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cannot build MaikTools for perl #96

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
What steps will reproduce the problem?
1.run make in MosaikTools/perl folder

What is the expected output? What do you see instead?
Get following error msgs:

swig -c++ -perl MosaikAlignment.i
MosaikAlignment.h:231: Warning(312): Nested union not currently supported 
(ignored).
cc -fpic -c fastlz.c
g++ -fpic -c MosaikAlignment.cpp MosaikAlignment_wrap.cxx 
-I/usr/lib64/5.10.1/CORE
In file included from MosaikAlignment.cpp:12:
MosaikAlignment.h:368: error: \u2018uint64_t\u2019 does not name a type
MosaikAlignment.h: In constructor 
\u2018Mosaik::ReferenceSequence::ReferenceSequence()\u2019:
MosaikAlignment.h:381: error: class \u2018Mosaik::ReferenceSequence\u2019 does 
not have any field named \u2018NumAligned\u2019
MosaikAlignment.h: At global scope:
MosaikAlignment.h:405: error: \u2018uint64_t\u2019 does not name a type
MosaikAlignment.h:407: error: \u2018uint64_t\u2019 does not name a type
In file included from MosaikAlignment.cpp:12:
MosaikAlignment.h:441: error: \u2018uint64_t\u2019 does not name a type
MosaikAlignment.h:442: error: \u2018uint64_t\u2019 does not name a type
MosaikAlignment.h:444: error: \u2018uint64_t\u2019 does not name a type
MosaikAlignment.h:495: error: \u2018uint64_t\u2019 does not name a type
MosaikAlignment.h:497: error: \u2018uint64_t\u2019 does not name a type
MosaikAlignment.h:527: error: \u2018uint64_t\u2019 does not name a type
MosaikAlignment.h:528: error: \u2018uint64_t\u2019 does not name a type
MosaikAlignment.h:579: error: \u2018uint64_t\u2019 does not name a type
MosaikAlignment.h:582: error: \u2018uint64_t\u2019 does not name a type
MosaikAlignment.h:584: error: \u2018uint64_t\u2019 does not name a type
MosaikAlignment.h:585: error: \u2018uint64_t\u2019 does not name a type
MosaikAlignment.cpp: In constructor 
\u2018Mosaik::CAlignmentReader::CAlignmentReader()\u2019:
MosaikAlignment.cpp:24: error: class \u2018Mosaik::CAlignmentReader\u2019 does 
not have any field named \u2018mNumReads\u2019
MosaikAlignment.cpp:25: error: class \u2018Mosaik::CAlignmentReader\u2019 does 
not have any field named \u2018mNumBases\u2019
MosaikAlignment.cpp:26: error: class \u2018Mosaik::CAlignmentReader\u2019 does 
not have any field named \u2018mCurrentRead\u2019
MosaikAlignment.cpp: In static member function \u2018static bool 
Mosaik::CAlignmentReader::CheckFile(const std::string&, bool)\u2019:
MosaikAlignment.cpp:64: error: \u2018fopen\u2019 was not declared in this scope
MosaikAlignment.cpp:67: error: \u2018printf\u2019 was not declared in this scope
MosaikAlignment.cpp:78: error: \u2018fread\u2019 was not declared in this scope
MosaikAlignment.cpp:80: error: \u2018printf\u2019 was not declared in this scope
MosaikAlignment.cpp:90: error: \u2018printf\u2019 was not declared in this scope
MosaikAlignment.cpp:100: error: \u2018printf\u2019 was not declared in this 
scope
MosaikAlignment.cpp:110: error: \u2018fclose\u2019 was not declared in this 
scope
MosaikAlignment.cpp: In member function \u2018void 
Mosaik::CAlignmentReader::Close()\u2019:
MosaikAlignment.cpp:120: error: \u2018fclose\u2019 was not declared in this 
scope
MosaikAlignment.cpp: At global scope:
MosaikAlignment.cpp:129: error: \u2018uint64_t\u2019 does not name a type
MosaikAlignment.cpp:135: error: \u2018uint64_t\u2019 does not name a type
MosaikAlignment.cpp: In member function \u2018Mosaik::ReadGroup 
Mosaik::CAlignmentReader::GetReadGroupFromCode(unsigned int)\u2019:
MosaikAlignment.cpp:145: error: \u2018printf\u2019 was not declared in this 
scope
MosaikAlignment.cpp: In member function \u2018void 
Mosaik::CAlignmentReader::Jump(unsigned int, unsigned int)\u2019:
MosaikAlignment.cpp:179: error: \u2018fseeko\u2019 was not declared in this 
scope
MosaikAlignment.cpp:183: error: \u2018fread\u2019 was not declared in this scope
MosaikAlignment.cpp:225: error: \u2018mCurrentRead\u2019 was not declared in 
this scope
MosaikAlignment.cpp: In member function \u2018bool 
Mosaik::CAlignmentReader::LoadNextRead(Mosaik::AlignedRead&)\u2019:
MosaikAlignment.cpp:239: error: \u2018mCurrentRead\u2019 was not declared in 
this scope
MosaikAlignment.cpp:239: error: \u2018mNumReads\u2019 was not declared in this 
scope
MosaikAlignment.cpp:277: error: \u2018mCurrentRead\u2019 was not declared in 
this scope
MosaikAlignment.cpp: In member function \u2018void 
Mosaik::CAlignmentReader::Open(const std::string&)\u2019:
MosaikAlignment.cpp:328: error: \u2018fopen\u2019 was not declared in this scope
MosaikAlignment.cpp:356: error: \u2018fseeko\u2019 was not declared in this 
scope
MosaikAlignment.cpp:359: error: \u2018fgetc\u2019 was not declared in this scope
MosaikAlignment.cpp:362: error: \u2018fread\u2019 was not declared in this scope
MosaikAlignment.cpp:375: error: \u2018mNumReads\u2019 was not declared in this 
scope
MosaikAlignment.cpp:378: error: \u2018mNumBases\u2019 was not declared in this 
scope
MosaikAlignment.cpp:456: error: \u2018printf\u2019 was not declared in this 
scope
MosaikAlignment.cpp:472: error: \u2018ftello\u2019 was not declared in this 
scope
MosaikAlignment.cpp:516: error: \u2018struct Mosaik::ReferenceSequence\u2019 
has no member named \u2018NumAligned\u2019
MosaikAlignment.cpp:557: error: \u2018printf\u2019 was not declared in this 
scope
MosaikAlignment.cpp: In member function \u2018bool 
Mosaik::CAlignmentReader::ReadPartition()\u2019:
MosaikAlignment.cpp:752: error: \u2018fread\u2019 was not declared in this scope
MosaikAlignment.cpp:754: error: \u2018feof\u2019 was not declared in this scope
MosaikAlignment.cpp: In member function \u2018void 
Mosaik::CAlignmentReader::ReadTag(Mosaik::Tag&)\u2019:
MosaikAlignment.cpp:793: error: \u2018fgetc\u2019 was not declared in this scope
MosaikAlignment.cpp:807: error: \u2018fread\u2019 was not declared in this scope
MosaikAlignment.cpp:838: error: \u2018printf\u2019 was not declared in this 
scope
MosaikAlignment.cpp: In member function \u2018void 
Mosaik::CAlignmentReader::Rewind()\u2019:
MosaikAlignment.cpp:845: error: \u2018fseeko\u2019 was not declared in this 
scope
MosaikAlignment.cpp:846: error: \u2018mCurrentRead\u2019 was not declared in 
this scope
MosaikAlignment.cpp: In constructor 
\u2018Mosaik::CAlignmentWriter::CAlignmentWriter()\u2019:
MosaikAlignment.cpp:859: error: class \u2018Mosaik::CAlignmentWriter\u2019 does 
not have any field named \u2018mNumReads\u2019
MosaikAlignment.cpp:860: error: class \u2018Mosaik::CAlignmentWriter\u2019 does 
not have any field named \u2018mNumBases\u2019
MosaikAlignment.cpp: In member function \u2018void 
Mosaik::CAlignmentWriter::AddHeaderTag(const Mosaik::Tag&)\u2019:
MosaikAlignment.cpp:899: error: \u2018printf\u2019 was not declared in this 
scope
MosaikAlignment.cpp: In member function \u2018void 
Mosaik::CAlignmentWriter::Close()\u2019:
MosaikAlignment.cpp:946: error: \u2018ftello\u2019 was not declared in this 
scope
MosaikAlignment.cpp:971: error: \u2018fputc\u2019 was not declared in this scope
MosaikAlignment.cpp:983: error: \u2018fwrite\u2019 was not declared in this 
scope
MosaikAlignment.cpp:986: error: \u2018const struct 
Mosaik::ReferenceSequence\u2019 has no member named \u2018NumAligned\u2019
MosaikAlignment.cpp:1024: error: \u2018fwrite\u2019 was not declared in this 
scope
MosaikAlignment.cpp:1052: error: \u2018fseeko\u2019 was not declared in this 
scope
MosaikAlignment.cpp:1053: error: \u2018mNumReads\u2019 was not declared in this 
scope
MosaikAlignment.cpp:1053: error: \u2018fwrite\u2019 was not declared in this 
scope
MosaikAlignment.cpp:1056: error: \u2018mNumBases\u2019 was not declared in this 
scope
MosaikAlignment.cpp:1077: error: \u2018fclose\u2019 was not declared in this 
scope
MosaikAlignment.cpp: At global scope:
MosaikAlignment.cpp:1081: error: \u2018uint64_t\u2019 does not name a type
MosaikAlignment.cpp:1086: error: \u2018uint64_t\u2019 does not name a type
MosaikAlignment.cpp: In member function \u2018void 
Mosaik::CAlignmentWriter::Open(const std::string&, const 
std::vector<Mosaik::ReferenceSequence, 
std::allocator<Mosaik::ReferenceSequence> >&, const 
std::vector<Mosaik::ReadGroup, std::allocator<Mosaik::ReadGroup> >&, 
Mosaik::AlignmentStatus)\u2019:
MosaikAlignment.cpp:1100: error: \u2018fopen\u2019 was not declared in this 
scope
MosaikAlignment.cpp:1124: error: \u2018struct Mosaik::ReferenceSequence\u2019 
has no member named \u2018NumAligned\u2019
MosaikAlignment.cpp:1163: error: \u2018fwrite\u2019 was not declared in this 
scope
MosaikAlignment.cpp:1166: error: \u2018fputc\u2019 was not declared in this 
scope
MosaikAlignment.cpp:1174: error: \u2018uint64_t\u2019 was not declared in this 
scope
MosaikAlignment.cpp:1174: error: expected \u2018;\u2019 before 
\u2018currentTime\u2019
MosaikAlignment.cpp:1175: error: \u2018currentTime\u2019 was not declared in 
this scope
MosaikAlignment.cpp:1184: error: \u2018fseeko\u2019 was not declared in this 
scope
MosaikAlignment.cpp: In member function \u2018void 
Mosaik::CAlignmentWriter::SaveAlignedRead(const Mosaik::AlignedRead&)\u2019:
MosaikAlignment.cpp:1290: error: \u2018mNumReads\u2019 was not declared in this 
scope
MosaikAlignment.cpp: In member function \u2018void 
Mosaik::CAlignmentWriter::WriteAlignment(const Mosaik::Alignment*, bool, bool, 
bool, bool)\u2019:
MosaikAlignment.cpp:1308: error: \u2018struct Mosaik::ReferenceSequence\u2019 
has no member named \u2018NumAligned\u2019
MosaikAlignment.cpp:1413: error: \u2018mNumBases\u2019 was not declared in this 
scope
MosaikAlignment.cpp: In member function \u2018void 
Mosaik::CAlignmentWriter::WritePartition()\u2019:
MosaikAlignment.cpp:1457: error: \u2018ftello\u2019 was not declared in this 
scope
MosaikAlignment.cpp:1471: error: \u2018fwrite\u2019 was not declared in this 
scope
MosaikAlignment.cpp: In member function \u2018void 
Mosaik::CAlignmentWriter::WriteTag(const 
std::_Rb_tree_const_iterator<std::pair<const unsigned char, Mosaik::Tag> 
>&)\u2019:
MosaikAlignment.cpp:1493: error: \u2018fputc\u2019 was not declared in this 
scope
MosaikAlignment.cpp:1506: error: \u2018fwrite\u2019 was not declared in this 
scope
MosaikAlignment.cpp:1538: error: \u2018printf\u2019 was not declared in this 
scope
MosaikAlignment.cpp: At global scope:
MosaikAlignment.cpp:1583: error: \u2018uint64_t\u2019 does not name a type
MosaikAlignment.cpp:1584: error: \u2018uint64_t\u2019 does not name a type
MosaikAlignment.cpp:1588: error: \u2018uint64_t\u2019 does not name a type
MosaikAlignment.cpp:1607: error: \u2018uint64_t\u2019 does not name a type
MosaikAlignment.cpp: In constructor \u2018Mosaik::CFastLZIO::CFastLZIO()\u2019:
MosaikAlignment.cpp:1624: error: \u2018printf\u2019 was not declared in this 
scope
MosaikAlignment.cpp: In member function \u2018void 
Mosaik::CFastLZIO::Read(char*&, unsigned int&, FILE*)\u2019:
MosaikAlignment.cpp:1648: error: \u2018fread\u2019 was not declared in this 
scope
MosaikAlignment.cpp:1657: error: \u2018printf\u2019 was not declared in this 
scope
MosaikAlignment.cpp: In member function \u2018void 
Mosaik::CFastLZIO::Read(std::string&, FILE*)\u2019:
MosaikAlignment.cpp:1691: error: \u2018fread\u2019 was not declared in this 
scope
MosaikAlignment.cpp: In member function \u2018void 
Mosaik::CFastLZIO::Write(const char*, unsigned int, FILE*)\u2019:
MosaikAlignment.cpp:1721: error: \u2018fwrite\u2019 was not declared in this 
scope
MosaikAlignment.cpp: In static member function \u2018static unsigned int 
Mosaik::CSHA1::GenerateReadGroupCode(const std::string&, const 
std::string&)\u2019:
MosaikAlignment.cpp:1756: error: \u2018sprintf\u2019 was not declared in this 
scope
MosaikAlignment.cpp: In static member function \u2018static void 
Mosaik::CSequenceUtilities::Pack(std::string&, const std::string&, const 
std::string&)\u2019:
MosaikAlignment.cpp:2011: error: \u2018printf\u2019 was not declared in this 
scope
MosaikAlignment_wrap.cxx:754:20: error: EXTERN.h: No such file or directory
MosaikAlignment_wrap.cxx:755:18: error: perl.h: No such file or directory
MosaikAlignment_wrap.cxx:756:18: error: XSUB.h: No such file or directory
MosaikAlignment_wrap.cxx:764:28: error: patchlevel.h: No such file or directory
MosaikAlignment_wrap.cxx:767:48: error: could_not_find_Perl_patchlevel.h: No 
such file or directory
MosaikAlignment_wrap.cxx:1024: error: typedef \u2018SwigMagicFunc\u2019 is 
initialized (use decltype instead)
MosaikAlignment_wrap.cxx:1024: error: \u2018SV\u2019 was not declared in this 
scope
MosaikAlignment_wrap.cxx:1024: error: expected primary-expression before 
\u2018,\u2019 token
MosaikAlignment_wrap.cxx:1024: error: \u2018MAGIC\u2019 was not declared in 
this scope
MosaikAlignment_wrap.cxx:1024: error: expected primary-expression before 
\u2018)\u2019 token
MosaikAlignment_wrap.cxx: In function \u2018void SWIG_croak_null()\u2019:
MosaikAlignment_wrap.cxx:1053: error: \u2018SV\u2019 was not declared in this 
scope
MosaikAlignment_wrap.cxx:1053: error: \u2018err\u2019 was not declared in this 
scope
MosaikAlignment_wrap.cxx:1053: error: \u2018FALSE\u2019 was not declared in 
this scope
MosaikAlignment_wrap.cxx:1053: error: \u2018perl_get_sv\u2019 was not declared 
in this scope
MosaikAlignment_wrap.cxx:1055: error: \u2018croak\u2019 was not declared in 
this scope
MosaikAlignment_wrap.cxx: At global scope:
MosaikAlignment_wrap.cxx:1138: error: \u2018SV\u2019 was not declared in this 
scope
MosaikAlignment_wrap.cxx:1138: error: \u2018sv\u2019 was not declared in this 
scope
MosaikAlignment_wrap.cxx:1138: error: expected primary-expression before 
\u2018void\u2019
MosaikAlignment_wrap.cxx:1138: error: expected primary-expression before 
\u2018*\u2019 token
MosaikAlignment_wrap.cxx:1138: error: \u2018_t\u2019 was not declared in this 
scope
MosaikAlignment_wrap.cxx:1138: error: expected primary-expression before 
\u2018int\u2019
MosaikAlignment_wrap.cxx:1138: error: expected primary-expression before 
\u2018int\u2019
MosaikAlignment_wrap.cxx:1138: error: initializer expression list treated as 
compound expression
MosaikAlignment_wrap.cxx:1138: error: expected \u2018,\u2019 or \u2018;\u2019 
before \u2018{\u2019 token
In file included from /usr/include/c++/4.4/stdexcept:38,
                 from MosaikAlignment_wrap.cxx:1560:
/usr/include/c++/4.4/exception:35: error: expected \u2018}\u2019 before end of 
line
/usr/include/c++/4.4/exception:35: error: expected declaration before end of 
line
make: *** [SWIG] Error 1

What version of the product are you using? On what operating system?
Mosaik 1.1.0021
Ubuntu 10.04 x64
gcc 4.4.3
swig 1.3.40

Please provide any additional information below.
btw, in sam/bed output from MosaikSort/MosaikText, is there anyway to tell 
which one is read1 and which one is read2? We are doing strand-specific paired 
end seq and need this info for downstream process.

Original issue reported on code.google.com by acc...@gmail.com on 30 Mar 2011 at 4:33

GoogleCodeExporter commented 8 years ago 
I think I am getting something similar with gcc-4.5.3 while not with gcc-4.3.6. 
I will attach the errors in a file.

Original comment by mmokr...@gmail.com on 1 Jun 2012 at 9:34

Attachments: