) state.
Then when it doesn't work, it will most likely be your configuration that is not quite right.
(And it is a pig to get going - I hate it - but when going it actually works rather nicely - and the
big thing is that it permits access to the suite of testers on lots of platforms and hardware and
compilers etc - which make portability assured).
> I am getting close to rolling out the first draft of our genetics library.
>
> https://github.com/andy-thomason/Boost.Genetics
>
>
> Don't expect it to build and run out of the box except for the unit tests and they might not wor
in 32 bit
> builds.
>
> I'd also apreciate help with the build system as getting a build on 64 bit windows is a challenge
for
> Boost.Python at present and some wisdom would go far.
I'm not a Python user, so can't help here. I use 64-bit windows VS 2013.
So here goes, noting 'features' as I hit / spot them.
I started by doing
I:\modular-boost\libs>git clone https://github.com/andy-thomason/Boost.Genetics.git
Cloning into 'Boost.Genetics'...
I:\modular-boost\libs>cd ./Boost.Genetics
Now file and folder names MUST be all lower case (and conventionally do not here include Boost.,
so I'd change to just /genetics
packed_test.cpp
packed_test.cpp(233) : error C3861: 'BOOST_MESSAGE': identifier not found
packed_test.cpp(239) : error C3861: 'BOOST_MESSAGE': identifier not found
I think this means that you haven't got a recent version of Boost.Test.
The newest version is in the Boost develop branch, so you should probably update and rebuild the
testing tool.
See
http://raffienficiaud.github.io/test/boost_test/adv_scenarios/build_utf.html
on building a library version
(if this is too much hassle, try using the header only /included/ version first - it is just a bit
slower to run)
The very much improved manual is (for now) at
http://raffienficiaud.github.io/test/index.html
http://raffienficiaud.github.io/test/boost_test/utf_reference/testout_reference/test_output_macro_me
ssage.html
http://raffienficiaud.github.io/test/boost_test/test_output/test_output_macro_message.html
noting
"Important
Messages generated by this tool do not appear in test log output with default value of the active
log level threshold. For these messages to appear the active log level threshold has to be set to a
value below or equal to "message"."
I changed all 'BOOST_MESSAGE' to 'BOOST_TEST_MESSAGE' and it compiled
The actual run ended thus
====== BEGIN OUTPUT ======
Running 9 test cases...
packed_test.cpp(250): error: in "rev_comp_test": check rev_comp(b) == "TGTGTGTTNCA" has failed
*** 1 failure is detected in the test module "Genetics"
Perhaps you'd like to comment on this first?
While I look at getting the docs started.
Paul
PS
http://www.boost.org/build/doc/html/bbv2/overview/configuration.html
"You can use the --debug-configuration option to find which configuration files are actually
loaded."
You *will* need to use this to get the b2 beast to tell you anything helpful and get configuration
right.
PPS Trying to us gcc didn't go well, but I suspect a configuration fault,
do I need --std=c++11?? or gnu++11
causing this
..\..\../boost/genetics/utils.hpp:284:19: error: 'nullptr' was not declared in this scope
dat = nullptr;
(nullptr was always a daft idea...)
in full below
I:\modular-boost\libs\Boost.Genetics\test>b2 --toolset=gcc
Performing configuration checks
- 32-bit : no (cached)
- 64-bit : yes (cached) <<<<<<<<<<<<<<<< note 64-bit used here
- arm : no (cached)
- mips1 : no (cached)
- power : no (cached)
- sparc : no (cached)
- x86 : yes (cached)
- symlinks supported : yes (cached)
...patience...
...patience...
...found 2597 targets...
...updating 37 targets...
common.mkdir ..\..\..\bin.v2\libs\Boost.Genetics\test\packed_test.test\gcc-mingw-4.8.1
common.mkdir ..\..\..\bin.v2\libs\Boost.Genetics\test\packed_test.test\gcc-mingw-4.8.1\debug
gcc.compile.c++ ..\..\..\bin.v2\libs\Boost.Genetics\test\packed_test.test\gcc-mingw-4.8.1\debug\pac
ed_test.o
In file included from packed_test.cpp:9:0:
..\..\../boost/genetics/utils.hpp:201:13: warning: identifier 'nullptr' is a keyword in C++11 [-Wc+
0x-compat]
if (end != nullptr && aptr + size <= end) {
^
..\..\../boost/genetics/utils.hpp: In member function 'void boost::genetics::writer::write(const Ty
e*, size_t, size_t)':
..\..\../boost/genetics/utils.hpp:201:24: error: 'nullptr' was not declared in this scope
if (end != nullptr && aptr + size <= end) {
^
..\..\../boost/genetics/utils.hpp: In constructor 'boost::genetics::mapped_vector<Type>::mapped_vec
or()':
..\..\../boost/genetics/utils.hpp:284:19: error: 'nullptr' was not declared in this scope
dat = nullptr;
^
In file included from packed_test.cpp:10:0:
..\..\../boost/genetics/dna_string.hpp: At global scope:
..\..\../boost/genetics/dna_string.hpp:339:19: error: declaration of 'class WordType'
template <class WordType, class ArrayType>
^
In file included from packed_test.cpp:10:0:
..\..\../boost/genetics/dna_string.hpp:21:14: error: shadows template parm 'class WordType'
template<class WordType, class ArrayType>
^
In file included from packed_test.cpp:10:0:
..\..\../boost/genetics/dna_string.hpp:339:35: error: declaration of 'class ArrayType'
template <class WordType, class ArrayType>
^
In file included from packed_test.cpp:10:0:
..\..\../boost/genetics/dna_string.hpp:21:30: error: shadows template parm 'class ArrayType'
template<class WordType, class ArrayType>
^
In file included from packed_test.cpp:10:0:
..\..\../boost/genetics/dna_string.hpp:447:5: error: explicit template specialization cannot have a
storage class
static inline int get_code<dna_string>(const dna_string &str, size_t index) {
^
In file included from packed_test.cpp:11:0:
..\..\../boost/genetics/augmented_string.hpp:124:19: error: 'basic_dna_string' is not a type
void swap(basic_dna_string &rhs) {
^
..\..\../boost/genetics/augmented_string.hpp: In member function 'void boost::genetics::basic_augme
ted_string<WordType, ParentType, IndexArrayType, RleArrayType>::swap(int&)':
..\..\../boost/genetics/augmented_string.hpp:126:28: error: request for member 'index' in 'rhs', wh
ch is of non-class type 'int'
index.swap(rhs.index);
^
..\..\../boost/genetics/augmented_string.hpp:127:26: error: request for member 'rle' in 'rhs', whic
is of non-class type 'int'
rle.swap(rhs.rle);
^
..\..\../boost/genetics/augmented_string.hpp: At global scope:
..\..\../boost/genetics/augmented_string.hpp:175:5: error: explicit template specialization cannot
ave a storage class
static inline int get_code<augmented_string>(const augmented_string &str, size_t index) {
^
In file included from packed_test.cpp:12:0:
..\..\../boost/genetics/two_stage_index.hpp:30:65: error: expected ',' or '...' before '&&' token
basic_two_stage_index &operator =(basic_two_stage_index &&rhs) {
^
In file included from packed_test.cpp:12:0:
..\..\../boost/genetics/two_stage_index.hpp:285:18: error: explicit specialization in non-namespace
scope 'class boost::genetics::basic_two_stage_index<StringType, IndexArrayType, AddrArrayType, Writ
ble>'
template<>
^
..\..\../boost/genetics/two_stage_index.hpp:286:33: error: template-id 'reindex_impl<true>' in decl
ration of primary template
void reindex_impl<true>() {
^
In file included from packed_test.cpp:12:0:
..\..\../boost/genetics/two_stage_index.hpp: In constructor 'boost::genetics::basic_two_stage_index
StringType, IndexArrayType, AddrArrayType, Writable>::basic_two_stage_index()':
..\..\../boost/genetics/two_stage_index.hpp:21:20: error: 'nullptr' was not declared in this scope
) : string(nullptr), num_indexed_chars(0) {
^
..\..\../boost/genetics/two_stage_index.hpp: In member function 'boost::genetics::basic_two_stage_i
dex<StringType, IndexArrayType, AddrArrayType, Writable>& boost::genetics::basic_two_stage_index<St
ingType, IndexArrayType, AddrArrayType, Writable>::operator=(boost::genetics::basic_two_stage_index
StringType, IndexArrayType, AddrArrayType, Writable>)':
..\..\../boost/genetics/two_stage_index.hpp:31:22: error: 'rhs' was not declared in this scope
string = rhs.string;
^
..\..\../boost/genetics/two_stage_index.hpp:32:21: error: 'move' is not a member of 'std'
index = std::move(rhs.index);
^
..\..\../boost/genetics/two_stage_index.hpp:33:20: error: 'move' is not a member of 'std'
addr = std::move(rhs.addr);
^
In file included from packed_test.cpp:9:0:
..\..\../boost/genetics/utils.hpp: In instantiation of 'Type* boost::genetics::mapper::map(size_t,
ize_t) [with Type = long long unsigned int; size_t = long long unsigned int]':
..\..\../boost/genetics/utils.hpp:249:54: required from here
..\..\../boost/genetics/utils.hpp:257:108: error: no matching function for call to 'std::exception:
exception(const char [57])'
if (ptr > end) throw(std::exception("mapped file: overflow reading vector (check file
ormat)"));
^
..\..\../boost/genetics/utils.hpp:257:108: note: candidates are:
In file included from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64
w64-mingw32\4.8.1\include\c++\ios:39:0,
from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64
w64-mingw32\4.8.1\include\c++\istream:38,
from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64
w64-mingw32\4.8.1\include\c++\fstream:38,
from packed_test.cpp:2:
c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc
ude\c++\exception:63:5: note: std::exception::exception()
exception() _GLIBCXX_USE_NOEXCEPT { }
^
c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc
ude\c++\exception:63:5: note: candidate expects 0 arguments, 1 provided
c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc
ude\c++\exception:60:9: note: std::exception::exception(const std::exception&)
class exception
^
c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc
ude\c++\exception:60:9: note: no known conversion for argument 1 from 'const char [57]' to 'const
std::exception&'
In file included from packed_test.cpp:9:0:
..\..\../boost/genetics/utils.hpp: In instantiation of 'void boost::genetics::basic_dna_string<Word
ype, ArrayType>::write_binary(boost::genetics::writer&) const [with WordType = long long unsigned i
t; ArrayType = std::vector<long long unsigned int>]':
packed_test.cpp:341:28: required from here
..\..\../boost/genetics/utils.hpp:212:61: error: dependent-name 'VecType:: value_type' is parsed as
a non-type, but instantiation yields a type
void write(const VecType &vec, size_t align = sizeof(VecType::value_type)) {
^
..\..\../boost/genetics/utils.hpp:212:61: note: say 'typename VecType:: value_type' if a type is me
nt
In file included from packed_test.cpp:10:0:
..\..\../boost/genetics/dna_string.hpp:406:13: note: when instantiating default argument for call
to void boost::genetics::writer::write(const VecType&, size_t) [with VecType = std::vector<long lon
unsigned int>; size_t = long long unsigned int]
wr.write(values);
^
In file included from packed_test.cpp:9:0:
..\..\../boost/genetics/utils.hpp: In instantiation of 'void boost::genetics::basic_augmented_strin
<WordType, ParentType, IndexArrayType, RleArrayType>::write_binary(boost::genetics::writer&) const
with WordType = long long unsigned int; ParentType = boost::genetics::basic_dna_string<long long un
igned int, std::vector<long long unsigned int> >; IndexArrayType = std::vector<unsigned int>; RleAr
ayType = std::vector<unsigned int>]':
packed_test.cpp:360:28: required from here
..\..\../boost/genetics/utils.hpp:212:61: error: dependent-name 'VecType:: value_type' is parsed as
a non-type, but instantiation yields a type
void write(const VecType &vec, size_t align = sizeof(VecType::value_type)) {
^
..\..\../boost/genetics/utils.hpp:212:61: note: say 'typename VecType:: value_type' if a type is me
nt
In file included from packed_test.cpp:11:0:
..\..\../boost/genetics/augmented_string.hpp:132:13: note: when instantiating default argument fo
call to void boost::genetics::writer::write(const VecType&, size_t) [with VecType = std::vector<un
igned int>; size_t = long long unsigned int]
wr.write(index);
^
In file included from packed_test.cpp:9:0:
..\..\../boost/genetics/utils.hpp:212:61: error: dependent-name 'VecType:: value_type' is parsed as
a non-type, but instantiation yields a type
void write(const VecType &vec, size_t align = sizeof(VecType::value_type)) {
^
..\..\../boost/genetics/utils.hpp:212:61: note: say 'typename VecType:: value_type' if a type is me
nt
In file included from packed_test.cpp:11:0:
..\..\../boost/genetics/augmented_string.hpp:133:13: note: when instantiating default argument fo
call to void boost::genetics::writer::write(const VecType&, size_t) [with VecType = std::vector<un
igned int>; size_t = long long unsigned int]
wr.write(rle);
^
In file included from packed_test.cpp:9:0:
..\..\../boost/genetics/utils.hpp: In instantiation of 'void boost::genetics::basic_two_stage_index
StringType, IndexArrayType, AddrArrayType, Writable>::write_binary(boost::genetics::writer&) const
with StringType = boost::genetics::basic_augmented_string<long long unsigned int, boost::genetics::
asic_dna_string<long long unsigned int, std::vector<long long unsigned int> >, std::vector<unsigned
int>, std::vector<unsigned int> >; IndexArrayType = std::vector<unsigned int>; AddrArrayType = std:
vector<unsigned int>; bool Writable = true]':
packed_test.cpp:376:28: required from here
..\..\../boost/genetics/utils.hpp:212:61: error: dependent-name 'VecType:: value_type' is parsed as
a non-type, but instantiation yields a type
void write(const VecType &vec, size_t align = sizeof(VecType::value_type)) {
^
..\..\../boost/genetics/utils.hpp:212:61: note: say 'typename VecType:: value_type' if a type is me
nt
In file included from packed_test.cpp:12:0:
..\..\../boost/genetics/two_stage_index.hpp:26:13: note: when instantiating default argument for
all to void boost::genetics::writer::write(const VecType&, size_t) [with VecType = std::vector<unsi
ned int>; size_t = long long unsigned int]
wr.write(index);
^
In file included from packed_test.cpp:9:0:
..\..\../boost/genetics/utils.hpp:212:61: error: dependent-name 'VecType:: value_type' is parsed as
a non-type, but instantiation yields a type
void write(const VecType &vec, size_t align = sizeof(VecType::value_type)) {
^
..\..\../boost/genetics/utils.hpp:212:61: note: say 'typename VecType:: value_type' if a type is me
nt
In file included from packed_test.cpp:12:0:
..\..\../boost/genetics/two_stage_index.hpp:27:13: note: when instantiating default argument for
all to void boost::genetics::writer::write(const VecType&, size_t) [with VecType = std::vector<unsi
ned int>; size_t = long long unsigned int]
wr.write(addr);
^
In file included from packed_test.cpp:12:0:
..\..\../boost/genetics/two_stage_index.hpp: In instantiation of 'void boost::genetics::basic_two_s
age_index<StringType, IndexArrayType, AddrArrayType, Writable>::iterator::find_next(bool) [with Str
ngType = boost::genetics::basic_augmented_string<long long unsigned int, boost::genetics::basic_dna
string<long long unsigned int, std::vector<long long unsigned int> >, std::vector<unsigned int>, st
::vector<unsigned int> >; IndexArrayType = std::vector<unsigned int>; AddrArrayType = std::vector<u
signed int>; bool Writable = true]':
..\..\../boost/genetics/two_stage_index.hpp:138:32: required from 'boost::genetics::basic_two_sta
e_index<StringType, IndexArrayType, AddrArrayType, Writable>::iterator& boost::genetics::basic_two_
tage_index<StringType, IndexArrayType, AddrArrayType, Writable>::iterator::operator++() [with Strin
Type = boost::genetics::basic_augmented_string<long long unsigned int, boost::genetics::basic_dna_s
ring<long long unsigned int, std::vector<long long unsigned int> >, std::vector<unsigned int>, std:
vector<unsigned int> >; IndexArrayType = std::vector<unsigned int>; AddrArrayType = std::vector<uns
gned int>; bool Writable = true]'
packed_test.cpp:308:9: required from here
..\..\../boost/genetics/two_stage_index.hpp:170:36: warning: unused variable 'erc' [-Wunused-variab
e]
size_t erc = 0;
^
In file included from packed_test.cpp:9:0:
..\..\../boost/genetics/utils.hpp: In instantiation of 'boost::genetics::mapped_vector<Type>::mappe
_vector(boost::genetics::mapper&) [with Type = long long unsigned int]':
..\..\../boost/genetics/dna_string.hpp:81:23: required from 'boost::genetics::basic_dna_string<Wo
dType, ArrayType>::basic_dna_string(Mapper&, typename Mapper::is_mapper*) [with Mapper = boost::gen
tics::mapper; WordType = long long unsigned int; ArrayType = boost::genetics::mapped_vector<long lo
g unsigned int>; typename Mapper::is_mapper = void]'
packed_test.cpp:352:34: required from here
..\..\../boost/genetics/utils.hpp:291:92: error: no matching function for call to 'std::exception::
xception(const char [52])'
throw(std::exception("mapped file: item size mismatch (check file format)"));
^
..\..\../boost/genetics/utils.hpp:291:92: note: candidates are:
In file included from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64
w64-mingw32\4.8.1\include\c++\ios:39:0,
from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64
w64-mingw32\4.8.1\include\c++\istream:38,
from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64
w64-mingw32\4.8.1\include\c++\fstream:38,
from packed_test.cpp:2:
c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc
ude\c++\exception:63:5: note: std::exception::exception()
exception() _GLIBCXX_USE_NOEXCEPT { }
^
c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc
ude\c++\exception:63:5: note: candidate expects 0 arguments, 1 provided
c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc
ude\c++\exception:60:9: note: std::exception::exception(const std::exception&)
class exception
^
c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc
ude\c++\exception:60:9: note: no known conversion for argument 1 from 'const char [52]' to 'const
std::exception&'
In file included from packed_test.cpp:9:0:
..\..\../boost/genetics/utils.hpp: In instantiation of 'boost::genetics::mapped_vector<Type>::mappe
_vector(boost::genetics::mapper&) [with Type = unsigned int]':
..\..\../boost/genetics/augmented_string.hpp:47:20: required from 'boost::genetics::basic_augment
d_string<WordType, ParentType, IndexArrayType, RleArrayType>::basic_augmented_string(Mapper&, typen
me Mapper::is_mapper*) [with Mapper = boost::genetics::mapper; WordType = long long unsigned int; P
rentType = boost::genetics::basic_dna_string<long long unsigned int, boost::genetics::mapped_vector
long long unsigned int> >; IndexArrayType = boost::genetics::mapped_vector<unsigned int>; RleArrayT
pe = boost::genetics::mapped_vector<unsigned int>; typename Mapper::is_mapper = void]'
packed_test.cpp:366:40: required from here
..\..\../boost/genetics/utils.hpp:291:92: error: no matching function for call to 'std::exception::
xception(const char [52])'
throw(std::exception("mapped file: item size mismatch (check file format)"));
^
..\..\../boost/genetics/utils.hpp:291:92: note: candidates are:
In file included from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64
w64-mingw32\4.8.1\include\c++\ios:39:0,
from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64
w64-mingw32\4.8.1\include\c++\istream:38,
from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64
w64-mingw32\4.8.1\include\c++\fstream:38,
from packed_test.cpp:2:
c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc
ude\c++\exception:63:5: note: std::exception::exception()
exception() _GLIBCXX_USE_NOEXCEPT { }
^
c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc
ude\c++\exception:63:5: note: candidate expects 0 arguments, 1 provided
c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc
ude\c++\exception:60:9: note: std::exception::exception(const std::exception&)
class exception
^
c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc
ude\c++\exception:60:9: note: no known conversion for argument 1 from 'const char [52]' to 'const
std::exception&'
In file included from packed_test.cpp:12:0:
..\..\../boost/genetics/two_stage_index.hpp: In instantiation of 'void boost::genetics::basic_two_s
age_index<StringType, IndexArrayType, AddrArrayType, Writable>::iterator::find_next(bool) [with Str
ngType = boost::genetics::basic_augmented_string<long long unsigned int, boost::genetics::basic_dna
string<long long unsigned int, boost::genetics::mapped_vector<long long unsigned int> >, boost::gen
tics::mapped_vector<unsigned int>, boost::genetics::mapped_vector<unsigned int> >; IndexArrayType =
boost::genetics::mapped_vector<unsigned int>; AddrArrayType = boost::genetics::mapped_vector<unsign
d int>; bool Writable = false]':
..\..\../boost/genetics/two_stage_index.hpp:143:32: required from 'boost::genetics::basic_two_sta
e_index<StringType, IndexArrayType, AddrArrayType, Writable>::iterator& boost::genetics::basic_two_
tage_index<StringType, IndexArrayType, AddrArrayType, Writable>::iterator::operator++(int) [with St
ingType = boost::genetics::basic_augmented_string<long long unsigned int, boost::genetics::basic_dn
_string<long long unsigned int, boost::genetics::mapped_vector<long long unsigned int> >, boost::ge
etics::mapped_vector<unsigned int>, boost::genetics::mapped_vector<unsigned int> >; IndexArrayType
boost::genetics::mapped_vector<unsigned int>; AddrArrayType = boost::genetics::mapped_vector<unsig
ed int>; bool Writable = false]'
packed_test.cpp:389:10: required from here
..\..\../boost/genetics/two_stage_index.hpp:170:36: warning: unused variable 'erc' [-Wunused-variab
e]
size_t erc = 0;
^
..\..\../boost/genetics/two_stage_index.hpp: In instantiation of 'void boost::genetics::basic_two_s
age_index<StringType, IndexArrayType, AddrArrayType, Writable>::reindex_impl() [with bool B = true;
StringType = boost::genetics::basic_augmented_string<long long unsigned int, boost::genetics::basic
dna_string<long long unsigned int, std::vector<long long unsigned int> >, std::vector<unsigned int>
std::vector<unsigned int> >; IndexArrayType = std::vector<unsigned int>; AddrArrayType = std::vect
r<unsigned int>; bool Writable = true]':
..\..\../boost/genetics/two_stage_index.hpp:59:25: required from 'void boost::genetics::basic_two
stage_index<StringType, IndexArrayType, AddrArrayType, Writable>::reindex() [with StringType = boos
::genetics::basic_augmented_string<long long unsigned int, boost::genetics::basic_dna_string<long l
ng unsigned int, std::vector<long long unsigned int> >, std::vector<unsigned int>, std::vector<unsi
ned int> >; IndexArrayType = std::vector<unsigned int>; AddrArrayType = std::vector<unsigned int>;
ool Writable = true]'
..\..\../boost/genetics/two_stage_index.hpp:55:21: required from 'boost::genetics::basic_two_stag
_index<StringType, IndexArrayType, AddrArrayType, Writable>::basic_two_stage_index(StringType&, siz
_t) [with StringType = boost::genetics::basic_augmented_string<long long unsigned int, boost::genet
cs::basic_dna_string<long long unsigned int, std::vector<long long unsigned int> >, std::vector<uns
gned int>, std::vector<unsigned int> >; IndexArrayType = std::vector<unsigned int>; AddrArrayType =
std::vector<unsigned int>; bool Writable = true; size_t = long long unsigned int]'
packed_test.cpp:301:30: required from here
..\..\../boost/genetics/two_stage_index.hpp:281:102: error: no matching function for call to 'std::
xception::exception(const char [65])'
throw (std::exception("two_stage_index::reindex(): attempt to reindex a read-only inde
"));
^
..\..\../boost/genetics/two_stage_index.hpp:281:102: note: candidates are:
In file included from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64
w64-mingw32\4.8.1\include\c++\ios:39:0,
from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64
w64-mingw32\4.8.1\include\c++\istream:38,
from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64
w64-mingw32\4.8.1\include\c++\fstream:38,
from packed_test.cpp:2:
c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc
ude\c++\exception:63:5: note: std::exception::exception()
exception() _GLIBCXX_USE_NOEXCEPT { }
^
c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc
ude\c++\exception:63:5: note: candidate expects 0 arguments, 1 provided
c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc
ude\c++\exception:60:9: note: std::exception::exception(const std::exception&)
class exception
^
c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc
ude\c++\exception:60:9: note: no known conversion for argument 1 from 'const char [65]' to 'const
std::exception&'
"C:\Program Files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\bin\g++.exe" -ftemplate-depth-
28 -O0 -fno-inline -Wall -g -m64 -DBOOST_ALL_NO_LIB=1 -DBOOST_CHRONO_STATIC_LINK=1 -DBOOST_CHRONO_
HREAD_DISABLED -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_SYSTEM_STATIC_LINK=1 -DBOOST_TEST_NO_AUTO_LINK=
-DBOOST_TIMER_STATIC_LINK=1 -I"..\..\.." -c -o "..\..\..\bin.v2\libs\Boost.Genetics\test\packed_t
st.test\gcc-mingw-4.8.1\debug\packed_test.o" "packed_test.cpp"
...failed gcc.compile.c++ ..\..\..\bin.v2\libs\Boost.Genetics\test\packed_test.test\gcc-mingw-4.8.1
debug\packed_test.o...
gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\compiler_log_form
tter.o
gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\debug.o
gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\decorator.o
gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\execution_monitor
o
gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\framework.o
gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\plain_report_form
tter.o
gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\progress_monitor.
gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\results_collector
o
gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\results_reporter.
gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\test_tools.o
gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\test_tree.o
gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\unit_test_log.o
gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\unit_test_main.o
gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\unit_test_monitor
o
gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\unit_test_paramet
rs.o
gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\xml_log_formatter
o
gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\xml_report_format
er.o
gcc.archive ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\libboost_unit_test_fr
mework-mgw48-d-1_59.a
gcc.compile.c++ ..\..\..\bin.v2\libs\timer\build\gcc-mingw-4.8.1\debug\link-static\auto_timers_cons
ruction.o
In file included from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64
w64-mingw32\4.8.1\include\stdint.h:9:0,
from ..\..\../boost/cstdint.hpp:60,
from ..\..\../boost/ratio/config.hpp:13,
from ..\..\../boost/ratio/ratio.hpp:35,
from ..\..\../boost/chrono/duration.hpp:41,
from ..\..\../boost/chrono/chrono.hpp:11,
from ..\..\../boost/timer/timer.hpp:14,
from ..\..\..\libs\timer\src\auto_timers_construction.cpp:23:
..\..\../boost/chrono/system_clocks.hpp:77:111: warning: use of C++0x long long integer constant [-
long-long]
# define BOOST_SYSTEM_CLOCK_DURATION boost::chrono::duration<boost::int_least64_t, ratio<BOOST_RAT
O_INTMAX_C(1), BOOST_RATIO_INTMAX_C(10000000)> >
^
..\..\../boost/chrono/system_clocks.hpp:77:90: note: in expansion of macro 'BOOST_RATIO_INTMAX_C'
# define BOOST_SYSTEM_CLOCK_DURATION boost::chrono::duration<boost::int_least64_t, ratio<BOOST_RAT
O_INTMAX_C(1), BOOST_RATIO_INTMAX_C(10000000)> >
^
..\..\../boost/chrono/system_clocks.hpp:130:15: note: in expansion of macro 'BOOST_SYSTEM_CLOCK_DUR
TION'
typedef BOOST_SYSTEM_CLOCK_DURATION duration;
^
..\..\../boost/chrono/system_clocks.hpp:77:136: warning: use of C++0x long long integer constant [-
long-long]
# define BOOST_SYSTEM_CLOCK_DURATION boost::chrono::duration<boost::int_least64_t, ratio<BOOST_RAT
O_INTMAX_C(1), BOOST_RATIO_INTMAX_C(10000000)> >
^
..\..\../boost/chrono/system_clocks.hpp:77:115: note: in expansion of macro 'BOOST_RATIO_INTMAX_C'
# define BOOST_SYSTEM_CLOCK_DURATION boost::chrono::duration<boost::int_least64_t, ratio<BOOST_RAT
O_INTMAX_C(1), BOOST_RATIO_INTMAX_C(10000000)> >
^
..\..\../boost/chrono/system_clocks.hpp:130:15: note: in expansion of macro 'BOOST_SYSTEM_CLOCK_DUR
TION'
typedef BOOST_SYSTEM_CLOCK_DURATION duration;
^
In file included from ..\..\..\libs\timer\src\auto_timers_construction.cpp:23:0:
..\..\../boost/timer/timer.hpp:44:43: warning: use of C++0x long long integer constant [-Wlong-long
void clear() { wall = user = system = 0LL; }
^
gcc.compile.c++ ..\..\..\bin.v2\libs\timer\build\gcc-mingw-4.8.1\debug\link-static\cpu_timer.o
In file included from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64
w64-mingw32\4.8.1\include\stdint.h:9:0,
from ..\..\../boost/cstdint.hpp:60,
from ..\..\../boost/ratio/config.hpp:13,
from ..\..\../boost/ratio/ratio.hpp:35,
from ..\..\../boost/chrono/duration.hpp:41,
from ..\..\../boost/chrono/chrono.hpp:11,
from ..\..\../boost/timer/timer.hpp:14,
from ..\..\..\libs\timer\src\cpu_timer.cpp:16:
..\..\../boost/chrono/system_clocks.hpp:77:111: warning: use of C++0x long long integer constant [-
long-long]
# define BOOST_SYSTEM_CLOCK_DURATION boost::chrono::duration<boost::int_least64_t, ratio<BOOST_RAT
O_INTMAX_C(1), BOOST_RATIO_INTMAX_C(10000000)> >
^
..\..\../boost/chrono/system_clocks.hpp:77:90: note: in expansion of macro 'BOOST_RATIO_INTMAX_C'
# define BOOST_SYSTEM_CLOCK_DURATION boost::chrono::duration<boost::int_least64_t, ratio<BOOST_RAT
O_INTMAX_C(1), BOOST_RATIO_INTMAX_C(10000000)> >
^
..\..\../boost/chrono/system_clocks.hpp:130:15: note: in expansion of macro 'BOOST_SYSTEM_CLOCK_DUR
TION'
typedef BOOST_SYSTEM_CLOCK_DURATION duration;
^
..\..\../boost/chrono/system_clocks.hpp:77:136: warning: use of C++0x long long integer constant [-
long-long]
# define BOOST_SYSTEM_CLOCK_DURATION boost::chrono::duration<boost::int_least64_t, ratio<BOOST_RAT
O_INTMAX_C(1), BOOST_RATIO_INTMAX_C(10000000)> >
^
..\..\../boost/chrono/system_clocks.hpp:77:115: note: in expansion of macro 'BOOST_RATIO_INTMAX_C'
# define BOOST_SYSTEM_CLOCK_DURATION boost::chrono::duration<boost::int_least64_t, ratio<BOOST_RAT
O_INTMAX_C(1), BOOST_RATIO_INTMAX_C(10000000)> >
^
..\..\../boost/chrono/system_clocks.hpp:130:15: note: in expansion of macro 'BOOST_SYSTEM_CLOCK_DUR
TION'
typedef BOOST_SYSTEM_CLOCK_DURATION duration;
^
In file included from ..\..\..\libs\timer\src\cpu_timer.cpp:16:0:
..\..\../boost/timer/timer.hpp:44:43: warning: use of C++0x long long integer constant [-Wlong-long
void clear() { wall = user = system = 0LL; }
^
gcc.archive ..\..\..\bin.v2\libs\timer\build\gcc-mingw-4.8.1\debug\link-static\libboost_timer-mgw48
d-1_59.a
gcc.compile.c++ ..\..\..\bin.v2\libs\chrono\build\gcc-mingw-4.8.1\debug\link-static\chrono.o
gcc.compile.c++ ..\..\..\bin.v2\libs\chrono\build\gcc-mingw-4.8.1\debug\link-static\thread_clock.o
gcc.compile.c++ ..\..\..\bin.v2\libs\chrono\build\gcc-mingw-4.8.1\debug\link-static\process_cpu_clo
ks.o
gcc.archive ..\..\..\bin.v2\libs\chrono\build\gcc-mingw-4.8.1\debug\link-static\libboost_chrono-mgw
8-d-1_59.a
gcc.compile.c++ ..\..\..\bin.v2\libs\system\build\gcc-mingw-4.8.1\debug\link-static\error_code.o
gcc.archive ..\..\..\bin.v2\libs\system\build\gcc-mingw-4.8.1\debug\link-static\libboost_system-mgw
8-d-1_59.a
...skipped <p..\..\..\bin.v2\libs\Boost.Genetics\test\packed_test.test\gcc-mingw-4.8.1\debug>packed
test.exe for lack of <p..\..\..\bin.v2\libs\Boost.Genetics\test\packed_test.test\gcc-mingw-4.8.1\de
ug>packed_test.o...
...skipped <p..\..\..\bin.v2\libs\Boost.Genetics\test\packed_test.test\gcc-mingw-4.8.1\debug>packed
test.run for lack of <p..\..\..\bin.v2\libs\Boost.Genetics\test\packed_test.test\gcc-mingw-4.8.1\de
ug>packed_test.exe...
...failed updating 1 target...
...skipped 3 targets...
...updated 33 targets...
I:\modular-boost\libs\Boost.Genetics\test>
Boost list run by bdawes at acm.org, gregod at cs.rpi.edu, cpdaniel at pacbell.net, john at johnmaddock.co.uk