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freebayes failed to build on Mac OS X 10.10.1 #14

Closed
RodrigoGM opened this issue Nov 27, 2014 · 9 comments
Closed

freebayes failed to build on Mac OS X 10.10.1 #14

RodrigoGM opened this issue Nov 27, 2014 · 9 comments

Comments

@RodrigoGM
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I'm attempting to build freebayes on a mac in several occasions. The build fails due to the smithwaterman library, though I'm not sure exactly why. When I attempt to install, the message below.
For more details I ran a brew gist-logs freebayes and it's located here https://gist.github.com/d748473463ac04ecc4b4

$brew install freebayes
...
==> cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/freebayes/0.9.14-15 -DCMAKE_BUILD_TYPE=None -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_VERBOSE_MAKEFILE=ON -Wno-dev
==> make
==> make
==> make
  * linking smithwaterman
ld: internal error: atom not found in symbolIndex(__ZNSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEE6assignINS_16reverse_iteratorINS_11__wrap_iterIPcEEEEEENS_9enable_ifIXsr21__is_forward_iteratorIT_EE5valueERS5_E4typeESD_SD_) for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [smithwaterman] Error 1
make: *** [smithwaterman/SmithWatermanGotoh.o] Error 2

READ THIS: http://git.io/brew-troubleshooting
If reporting this issue please do so at (not Homebrew/homebrew):
  https://github.com/chapmanb/homebrew-cbl/issues

Any help is appreciated !
hope all is well,

Rodrigo
@chapmanb
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Owner

Rodrigo;
Apologies about the issue. We do most of our evaluation of these recipes on Linux, using Linuxbrew, so I'm not sure they will all build reliably on Mac OS X. We're happy to accept patches to make them work but I run Linux myself so would rely on you for testing. Regarding this failure, it looks like it might be this open issue on FreeBayes:

freebayes/freebayes#83

So trying the change suggested there might fix it. Hope this helps.

@RodrigoGM
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Author

Hello Brad,
Thank you for such a quick reply.
I built freebayes with the fix suggested on freebayes/freebayes#83. It built and seems to be working properly. Enclosed is the terminal transcript. If you require more in-depth testing we can do so as well. I can compare the outputs of this version with the one on our server.

Would it be possible to have a recipe on homebrew to do this ? I’m decent at keeping all my programs in /opt/src, but homebrew does a much nicer job in keeping up to date than anything I do. I can gladly run the tests for the patch.

Thank you in advance,

Rodrigo

On 28 Nov 2014, at 13:09, Brad Chapman notifications@github.com wrote:

Rodrigo;
Apologies about the issue. We do most of our evaluation of these recipes on Linux, using Linuxbrew, so I'm not sure they will all build reliably on Mac OS X. We're happy to accept patches to make them work but I run Linux myself so would rely on you for testing. Regarding this failure, it looks like it might be this open issue on FreeBayes:

freebayes/freebayes#83 freebayes/freebayes#83
So trying the change suggested there might fix it. Hope this helps.

—
Reply to this email directly or view it on GitHub #14 (comment).

Last login: Fri Nov 28 13:23:09 on ttys003
You have mail.
lycaste:~ rjgularte$ cd /opt/src/
lycaste:src rjgularte$ git clone --recursive https://github.com/ekg/freebayes.git
Cloning into 'freebayes'...
remote: Counting objects: 4220, done.
remote: Total 4220 (delta 0), reused 0 (delta 0)
Receiving objects: 100% (4220/4220), 6.34 MiB | 3.47 MiB/s, done.
Resolving deltas: 100% (2717/2717), done.
Checking connectivity... done.
Submodule 'bamtools' (https://github.com/ekg/bamtools.git) registered for path 'bamtools'
Submodule 'intervaltree' (https://github.com/ekg/intervaltree.git) registered for path 'intervaltree'
Submodule 'vcflib' (https://github.com/ekg/vcflib.git) registered for path 'vcflib'
Cloning into 'bamtools'...
remote: Counting objects: 4015, done.
remote: Compressing objects: 100% (2/2), done.
remote: Total 4015 (delta 0), reused 2 (delta 0)
Receiving objects: 100% (4015/4015), 2.84 MiB | 2.53 MiB/s, done.
Resolving deltas: 100% (2437/2437), done.
Checking connectivity... done.
Submodule path 'bamtools': checked out '13cac54de711abc914c92828e469c0bc5a0a2543'
Cloning into 'intervaltree'...
remote: Counting objects: 86, done.
remote: Total 86 (delta 0), reused 0 (delta 0)
Unpacking objects: 100% (86/86), done.
Checking connectivity... done.
Submodule path 'intervaltree': checked out 'd151b487804861dc9f932e9f1fe4f8c499673cec'
Cloning into 'vcflib'...
remote: Counting objects: 1547, done.
remote: Total 1547 (delta 0), reused 0 (delta 0)
Receiving objects: 100% (1547/1547), 1.06 MiB | 1.02 MiB/s, done.
Resolving deltas: 100% (884/884), done.
Checking connectivity... done.
Submodule path 'vcflib': checked out '5ac091365fdc716cc47cc5410bb97ee5dc2a2c92'
Submodule 'fastahack' (https://github.com/ekg/fastahack.git) registered for path 'fastahack'
Submodule 'filevercmp' (https://github.com/ekg/filevercmp.git) registered for path 'filevercmp'
Submodule 'fsom' (https://github.com/ekg/fsom.git) registered for path 'fsom'
Submodule 'intervaltree' (https://github.com/ekg/intervaltree.git) registered for path 'intervaltree'
Submodule 'multichoose' (https://github.com/ekg/multichoose.git) registered for path 'multichoose'
Submodule 'smithwaterman' (https://github.com/ekg/smithwaterman.git) registered for path 'smithwaterman'
Submodule 'tabixpp' (https://github.com/ekg/tabixpp.git) registered for path 'tabixpp'
Cloning into 'fastahack'...
remote: Counting objects: 187, done.
remote: Total 187 (delta 0), reused 0 (delta 0)
Receiving objects: 100% (187/187), 43.59 KiB | 0 bytes/s, done.
Resolving deltas: 100% (108/108), done.
Checking connectivity... done.
Submodule path 'vcflib/fastahack': checked out 'c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd'
Cloning into 'filevercmp'...
remote: Counting objects: 22, done.
remote: Total 22 (delta 0), reused 0 (delta 0)
Unpacking objects: 100% (22/22), done.
Checking connectivity... done.
Submodule path 'vcflib/filevercmp': checked out '1a9b779b93d0b244040274794d402106907b71b7'
Cloning into 'fsom'...
remote: Counting objects: 38, done.
remote: Compressing objects: 100% (23/23), done.
remote: Total 38 (delta 13), reused 38 (delta 13)
Unpacking objects: 100% (38/38), done.
Checking connectivity... done.
Submodule path 'vcflib/fsom': checked out 'a6ef318fbd347c53189384aef7f670c0e6ce89a3'
Cloning into 'intervaltree'...
remote: Counting objects: 86, done.
remote: Total 86 (delta 0), reused 0 (delta 0)
Unpacking objects: 100% (86/86), done.
Checking connectivity... done.
Submodule path 'vcflib/intervaltree': checked out '1290744283cef8076bb8a2968d4899b7228435f4'
Cloning into 'multichoose'...
remote: Counting objects: 70, done.
remote: Total 70 (delta 0), reused 0 (delta 0)
Unpacking objects: 100% (70/70), done.
Checking connectivity... done.
Submodule path 'vcflib/multichoose': checked out '73d35daa18bf35729b9ba758041a9247a72484a5'
Cloning into 'smithwaterman'...
remote: Counting objects: 287, done.
remote: Total 287 (delta 0), reused 0 (delta 0)
Receiving objects: 100% (287/287), 84.91 KiB | 0 bytes/s, done.
Resolving deltas: 100% (186/186), done.
Checking connectivity... done.
Submodule path 'vcflib/smithwaterman': checked out '203218b47d45ac56ef234716f1bd4c741b289be1'
Cloning into 'tabixpp'...
remote: Counting objects: 70, done.
remote: Total 70 (delta 0), reused 0 (delta 0)
Unpacking objects: 100% (70/70), done.
Checking connectivity... done.
Submodule path 'vcflib/tabixpp': checked out 'bbc63a49acc52212199f92e9e3b8fba0a593e3f7'
lycaste:src rjgularte$ cd freebayes/
lycaste:freebayes rjgularte$ ls
LICENSE README.md bin intervaltree python src vcflib
Makefile bamtools examples paper scripts ttmath
lycaste:freebayes rjgularte$ cd vcflib/
lycaste:vcflib rjgularte$ ls
LICENSE README.md fastahack fsom multichoose smithwaterman tabixpp
Makefile bin filevercmp intervaltree samples src
lycaste:vcflib rjgularte$ cd smithwaterman/
lycaste:smithwaterman rjgularte$ ls
BandedSmithWaterman.cpp LeftAlign.cpp Repeats.cpp SmithWatermanGotoh.h examples.txt
BandedSmithWaterman.h LeftAlign.h Repeats.h convert.h libdisorder.LICENSE
IndelAllele.cpp Makefile SWMain.cpp disorder.c smithwaterman.cpp
IndelAllele.h Mosaik.h SmithWatermanGotoh.cpp disorder.h
lycaste:smithwaterman rjgularte$ emacs Makefile
lycaste:smithwaterman rjgularte$ cd ../../
lycaste:freebayes rjgularte$ make
cd src && /Applications/Xcode.app/Contents/Developer/usr/bin/make autoversion
DETECTED_VERSION = v0.9.18-24-gc4aed4f-dirty
CURRENT_VERSION =
Updating version file.
touch src/version_git.h
wget -q http://hypervolu.me/freebayes/build/v0.9.18-24-gc4aed4f-dirty &
cd src && /Applications/Xcode.app/Contents/Developer/usr/bin/make
DETECTED_VERSION = v0.9.18-24-gc4aed4f-dirty
CURRENT_VERSION = v0.9.18-24-gc4aed4f-dirty
cd ../bamtools && mkdir -p build && cd build && cmake .. && /Applications/Xcode.app/Contents/Developer/usr/bin/make
-- The C compiler identification is AppleClang 6.0.0.6000054
-- The CXX compiler identification is AppleClang 6.0.0.6000054
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Configuring done
CMake Warning (dev):
Policy CMP0042 is not set: MACOSX_RPATH is enabled by default. Run "cmake
--help-policy CMP0042" for policy details. Use the cmake_policy command to
set the policy and suppress this warning.

MACOSX_RPATH is not specified for the following targets:

BamTools

This warning is for project developers. Use -Wno-dev to suppress it.

-- Generating done
-- Build files have been written to: /opt/src/freebayes/bamtools/build
Scanning dependencies of target SharedHeaders
[ 1%] Exporting SharedHeaders
[ 1%] Built target SharedHeaders
Scanning dependencies of target APIHeaders
[ 2%] Exporting APIHeaders
[ 2%] Built target APIHeaders
Scanning dependencies of target AlgorithmsHeaders
[ 3%] Exporting AlgorithmsHeaders
[ 3%] Built target AlgorithmsHeaders
Scanning dependencies of target BamTools
[ 4%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o
[ 5%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o
[ 6%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/BamReader.cpp:11:
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:28:
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was
previously declared as a struct [-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 7%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/BamWriter.cpp:11:
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct
[-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
In file included from /opt/src/freebayes/bamtools/src/api/BamWriter.cpp:12:
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:1: warning: 'SamHeader' defined as a struct here but previously
declared as a class [-Wmismatched-tags]
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
2 warnings generated.
[ 8%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/SamHeader.cpp:13:
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: warning: class 'SamHeader' was previously
declared as a struct [-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
In file included from /opt/src/freebayes/bamtools/src/api/SamHeader.cpp:15:
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: warning: class 'SamReadGroup' was
previously declared as a struct [-Wmismatched-tags]
class SamReadGroup;
^
/opt/src/freebayes/bamtools/src/api/SamReadGroup.h:18:19: note: previous use is here
struct API_EXPORT SamReadGroup {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: note: did you mean struct here?
class SamReadGroup;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: warning: class 'SamSequence' was
previously declared as a struct [-Wmismatched-tags]
class SamSequence;
^
/opt/src/freebayes/bamtools/src/api/SamSequence.h:18:19: note: previous use is here
struct API_EXPORT SamSequence {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: note: did you mean struct here?
class SamSequence;
^~~~~
struct
3 warnings generated.
[ 9%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o
[ 10%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o
[ 11%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o
[ 12%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o
[ 13%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o
[ 14%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o
[ 15%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o
[ 16%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o
[ 17%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.cpp:12:
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:23:
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:1: warning: 'BamAlignment' defined as a struct here but previously
declared as a class [-Wmismatched-tags]
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 18%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamReader_p.cpp:14:
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was
previously declared as a struct [-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 19%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamWriter_p.cpp:13:
/opt/src/freebayes/bamtools/src/api/internal/bam/BamWriter_p.h:30:1: warning: class 'BamAlignment' was previously
declared as a struct [-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamWriter_p.h:30:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 20%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o
[ 21%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:11:
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:28:
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was
previously declared as a struct [-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 22%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:11:
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:28:
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was
previously declared as a struct [-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 23%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o
[ 24%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o
[ 25%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o
[ 26%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o
[ 27%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o
[ 28%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o
[ 29%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o
[ 30%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o
/opt/src/freebayes/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to
false [-Wtautological-compare]
return m_ip4Address < m_ip4Address;
^
1 warning generated.
[ 31%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o
[ 32%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o
/opt/src/freebayes/bamtools/src/api/internal/io/HttpHeader_p.cpp:33:19: warning: unused variable 'TAB_CHAR'
[-Wunused-const-variable]
static const char TAB_CHAR = '\t';
^
1 warning generated.
[ 33%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o
[ 34%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o
[ 35%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/io/TcpSocket_p.cpp:12:
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.h:33:1: warning: 'TcpSocketEngine' defined as a struct
here but previously declared as a class [-Wmismatched-tags]
struct TcpSocketEngine {
^
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here?
class TcpSocketEngine;
^~~~~
struct
1 warning generated.
[ 36%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.cpp:15:
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.h:33:1: warning: 'TcpSocketEngine' defined as a struct
here but previously declared as a class [-Wmismatched-tags]
struct TcpSocketEngine {
^
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here?
class TcpSocketEngine;
^~~~~
struct
1 warning generated.
[ 37%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_unix_p.cpp:10:
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.h:33:1: warning: 'TcpSocketEngine' defined as a struct
here but previously declared as a class [-Wmismatched-tags]
struct TcpSocketEngine {
^
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here?
class TcpSocketEngine;
^~~~~
struct
1 warning generated.
[ 38%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.cpp:12:
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: warning: class 'SamHeader' was previously
declared as a struct [-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
1 warning generated.
[ 39%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatPrinter_p.cpp:12:
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatPrinter_p.h:28:1: warning: class 'SamHeader' was previously
declared as a struct [-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatPrinter_p.h:28:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
1 warning generated.
[ 40%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.cpp:12:
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:29:1: warning: class 'SamHeader' was previously
declared as a struct [-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:29:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: warning: class 'SamReadGroup' was
previously declared as a struct [-Wmismatched-tags]
class SamReadGroup;
^
/opt/src/freebayes/bamtools/src/api/SamReadGroup.h:18:19: note: previous use is here
struct API_EXPORT SamReadGroup {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: note: did you mean struct here?
class SamReadGroup;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: warning: class 'SamSequence' was
previously declared as a struct [-Wmismatched-tags]
class SamSequence;
^
/opt/src/freebayes/bamtools/src/api/SamSequence.h:18:19: note: previous use is here
struct API_EXPORT SamSequence {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: note: did you mean struct here?
class SamSequence;
^~~~~
struct
3 warnings generated.
[ 41%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o
Linking CXX shared library ../../../lib/libbamtools.dylib
[ 41%] Built target BamTools
Scanning dependencies of target BamTools-static
[ 42%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o
[ 43%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o
[ 44%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamReader.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/BamReader.cpp:11:
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:28:
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was
previously declared as a struct [-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 45%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamWriter.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/BamWriter.cpp:11:
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct
[-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
In file included from /opt/src/freebayes/bamtools/src/api/BamWriter.cpp:12:
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:1: warning: 'SamHeader' defined as a struct here but previously
declared as a class [-Wmismatched-tags]
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
2 warnings generated.
[ 46%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamHeader.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/SamHeader.cpp:13:
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: warning: class 'SamHeader' was previously
declared as a struct [-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
In file included from /opt/src/freebayes/bamtools/src/api/SamHeader.cpp:15:
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: warning: class 'SamReadGroup' was
previously declared as a struct [-Wmismatched-tags]
class SamReadGroup;
^
/opt/src/freebayes/bamtools/src/api/SamReadGroup.h:18:19: note: previous use is here
struct API_EXPORT SamReadGroup {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: note: did you mean struct here?
class SamReadGroup;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: warning: class 'SamSequence' was
previously declared as a struct [-Wmismatched-tags]
class SamSequence;
^
/opt/src/freebayes/bamtools/src/api/SamSequence.h:18:19: note: previous use is here
struct API_EXPORT SamSequence {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: note: did you mean struct here?
class SamSequence;
^~~~~
struct
3 warnings generated.
[ 47%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgram.cpp.o
[ 48%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o
[ 49%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o
[ 50%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o
[ 51%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequence.cpp.o
[ 52%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o
[ 53%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamHeader_p.cpp.o
[ 54%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamMultiReader_p.cpp.o
[ 55%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamRandomAccessController_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.cpp:12:
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:23:
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:1: warning: 'BamAlignment' defined as a struct here but previously
declared as a class [-Wmismatched-tags]
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 56%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamReader_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamReader_p.cpp:14:
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was
previously declared as a struct [-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 57%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamWriter_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamWriter_p.cpp:13:
/opt/src/freebayes/bamtools/src/api/internal/bam/BamWriter_p.h:30:1: warning: class 'BamAlignment' was previously
declared as a struct [-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamWriter_p.h:30:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 58%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamIndexFactory_p.cpp.o
[ 59%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamStandardIndex_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:11:
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:28:
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was
previously declared as a struct [-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 60%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamToolsIndex_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:11:
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:28:
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was
previously declared as a struct [-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 61%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamDeviceFactory_p.cpp.o
[ 62%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFile_p.cpp.o
[ 63%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFtp_p.cpp.o
[ 64%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamHttp_p.cpp.o
[ 65%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o
[ 66%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BgzfStream_p.cpp.o
[ 67%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ByteArray_p.cpp.o
[ 68%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o
/opt/src/freebayes/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to
false [-Wtautological-compare]
return m_ip4Address < m_ip4Address;
^
1 warning generated.
[ 69%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o
[ 70%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o
/opt/src/freebayes/bamtools/src/api/internal/io/HttpHeader_p.cpp:33:19: warning: unused variable 'TAB_CHAR'
[-Wunused-const-variable]
static const char TAB_CHAR = '\t';
^
1 warning generated.
[ 71%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o
[ 72%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o
[ 73%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/io/TcpSocket_p.cpp:12:
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.h:33:1: warning: 'TcpSocketEngine' defined as a struct
here but previously declared as a class [-Wmismatched-tags]
struct TcpSocketEngine {
^
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here?
class TcpSocketEngine;
^~~~~
struct
1 warning generated.
[ 74%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.cpp:15:
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.h:33:1: warning: 'TcpSocketEngine' defined as a struct
here but previously declared as a class [-Wmismatched-tags]
struct TcpSocketEngine {
^
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here?
class TcpSocketEngine;
^~~~~
struct
1 warning generated.
[ 75%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_unix_p.cpp:10:
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.h:33:1: warning: 'TcpSocketEngine' defined as a struct
here but previously declared as a class [-Wmismatched-tags]
struct TcpSocketEngine {
^
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here?
class TcpSocketEngine;
^~~~~
struct
1 warning generated.
[ 76%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.cpp:12:
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: warning: class 'SamHeader' was previously
declared as a struct [-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
1 warning generated.
[ 77%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatPrinter_p.cpp:12:
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatPrinter_p.h:28:1: warning: class 'SamHeader' was previously
declared as a struct [-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatPrinter_p.h:28:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
1 warning generated.
[ 78%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.cpp:12:
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:29:1: warning: class 'SamHeader' was previously
declared as a struct [-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:29:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: warning: class 'SamReadGroup' was
previously declared as a struct [-Wmismatched-tags]
class SamReadGroup;
^
/opt/src/freebayes/bamtools/src/api/SamReadGroup.h:18:19: note: previous use is here
struct API_EXPORT SamReadGroup {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: note: did you mean struct here?
class SamReadGroup;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: warning: class 'SamSequence' was
previously declared as a struct [-Wmismatched-tags]
class SamSequence;
^
/opt/src/freebayes/bamtools/src/api/SamSequence.h:18:19: note: previous use is here
struct API_EXPORT SamSequence {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: note: did you mean struct here?
class SamSequence;
^~~~~
struct
3 warnings generated.
[ 79%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o
Linking CXX static library ../../../lib/libbamtools.a
[ 79%] Built target BamTools-static
Scanning dependencies of target jsoncpp
[ 80%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_reader.cpp.o
[ 81%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_value.cpp.o
[ 82%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_writer.cpp.o
Linking CXX static library ../../../../lib/libjsoncpp.a
[ 82%] Built target jsoncpp
Scanning dependencies of target BamTools-utils
[ 83%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o
/opt/src/freebayes/bamtools/src/utils/bamtools_fasta.cpp:90:23: warning: comparison of unsigned expression < 0 is always
false [-Wtautological-compare]
if (seqLength < 0)
~~~~~~~~~ ^ ~
1 warning generated.
[ 84%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o
[ 85%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o
[ 86%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o
Linking CXX static library ../../../lib/libbamtools-utils.a
[ 86%] Built target BamTools-utils
Scanning dependencies of target bamtools_cmd
[ 87%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o
[ 88%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o
[ 89%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o
[ 90%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o
In file included from /opt/src/freebayes/bamtools/src/toolkit/bamtools_filter.cpp:13:
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct
[-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct
[-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
/opt/src/freebayes/bamtools/src/toolkit/bamtools_filter.cpp:368:1: warning: 'FilterToolPrivate' defined as a class here
but previously declared as a struct [-Wmismatched-tags]
class FilterTool::FilterToolPrivate {
^
/opt/src/freebayes/bamtools/src/toolkit/bamtools_filter.h:31:9: note: did you mean class here?
struct FilterToolPrivate;
^~~~~~
class
3 warnings generated.
[ 91%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o
[ 92%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o
[ 93%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o
In file included from /opt/src/freebayes/bamtools/src/toolkit/bamtools_merge.cpp:13:
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct
[-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct
[-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
2 warnings generated.
[ 94%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o
In file included from /opt/src/freebayes/bamtools/src/toolkit/bamtools_random.cpp:13:
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct
[-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct
[-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
2 warnings generated.
[ 95%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o
In file included from /opt/src/freebayes/bamtools/src/toolkit/bamtools_resolve.cpp:13:
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct
[-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct
[-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
/opt/src/freebayes/bamtools/src/toolkit/bamtools_resolve.cpp:48:19: warning: unused variable 'OPEN_BRACE_CHAR'
[-Wunused-const-variable]
static const char OPEN_BRACE_CHAR = '[';
^
/opt/src/freebayes/bamtools/src/toolkit/bamtools_resolve.cpp:49:19: warning: unused variable 'CLOSE_BRACE_CHAR'
[-Wunused-const-variable]
static const char CLOSE_BRACE_CHAR = ']';
^
4 warnings generated.
[ 96%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o
In file included from /opt/src/freebayes/bamtools/src/toolkit/bamtools_revert.cpp:13:
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct
[-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct
[-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
2 warnings generated.
[ 97%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o
In file included from /opt/src/freebayes/bamtools/src/toolkit/bamtools_sort.cpp:14:
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct
[-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct
[-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
/opt/src/freebayes/bamtools/src/toolkit/bamtools_sort.cpp:79:1: warning: 'SortToolPrivate' defined as a class here but
previously declared as a struct [-Wmismatched-tags]
class SortTool::SortToolPrivate {
^
/opt/src/freebayes/bamtools/src/toolkit/bamtools_sort.h:31:9: note: did you mean class here?
struct SortToolPrivate;
^~~~~~
class
3 warnings generated.
[ 98%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o
In file included from /opt/src/freebayes/bamtools/src/toolkit/bamtools_split.cpp:15:
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct
[-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct
[-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
/opt/src/freebayes/bamtools/src/toolkit/bamtools_split.cpp:108:1: warning: 'SplitToolPrivate' defined as a class here
but previously declared as a struct [-Wmismatched-tags]
class SplitTool::SplitToolPrivate {
^
/opt/src/freebayes/bamtools/src/toolkit/bamtools_split.h:32:9: note: did you mean class here?
struct SplitToolPrivate;
^~~~~~
class
3 warnings generated.
[ 99%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o
[100%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o
/opt/src/freebayes/bamtools/src/toolkit/bamtools.cpp:149:16: warning: equality comparison with extraneous parentheses
[-Wparentheses-equality]
if ( (argc == 1) ) return Help(argc, argv);
~~~~~^~~~
/opt/src/freebayes/bamtools/src/toolkit/bamtools.cpp:149:16: note: remove extraneous parentheses around the comparison
to silence this warning
if ( (argc == 1) ) return Help(argc, argv);
~ ^ ~
/opt/src/freebayes/bamtools/src/toolkit/bamtools.cpp:149:16: note: use '=' to turn this equality comparison into an
assignment
if ( (argc == 1) ) return Help(argc, argv);
^~
=
1 warning generated.
Linking CXX executable ../../../bin/bamtools
[100%] Built target bamtools_cmd
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c freebayes.cpp
freebayes.cpp:695:27: warning: '&&' within '||' [-Wlogical-op-parentheses]
if (!alts.empty() && (1 - pHom.ToDouble()) >= parameters.PVL || parameters.PVL == 0) {
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~
freebayes.cpp:695:27: note: place parentheses around the '&&' expression to silence this warning
if (!alts.empty() && (1 - pHom.ToDouble()) >= parameters.PVL || parameters.PVL == 0) {
^
( )
1 warning generated.
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c BedReader.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c CNV.cpp
gcc -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c fastlz.c
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Fasta.cpp
Fasta.cpp:90:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
1 warning generated.
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Parameters.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Allele.cpp
Allele.cpp:160:13: warning: enumeration values 'ALLELE_GENOTYPE' and 'ALLELE_NULL' not handled in switch [-Wswitch]
switch (this->type) {
^
Allele.cpp:183:1: warning: control may reach end of non-void function [-Wreturn-type]
}
^
2 warnings generated.
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Sample.cpp
Sample.cpp:146:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
Sample.cpp:158:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
2 warnings generated.
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Result.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c AlleleParser.cpp
AlleleParser.cpp:1002:37: warning: '&&' within '||' [-Wlogical-op-parentheses]
newAllele.isReference() && newAllele.referenceLength == 0) {
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlleleParser.cpp:1002:37: note: place parentheses around the '&&' expression to silence this warning
newAllele.isReference() && newAllele.referenceLength == 0) {
^
( )
AlleleParser.cpp:1086:52: warning: '&&' within '||' [-Wlogical-op-parentheses]
if (cigar.back().second == "X" && newAllele.isSNP() || newAllele.isMNP()) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ ~~
AlleleParser.cpp:1086:52: note: place parentheses around the '&&' expression to silence this warning
if (cigar.back().second == "X" && newAllele.isSNP() || newAllele.isMNP()) {
^
( )
AlleleParser.cpp:2117:23: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while (ok = variantCallInputFile.getNextVariant(currentVariant)) {
~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlleleParser.cpp:2117:23: note: place parentheses around the assignment to silence this warning
while (ok = variantCallInputFile.getNextVariant(currentVariant)) {
^
( )
AlleleParser.cpp:2117:23: note: use '==' to turn this assignment into an equality comparison
while (ok = variantCallInputFile.getNextVariant(*currentVariant)) {
^
==
AlleleParser.cpp:2577:20: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
if (ok = getFirstAlignment()) {
~~~^~~~~~~~~~~~~~~~~~~~~
AlleleParser.cpp:2577:20: note: place parentheses around the assignment to silence this warning
if (ok = getFirstAlignment()) {
^
( )
AlleleParser.cpp:2577:20: note: use '==' to turn this assignment into an equality comparison
if (ok = getFirstAlignment()) {
^
==
AlleleParser.cpp:2801:49: warning: '&&' within '||' [-Wlogical-op-parentheses]
|| registeredAlignments.empty() && currentRefID != currentAlignment.RefID) {
~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlleleParser.cpp:2801:49: note: place parentheses around the '&&' expression to silence this warning
|| registeredAlignments.empty() && currentRefID != currentAlignment.RefID) {
^
( )
AlleleParser.cpp:3148:52: warning: '&&' within '||' [-Wlogical-op-parentheses]
if (ra.start > currentPosition && ra.start < currentPosition + haplotypeLength
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlleleParser.cpp:3148:52: note: place parentheses around the '&&' expression to silence this warning
if (ra.start > currentPosition && ra.start < currentPosition + haplotypeLength
^
( )
AlleleParser.cpp:3149:53: warning: '&&' within '||' [-Wlogical-op-parentheses]
|| ra.end > currentPosition && ra.end < currentPosition + haplotypeLength) {
~~ ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlleleParser.cpp:3149:53: note: place parentheses around the '&&' expression to silence this warning
|| ra.end > currentPosition && ra.end < currentPosition + haplotypeLength) {
^
( )
AlleleParser.cpp:3473:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
AlleleParser.cpp:3506:44: warning: '&&' within '||' [-Wlogical-op-parentheses]
if (ra.start > currentPosition && ra.start < currentPosition + haplotypeLength
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlleleParser.cpp:3506:44: note: place parentheses around the '&&' expression to silence this warning
if (ra.start > currentPosition && ra.start < currentPosition + haplotypeLength
^
( )
AlleleParser.cpp:3507:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
|| ra.end > currentPosition && ra.end < currentPosition + haplotypeLength) {
~~ ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlleleParser.cpp:3507:45: note: place parentheses around the '&&' expression to silence this warning
|| ra.end > currentPosition && ra.end < currentPosition + haplotypeLength) {
^
( )
AlleleParser.cpp:3532:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
11 warnings generated.
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Utility.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Genotype.cpp
Genotype.cpp:1296:67: warning: equality comparison result unused [-Wunused-comparison]
allelesWithHomozygousCombos[genotype->front().allele] == true;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
Genotype.cpp:1296:67: note: use '=' to turn this equality comparison into an assignment
allelesWithHomozygousCombos[genotype->front().allele] == true;
^~
=
1 warning generated.
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c DataLikelihood.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Multinomial.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Ewens.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c ResultData.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Dirichlet.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Marginals.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c split.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c LeftAlign.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c IndelAllele.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Bias.cpp
c++ -c -o Contamination.o Contamination.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c SegfaultHandler.cpp
c++ -c -o ../vcflib/tabixpp/tabix.o ../vcflib/tabixpp/tabix.cpp
cd ../vcflib/tabixpp && /Applications/Xcode.app/Contents/Developer/usr/bin/make
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bgzf.c -o bgzf.o
bgzf.c:44:1: warning: unused function 'kh_clear_cache' [-Wunused-function]
KHASH_MAP_INIT_INT64(cache, cache_t)
^
./khash.h:468:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
KHASH_INIT(name, uint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
^
./khash.h:140:21: note: expanded from macro 'KHASH_INIT'
static inline void kh_clear##name(kh##name##t *h)
^
:31:1: note: expanded from here
kh_clear_cache
^
1 warning generated.
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE kstring.c -o kstring.o
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE knetfile.c -o knetfile.o
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE index.c -o index.o
index.c:34:1: warning: unused function 'kh_clear_i' [-Wunused-function]
KHASH_MAP_INIT_INT(i, ti_binlist_t)
^
./khash.h:453:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
^
./khash.h:140:21: note: expanded from macro 'KHASH_INIT'
static inline void kh_clear##name(kh_##name##t *h)
^
:55:1: note: expanded from here
kh_clear_i
^
index.c:34:1: warning: unused function 'kh_del_i' [-Wunused-function]
./khash.h:453:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
^
./khash.h:259:21: note: expanded from macro 'KHASH_INIT'
static inline void kh_del##name(kh_##name##t *h, khint_t x)
^
:69:1: note: expanded from here
kh_del_i
^
index.c:35:1: warning: unused function 'kh_clear_s' [-Wunused-function]
KHASH_MAP_INIT_STR(s, int)
^
./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:140:21: note: expanded from macro 'KHASH_INIT'
static inline void kh_clear##name(kh_##name##t *h)
^
:84:1: note: expanded from here
kh_clear_s
^
index.c:35:1: warning: unused function 'kh_del_s' [-Wunused-function]
./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:259:21: note: expanded from macro 'KHASH_INIT'
static inline void kh_del##name(kh_##name##t *h, khint_t x)
^
:98:1: note: expanded from here
kh_del_s
^
4 warnings generated.
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bedidx.c -o bedidx.o
bedidx.c:20:1: warning: unused function 'kh_clear_reg' [-Wunused-function]
KHASH_MAP_INIT_STR(reg, bed_reglist_t)
^
./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:140:21: note: expanded from macro 'KHASH_INIT'
static inline void kh_clear##name(kh_##name##t *h)
^
:238:1: note: expanded from here
kh_clear_reg
^
bedidx.c:20:1: warning: unused function 'kh_del_reg' [-Wunused-function]
./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:259:21: note: expanded from macro 'KHASH_INIT'
static inline void kh_del##name(kh_##name##_t *h, khint_t x)
^
:2:1: note: expanded from here
kh_del_reg
^
2 warnings generated.
ar -cru libtabix.a bgzf.o kstring.o knetfile.o index.o bedidx.o
ranlib libtabix.a
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE main.c -o main.o
gcc -g -Wall -O2 -fPIC -o tabix main.o -lm -L. -ltabix -lz
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bgzip.c -o bgzip.o
gcc -g -Wall -O2 -fPIC -o bgzip bgzip.o bgzf.o knetfile.o -lz
g++ -g -Wall -O2 -fPIC -o tabix++ main.cpp tabix.o bgzf.o -lm -L. -ltabix -lz
cd ../vcflib/smithwaterman && /Applications/Xcode.app/Contents/Developer/usr/bin/make
c++ -c -o smithwaterman.o smithwaterman.cpp
c++ -c -o BandedSmithWaterman.o BandedSmithWaterman.cpp
c++ -c -o SmithWatermanGotoh.o SmithWatermanGotoh.cpp
c++ -c -o Repeats.o Repeats.cpp
c++ -c -o LeftAlign.o LeftAlign.cpp
LeftAlign.cpp:679:26: warning: '&&' within '||' [-Wlogical-op-parentheses]
&& (indel.insertion && indel.position == referenceSequence.size()
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
LeftAlign.cpp:679:26: note: place parentheses around the '&&' expression to silence this warning
&& (indel.insertion && indel.position == referenceSequence.size()
^
( )
1 warning generated.
c++ -c -o IndelAllele.o IndelAllele.cpp
g++ -c -o disorder.o disorder.c
clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated

  • linking smithwa

@chapmanb
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Owner

chapmanb commented Dec 4, 2014

Rodrigo;
Thanks much for testing this. I pushed this patch to the freebayes recipe so if you do a brew update it should hopefully install cleanly out of the box on Mac. Great to have this working cleanly there and thanks again.

@RodrigoGM
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Author

Hi Brad,
I ran brew install freebayesand it failed again. The gist logs for freebayes are at https://gist.github.com/3eeeca13cfbd9edb3f1a https://gist.github.com/3eeeca13cfbd9edb3f1a .

Here are the changes I made to compile it by source (Screen 1), and a text file with the transcript from the compilation (file enclosed).
I saw that with homebrew, the smithwaterman is compiled with g++; whereas when I typed make, it was compiled with c++. I checked two other mac’s in the lab, they all have something similar to Screen 2 and Screen 3. Lastly, I checked which g++ and c++ were used, and checked if they were linked. c++ is a symlink to clang++; though both appear to be the same compiler with the exception of the conf flags.

Hope all is well, and I hope this helps,

Rodrigo

Screen 1
1 bash-3.2$ cd /opt/src
2 bash-3.2$ git clone --recursive https://github.com/ekg/freebayes.git
3 *** output flushed ***
4 bash-3.2$ cd freebayes/vcflib/smithwaterman/
5 bash-3.2$ sed 's/LDFLAGS=-Wl,-s/LDFLAGS=-Wl,-v/' Makefile
6 *** output flushed ***
7 bash-3.2$ sed -i.bak 's/LDFLAGS=-Wl,-s/LDFLAGS=-Wl,-v/' Makefile
8 bash-3.2$ git diff Makefile
9 WARNING: terminal is not fully functional
10 - (press RETURN)
11 diff --git a/Makefile b/Makefile
12 index 610088f..942c71c 100644
13 --- a/Makefile
14 +++ b/Makefile
15 @@ -15,7 +15,7 @@ OBJECTS_NO_MAIN= disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o
16 # ----------------
17
18 CFLAGS=-Wall -O3
19 -LDFLAGS=-Wl,-s
20 +LDFLAGS=-Wl,-v
21 #CFLAGS=-g
22 PROGRAM=smithwaterman
23 LIBS=
24 bash-3.2$ cd ../../
25 bash-3.2$ make
26 *** output flushed ***
27 bash-3.2$

Screen 2
1 bash-3.2$ g++ -v
2 Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
3 Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn)
4 Target: x86_64-apple-darwin14.0.0
5 Thread model: posix
6 bash-3.2$ c++ -v
7 Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn)
8 Target: x86_64-apple-darwin14.0.0
9 Thread model: posix
10 bash-3.2$

Screen 3
1 aeon:~ chhar0$ c++ -v
2 Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn)
3 Target: x86_64-apple-darwin14.0.0
4 Thread model: posix
5 aeon:~ chhar0$ g++ -v
6 Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platfo
rms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/c++/4.2.1
7 Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn)
8 Target: x86_64-apple-darwin14.0.0
9 Thread model: posix

Screen 4
27 bash-3.2$ which g++
28 /usr/bin/g++
29 bash-3.2$ ls -l /usr/bin/g++
30 -rwxr-xr-x 1 root wheel 14160 Sep 27 04:07 /usr/bin/g++
31 bash-3.2$ which c++
32 /usr/bin/c++
33 bash-3.2$ ls -l /usr/bin/c++
lrwxr-xr-x 1 root wheel 7 Oct 22 17:29 /usr/bin/c++ -> clang++

On 04 Dec 2014, at 03:15, Brad Chapman notifications@github.com wrote:

Rodrigo;
Thanks much for testing this. I pushed this patch to the freebayes recipe so if you do a brew update it should hopefully install cleanly out of the box on Mac. Great to have this working cleanly there and thanks again.

—
Reply to this email directly or view it on GitHub #14 (comment).

bash-3.2$ cd /opt/src
bash-3.2$ git clone --recursive https://github.com/ekg/freebayes.git
*** output flushed ***
bash-3.2$ cd freebayes/vcflib/smithwaterman/
bash-3.2$ sed 's/LDFLAGS=-Wl,-s/LDFLAGS=-Wl,-v/' Makefile
*** output flushed ***
bash-3.2$ sed -i.bak 's/LDFLAGS=-Wl,-s/LDFLAGS=-Wl,-v/' Makefile
bash-3.2$ git diff Makefile
WARNING: terminal is not fully functional

  • (press RETURN)
    diff --git a/Makefile b/Makefile
    index 610088f..942c71c 100644
    --- a/Makefile
    +++ b/Makefile
    @@ -15,7 +15,7 @@ OBJECTS_NO_MAIN= disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o

----------------

CFLAGS=-Wall -O3
-LDFLAGS=-Wl,-s
+LDFLAGS=-Wl,-v
#CFLAGS=-g
PROGRAM=smithwaterman
LIBS=
bash-3.2$ cd ../../
bash-3.2$ make
cd src && /Applications/Xcode.app/Contents/Developer/usr/bin/make autoversion
DETECTED_VERSION = v0.9.18-25-g5781407-dirty
CURRENT_VERSION =
Updating version file.
touch src/version_git.h
wget -q http://hypervolu.me/freebayes/build/v0.9.18-25-g5781407-dirty &
cd src && /Applications/Xcode.app/Contents/Developer/usr/bin/make
DETECTED_VERSION = v0.9.18-25-g5781407-dirty
CURRENT_VERSION = v0.9.18-25-g5781407-dirty
cd ../bamtools && mkdir -p build && cd build && cmake .. && /Applications/Xcode.app/Contents/Developer/usr/bin/make
-- The C compiler identification is AppleClang 6.0.0.6000054
-- The CXX compiler identification is AppleClang 6.0.0.6000054
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Configuring done
CMake Warning (dev):
Policy CMP0042 is not set: MACOSX_RPATH is enabled by default. Run "cmake
--help-policy CMP0042" for policy details. Use the cmake_policy command to
set the policy and suppress this warning.

MACOSX_RPATH is not specified for the following targets:

BamTools

This warning is for project developers. Use -Wno-dev to suppress it.

-- Generating done
-- Build files have been written to: /opt/src/freebayes/bamtools/build
Scanning dependencies of target SharedHeaders
[ 1%] Exporting SharedHeaders
[ 1%] Built target SharedHeaders
Scanning dependencies of target APIHeaders
[ 2%] Exporting APIHeaders
[ 2%] Built target APIHeaders
Scanning dependencies of target AlgorithmsHeaders
[ 3%] Exporting AlgorithmsHeaders
[ 3%] Built target AlgorithmsHeaders
Scanning dependencies of target BamTools
[ 4%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o
[ 5%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o
[ 6%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/BamReader.cpp:11:
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:28:
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was
previously declared as a struct [-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 7%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/BamWriter.cpp:11:
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct
[-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
In file included from /opt/src/freebayes/bamtools/src/api/BamWriter.cpp:12:
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:1: warning: 'SamHeader' defined as a struct here but previously
declared as a class [-Wmismatched-tags]
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
2 warnings generated.
[ 8%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/SamHeader.cpp:13:
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: warning: class 'SamHeader' was previously
declared as a struct [-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
In file included from /opt/src/freebayes/bamtools/src/api/SamHeader.cpp:15:
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: warning: class 'SamReadGroup' was
previously declared as a struct [-Wmismatched-tags]
class SamReadGroup;
^
/opt/src/freebayes/bamtools/src/api/SamReadGroup.h:18:19: note: previous use is here
struct API_EXPORT SamReadGroup {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: note: did you mean struct here?
class SamReadGroup;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: warning: class 'SamSequence' was
previously declared as a struct [-Wmismatched-tags]
class SamSequence;
^
/opt/src/freebayes/bamtools/src/api/SamSequence.h:18:19: note: previous use is here
struct API_EXPORT SamSequence {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: note: did you mean struct here?
class SamSequence;
^~~~~
struct
3 warnings generated.
[ 9%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o
[ 10%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o
[ 11%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o
[ 12%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o
[ 13%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o
[ 14%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o
[ 15%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o
[ 16%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o
[ 17%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.cpp:12:
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:23:
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:1: warning: 'BamAlignment' defined as a struct here but previously
declared as a class [-Wmismatched-tags]
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 18%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamReader_p.cpp:14:
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was
previously declared as a struct [-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 19%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamWriter_p.cpp:13:
/opt/src/freebayes/bamtools/src/api/internal/bam/BamWriter_p.h:30:1: warning: class 'BamAlignment' was previously
declared as a struct [-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamWriter_p.h:30:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 20%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o
[ 21%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:11:
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:28:
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was
previously declared as a struct [-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 22%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:11:
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:28:
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was
previously declared as a struct [-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 23%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o
[ 24%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o
[ 25%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o
[ 26%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o
[ 27%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o
[ 28%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o
[ 29%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o
[ 30%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o
/opt/src/freebayes/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to
false [-Wtautological-compare]
return m_ip4Address < m_ip4Address;
^
1 warning generated.
[ 31%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o
[ 32%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o
/opt/src/freebayes/bamtools/src/api/internal/io/HttpHeader_p.cpp:33:19: warning: unused variable 'TAB_CHAR'
[-Wunused-const-variable]
static const char TAB_CHAR = '\t';
^
1 warning generated.
[ 33%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o
[ 34%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o
[ 35%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/io/TcpSocket_p.cpp:12:
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.h:33:1: warning: 'TcpSocketEngine' defined as a struct
here but previously declared as a class [-Wmismatched-tags]
struct TcpSocketEngine {
^
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here?
class TcpSocketEngine;
^~~~~
struct
1 warning generated.
[ 36%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.cpp:15:
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.h:33:1: warning: 'TcpSocketEngine' defined as a struct
here but previously declared as a class [-Wmismatched-tags]
struct TcpSocketEngine {
^
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here?
class TcpSocketEngine;
^~~~~
struct
1 warning generated.
[ 37%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_unix_p.cpp:10:
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.h:33:1: warning: 'TcpSocketEngine' defined as a struct
here but previously declared as a class [-Wmismatched-tags]
struct TcpSocketEngine {
^
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here?
class TcpSocketEngine;
^~~~~
struct
1 warning generated.
[ 38%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.cpp:12:
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: warning: class 'SamHeader' was previously
declared as a struct [-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
1 warning generated.
[ 39%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatPrinter_p.cpp:12:
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatPrinter_p.h:28:1: warning: class 'SamHeader' was previously
declared as a struct [-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatPrinter_p.h:28:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
1 warning generated.
[ 40%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.cpp:12:
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:29:1: warning: class 'SamHeader' was previously
declared as a struct [-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:29:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: warning: class 'SamReadGroup' was
previously declared as a struct [-Wmismatched-tags]
class SamReadGroup;
^
/opt/src/freebayes/bamtools/src/api/SamReadGroup.h:18:19: note: previous use is here
struct API_EXPORT SamReadGroup {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: note: did you mean struct here?
class SamReadGroup;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: warning: class 'SamSequence' was
previously declared as a struct [-Wmismatched-tags]
class SamSequence;
^
/opt/src/freebayes/bamtools/src/api/SamSequence.h:18:19: note: previous use is here
struct API_EXPORT SamSequence {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: note: did you mean struct here?
class SamSequence;
^~~~~
struct
3 warnings generated.
[ 41%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o
Linking CXX shared library ../../../lib/libbamtools.dylib
[ 41%] Built target BamTools
Scanning dependencies of target BamTools-static
[ 42%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o
[ 43%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o
[ 44%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamReader.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/BamReader.cpp:11:
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:28:
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was
previously declared as a struct [-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 45%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamWriter.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/BamWriter.cpp:11:
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct
[-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
In file included from /opt/src/freebayes/bamtools/src/api/BamWriter.cpp:12:
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:1: warning: 'SamHeader' defined as a struct here but previously
declared as a class [-Wmismatched-tags]
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
2 warnings generated.
[ 46%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamHeader.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/SamHeader.cpp:13:
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: warning: class 'SamHeader' was previously
declared as a struct [-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
In file included from /opt/src/freebayes/bamtools/src/api/SamHeader.cpp:15:
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: warning: class 'SamReadGroup' was
previously declared as a struct [-Wmismatched-tags]
class SamReadGroup;
^
/opt/src/freebayes/bamtools/src/api/SamReadGroup.h:18:19: note: previous use is here
struct API_EXPORT SamReadGroup {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: note: did you mean struct here?
class SamReadGroup;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: warning: class 'SamSequence' was
previously declared as a struct [-Wmismatched-tags]
class SamSequence;
^
/opt/src/freebayes/bamtools/src/api/SamSequence.h:18:19: note: previous use is here
struct API_EXPORT SamSequence {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: note: did you mean struct here?
class SamSequence;
^~~~~
struct
3 warnings generated.
[ 47%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgram.cpp.o
[ 48%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o
[ 49%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o
[ 50%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o
[ 51%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequence.cpp.o
[ 52%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o
[ 53%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamHeader_p.cpp.o
[ 54%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamMultiReader_p.cpp.o
[ 55%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamRandomAccessController_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.cpp:12:
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:23:
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:1: warning: 'BamAlignment' defined as a struct here but previously
declared as a class [-Wmismatched-tags]
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 56%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamReader_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamReader_p.cpp:14:
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was
previously declared as a struct [-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 57%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamWriter_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamWriter_p.cpp:13:
/opt/src/freebayes/bamtools/src/api/internal/bam/BamWriter_p.h:30:1: warning: class 'BamAlignment' was previously
declared as a struct [-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamWriter_p.h:30:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 58%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamIndexFactory_p.cpp.o
[ 59%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamStandardIndex_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:11:
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:28:
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was
previously declared as a struct [-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 60%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamToolsIndex_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:11:
In file included from /opt/src/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:28:
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was
previously declared as a struct [-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
1 warning generated.
[ 61%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamDeviceFactory_p.cpp.o
[ 62%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFile_p.cpp.o
[ 63%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFtp_p.cpp.o
[ 64%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamHttp_p.cpp.o
[ 65%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o
[ 66%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BgzfStream_p.cpp.o
[ 67%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ByteArray_p.cpp.o
[ 68%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o
/opt/src/freebayes/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to
false [-Wtautological-compare]
return m_ip4Address < m_ip4Address;
^
1 warning generated.
[ 69%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o
[ 70%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o
/opt/src/freebayes/bamtools/src/api/internal/io/HttpHeader_p.cpp:33:19: warning: unused variable 'TAB_CHAR'
[-Wunused-const-variable]
static const char TAB_CHAR = '\t';
^
1 warning generated.
[ 71%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o
[ 72%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o
[ 73%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/io/TcpSocket_p.cpp:12:
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.h:33:1: warning: 'TcpSocketEngine' defined as a struct
here but previously declared as a class [-Wmismatched-tags]
struct TcpSocketEngine {
^
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here?
class TcpSocketEngine;
^~~~~
struct
1 warning generated.
[ 74%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.cpp:15:
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.h:33:1: warning: 'TcpSocketEngine' defined as a struct
here but previously declared as a class [-Wmismatched-tags]
struct TcpSocketEngine {
^
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here?
class TcpSocketEngine;
^~~~~
struct
1 warning generated.
[ 75%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_unix_p.cpp:10:
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.h:33:1: warning: 'TcpSocketEngine' defined as a struct
here but previously declared as a class [-Wmismatched-tags]
struct TcpSocketEngine {
^
/opt/src/freebayes/bamtools/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here?
class TcpSocketEngine;
^~~~~
struct
1 warning generated.
[ 76%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.cpp:12:
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: warning: class 'SamHeader' was previously
declared as a struct [-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
1 warning generated.
[ 77%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatPrinter_p.cpp:12:
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatPrinter_p.h:28:1: warning: class 'SamHeader' was previously
declared as a struct [-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamFormatPrinter_p.h:28:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
1 warning generated.
[ 78%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o
In file included from /opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.cpp:12:
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:29:1: warning: class 'SamHeader' was previously
declared as a struct [-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:29:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: warning: class 'SamReadGroup' was
previously declared as a struct [-Wmismatched-tags]
class SamReadGroup;
^
/opt/src/freebayes/bamtools/src/api/SamReadGroup.h:18:19: note: previous use is here
struct API_EXPORT SamReadGroup {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: note: did you mean struct here?
class SamReadGroup;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: warning: class 'SamSequence' was
previously declared as a struct [-Wmismatched-tags]
class SamSequence;
^
/opt/src/freebayes/bamtools/src/api/SamSequence.h:18:19: note: previous use is here
struct API_EXPORT SamSequence {
^
/opt/src/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: note: did you mean struct here?
class SamSequence;
^~~~~
struct
3 warnings generated.
[ 79%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o
Linking CXX static library ../../../lib/libbamtools.a
[ 79%] Built target BamTools-static
Scanning dependencies of target jsoncpp
[ 80%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_reader.cpp.o
[ 81%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_value.cpp.o
[ 82%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_writer.cpp.o
Linking CXX static library ../../../../lib/libjsoncpp.a
[ 82%] Built target jsoncpp
Scanning dependencies of target BamTools-utils
[ 83%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o
/opt/src/freebayes/bamtools/src/utils/bamtools_fasta.cpp:90:23: warning: comparison of unsigned expression < 0 is always
false [-Wtautological-compare]
if (seqLength < 0)
~~~~~~~~~ ^ ~
1 warning generated.
[ 84%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o
[ 85%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o
[ 86%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o
Linking CXX static library ../../../lib/libbamtools-utils.a
[ 86%] Built target BamTools-utils
Scanning dependencies of target bamtools_cmd
[ 87%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o
[ 88%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o
[ 89%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o
[ 90%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o
In file included from /opt/src/freebayes/bamtools/src/toolkit/bamtools_filter.cpp:13:
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct
[-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct
[-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
/opt/src/freebayes/bamtools/src/toolkit/bamtools_filter.cpp:368:1: warning: 'FilterToolPrivate' defined as a class here
but previously declared as a struct [-Wmismatched-tags]
class FilterTool::FilterToolPrivate {
^
/opt/src/freebayes/bamtools/src/toolkit/bamtools_filter.h:31:9: note: did you mean class here?
struct FilterToolPrivate;
^~~~~~
class
3 warnings generated.
[ 91%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o
[ 92%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o
[ 93%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o
In file included from /opt/src/freebayes/bamtools/src/toolkit/bamtools_merge.cpp:13:
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct
[-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct
[-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
2 warnings generated.
[ 94%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o
In file included from /opt/src/freebayes/bamtools/src/toolkit/bamtools_random.cpp:13:
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct
[-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct
[-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
2 warnings generated.
[ 95%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o
In file included from /opt/src/freebayes/bamtools/src/toolkit/bamtools_resolve.cpp:13:
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct
[-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct
[-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
/opt/src/freebayes/bamtools/src/toolkit/bamtools_resolve.cpp:48:19: warning: unused variable 'OPEN_BRACE_CHAR'
[-Wunused-const-variable]
static const char OPEN_BRACE_CHAR = '[';
^
/opt/src/freebayes/bamtools/src/toolkit/bamtools_resolve.cpp:49:19: warning: unused variable 'CLOSE_BRACE_CHAR'
[-Wunused-const-variable]
static const char CLOSE_BRACE_CHAR = ']';
^
4 warnings generated.
[ 96%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o
In file included from /opt/src/freebayes/bamtools/src/toolkit/bamtools_revert.cpp:13:
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct
[-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct
[-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
2 warnings generated.
[ 97%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o
In file included from /opt/src/freebayes/bamtools/src/toolkit/bamtools_sort.cpp:14:
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct
[-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct
[-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
/opt/src/freebayes/bamtools/src/toolkit/bamtools_sort.cpp:79:1: warning: 'SortToolPrivate' defined as a class here but
previously declared as a struct [-Wmismatched-tags]
class SortTool::SortToolPrivate {
^
/opt/src/freebayes/bamtools/src/toolkit/bamtools_sort.h:31:9: note: did you mean class here?
struct SortToolPrivate;
^~~~~~
class
3 warnings generated.
[ 98%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o
In file included from /opt/src/freebayes/bamtools/src/toolkit/bamtools_split.cpp:15:
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct
[-Wmismatched-tags]
class BamAlignment;
^
/opt/src/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here
struct API_EXPORT BamAlignment {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here?
class BamAlignment;
^~~~~
struct
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct
[-Wmismatched-tags]
class SamHeader;
^
/opt/src/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here
struct API_EXPORT SamHeader {
^
/opt/src/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here?
class SamHeader;
^~~~~
struct
/opt/src/freebayes/bamtools/src/toolkit/bamtools_split.cpp:108:1: warning: 'SplitToolPrivate' defined as a class here
but previously declared as a struct [-Wmismatched-tags]
class SplitTool::SplitToolPrivate {
^
/opt/src/freebayes/bamtools/src/toolkit/bamtools_split.h:32:9: note: did you mean class here?
struct SplitToolPrivate;
^~~~~~
class
3 warnings generated.
[ 99%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o
[100%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o
/opt/src/freebayes/bamtools/src/toolkit/bamtools.cpp:149:16: warning: equality comparison with extraneous parentheses
[-Wparentheses-equality]
if ( (argc == 1) ) return Help(argc, argv);
~~~~~^~~~
/opt/src/freebayes/bamtools/src/toolkit/bamtools.cpp:149:16: note: remove extraneous parentheses around the comparison
to silence this warning
if ( (argc == 1) ) return Help(argc, argv);
~ ^ ~
/opt/src/freebayes/bamtools/src/toolkit/bamtools.cpp:149:16: note: use '=' to turn this equality comparison into an
assignment
if ( (argc == 1) ) return Help(argc, argv);
^~
=
1 warning generated.
Linking CXX executable ../../../bin/bamtools
[100%] Built target bamtools_cmd
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c freebayes.cpp
freebayes.cpp:695:27: warning: '&&' within '||' [-Wlogical-op-parentheses]
if (!alts.empty() && (1 - pHom.ToDouble()) >= parameters.PVL || parameters.PVL == 0) {
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~
freebayes.cpp:695:27: note: place parentheses around the '&&' expression to silence this warning
if (!alts.empty() && (1 - pHom.ToDouble()) >= parameters.PVL || parameters.PVL == 0) {
^
( )
1 warning generated.
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c BedReader.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c CNV.cpp
gcc -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c fastlz.c
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Fasta.cpp
Fasta.cpp:90:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
1 warning generated.
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Parameters.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Allele.cpp
Allele.cpp:160:13: warning: enumeration values 'ALLELE_GENOTYPE' and 'ALLELE_NULL' not handled in switch [-Wswitch]
switch (this->type) {
^
Allele.cpp:183:1: warning: control may reach end of non-void function [-Wreturn-type]
}
^
2 warnings generated.
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Sample.cpp
Sample.cpp:146:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
Sample.cpp:158:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
2 warnings generated.
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Result.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c AlleleParser.cpp
AlleleParser.cpp:1002:37: warning: '&&' within '||' [-Wlogical-op-parentheses]
newAllele.isReference() && newAllele.referenceLength == 0) {
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlleleParser.cpp:1002:37: note: place parentheses around the '&&' expression to silence this warning
newAllele.isReference() && newAllele.referenceLength == 0) {
^
( )
AlleleParser.cpp:1086:52: warning: '&&' within '||' [-Wlogical-op-parentheses]
if (cigar.back().second == "X" && newAllele.isSNP() || newAllele.isMNP()) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ ~~
AlleleParser.cpp:1086:52: note: place parentheses around the '&&' expression to silence this warning
if (cigar.back().second == "X" && newAllele.isSNP() || newAllele.isMNP()) {
^
( )
AlleleParser.cpp:2117:23: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while (ok = variantCallInputFile.getNextVariant(currentVariant)) {
~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlleleParser.cpp:2117:23: note: place parentheses around the assignment to silence this warning
while (ok = variantCallInputFile.getNextVariant(currentVariant)) {
^
( )
AlleleParser.cpp:2117:23: note: use '==' to turn this assignment into an equality comparison
while (ok = variantCallInputFile.getNextVariant(*currentVariant)) {
^
==
AlleleParser.cpp:2577:20: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
if (ok = getFirstAlignment()) {
~~~^~~~~~~~~~~~~~~~~~~~~
AlleleParser.cpp:2577:20: note: place parentheses around the assignment to silence this warning
if (ok = getFirstAlignment()) {
^
( )
AlleleParser.cpp:2577:20: note: use '==' to turn this assignment into an equality comparison
if (ok = getFirstAlignment()) {
^
==
AlleleParser.cpp:2801:49: warning: '&&' within '||' [-Wlogical-op-parentheses]
|| registeredAlignments.empty() && currentRefID != currentAlignment.RefID) {
~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlleleParser.cpp:2801:49: note: place parentheses around the '&&' expression to silence this warning
|| registeredAlignments.empty() && currentRefID != currentAlignment.RefID) {
^
( )
AlleleParser.cpp:3148:52: warning: '&&' within '||' [-Wlogical-op-parentheses]
if (ra.start > currentPosition && ra.start < currentPosition + haplotypeLength
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlleleParser.cpp:3148:52: note: place parentheses around the '&&' expression to silence this warning
if (ra.start > currentPosition && ra.start < currentPosition + haplotypeLength
^
( )
AlleleParser.cpp:3149:53: warning: '&&' within '||' [-Wlogical-op-parentheses]
|| ra.end > currentPosition && ra.end < currentPosition + haplotypeLength) {
~~ ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlleleParser.cpp:3149:53: note: place parentheses around the '&&' expression to silence this warning
|| ra.end > currentPosition && ra.end < currentPosition + haplotypeLength) {
^
( )
AlleleParser.cpp:3473:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
AlleleParser.cpp:3506:44: warning: '&&' within '||' [-Wlogical-op-parentheses]
if (ra.start > currentPosition && ra.start < currentPosition + haplotypeLength
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlleleParser.cpp:3506:44: note: place parentheses around the '&&' expression to silence this warning
if (ra.start > currentPosition && ra.start < currentPosition + haplotypeLength
^
( )
AlleleParser.cpp:3507:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
|| ra.end > currentPosition && ra.end < currentPosition + haplotypeLength) {
~~ ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlleleParser.cpp:3507:45: note: place parentheses around the '&&' expression to silence this warning
|| ra.end > currentPosition && ra.end < currentPosition + haplotypeLength) {
^
( )
AlleleParser.cpp:3532:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
11 warnings generated.
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Utility.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Genotype.cpp
Genotype.cpp:1296:67: warning: equality comparison result unused [-Wunused-comparison]
allelesWithHomozygousCombos[genotype->front().allele] == true;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
Genotype.cpp:1296:67: note: use '=' to turn this equality comparison into an assignment
allelesWithHomozygousCombos[genotype->front().allele] == true;
^~
=
1 warning generated.
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c DataLikelihood.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Multinomial.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Ewens.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c ResultData.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Dirichlet.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Marginals.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c split.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c LeftAlign.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c IndelAllele.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Bias.cpp
c++ -c -o Contamination.o Contamination.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c SegfaultHandler.cpp
c++ -c -o ../vcflib/tabixpp/tabix.o ../vcflib/tabixpp/tabix.cpp
cd ../vcflib/tabixpp && /Applications/Xcode.app/Contents/Developer/usr/bin/make
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bgzf.c -o bgzf.o
bgzf.c:44:1: warning: unused function 'kh_clear_cache' [-Wunused-function]
KHASH_MAP_INIT_INT64(cache, cache_t)
^
./khash.h:468:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
KHASH_INIT(name, uint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
^
./khash.h:140:21: note: expanded from macro 'KHASH_INIT'
static inline void kh_clear##name(kh##name##t *h)
^
:31:1: note: expanded from here
kh_clear_cache
^
1 warning generated.
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE kstring.c -o kstring.o
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE knetfile.c -o knetfile.o
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE index.c -o index.o
index.c:34:1: warning: unused function 'kh_clear_i' [-Wunused-function]
KHASH_MAP_INIT_INT(i, ti_binlist_t)
^
./khash.h:453:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
^
./khash.h:140:21: note: expanded from macro 'KHASH_INIT'
static inline void kh_clear##name(kh_##name##t *h)
^
:55:1: note: expanded from here
kh_clear_i
^
index.c:34:1: warning: unused function 'kh_del_i' [-Wunused-function]
./khash.h:453:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
^
./khash.h:259:21: note: expanded from macro 'KHASH_INIT'
static inline void kh_del##name(kh_##name##t *h, khint_t x)
^
:69:1: note: expanded from here
kh_del_i
^
index.c:35:1: warning: unused function 'kh_clear_s' [-Wunused-function]
KHASH_MAP_INIT_STR(s, int)
^
./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:140:21: note: expanded from macro 'KHASH_INIT'
static inline void kh_clear##name(kh_##name##t *h)
^
:84:1: note: expanded from here
kh_clear_s
^
index.c:35:1: warning: unused function 'kh_del_s' [-Wunused-function]
./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:259:21: note: expanded from macro 'KHASH_INIT'
static inline void kh_del##name(kh_##name##t *h, khint_t x)
^
:98:1: note: expanded from here
kh_del_s
^
4 warnings generated.
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bedidx.c -o bedidx.o
bedidx.c:20:1: warning: unused function 'kh_clear_reg' [-Wunused-function]
KHASH_MAP_INIT_STR(reg, bed_reglist_t)
^
./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:140:21: note: expanded from macro 'KHASH_INIT'
static inline void kh_clear##name(kh_##name##t *h)
^
:238:1: note: expanded from here
kh_clear_reg
^
bedidx.c:20:1: warning: unused function 'kh_del_reg' [-Wunused-function]
./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./khash.h:259:21: note: expanded from macro 'KHASH_INIT'
static inline void kh_del##name(kh_##name##_t *h, khint_t x)
^
:2:1: note: expanded from here
kh_del_reg
^
2 warnings generated.
ar -cru libtabix.a bgzf.o kstring.o knetfile.o index.o bedidx.o
ranlib libtabix.a
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE main.c -o main.o
gcc -g -Wall -O2 -fPIC -o tabix main.o -lm -L. -ltabix -lz
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bgzip.c -o bgzip.o
gcc -g -Wall -O2 -fPIC -o bgzip bgzip.o bgzf.o knetfile.o -lz
g++ -g -Wall -O2 -fPIC -o tabix++ main.cpp tabix.o bgzf.o -lm -L. -ltabix -lz
cd ../vcflib/smithwaterman && /Applications/Xcode.app/Contents/Developer/usr/bin/make
c++ -c -o smithwaterman.o smithwaterman.cpp
c++ -c -o BandedSmithWaterman.o BandedSmithWaterman.cpp
c++ -c -o SmithWatermanGotoh.o SmithWatermanGotoh.cpp
c++ -c -o Repeats.o Repeats.cpp
c++ -c -o LeftAlign.o LeftAlign.cpp
LeftAlign.cpp:679:26: warning: '&&' within '||' [-Wlogical-op-parentheses]
&& (indel.insertion && indel.position == referenceSequence.size()
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
LeftAlign.cpp:679:26: note: place parentheses around the '&&' expression to silence this warning
&& (indel.insertion && indel.position == referenceSequence.size()
^
( )
1 warning generated.
c++ -c -o IndelAllele.o IndelAllele.cpp
g++ -c -o disorder.o disorder.c
clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated

  • linking smithwaterman
    @(#)PROGRAM:ld PROJECT:ld64-241.9
    configured to support archs: armv6 armv7 armv7s arm64 i386 x86_64 x86_64h armv6m armv7m armv7em
    Library search paths:
    /usr/lib
    /usr/local/lib
    Framework search paths:
    /Library/Frameworks/
    /System/Library/Frameworks/
    ld -r disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o -o sw.o
    g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c ../vcflib/src/Variant.cpp
    ../vcflib/src/Variant.cpp:214:5: warning: control may reach end of non-void function [-Wreturn-type]
    }
    ^
    ../vcflib/src/Variant.cpp:336:5: warning: control may reach end of non-void function [-Wreturn-type]
    }
    ^
    ../vcflib/src/Variant.cpp:370:5: warning: control may reach end of non-void function [-Wreturn-type]
    }
    ^
    ../vcflib/src/Variant.cpp:408:5: warning: control may reach end of non-void function [-Wreturn-type]
    }
    ^
    4 warnings generated.
    g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ freebayes.o BedReader.o CNV.o fastlz.o Fasta.o Parameters.o Allele.o Sample.o Result.o AlleleParser.o Utility.o Genotype.o DataLikelihood.o Multinomial.o Ewens.o ResultData.o Dirichlet.o Marginals.o split.o LeftAlign.o IndelAllele.o Bias.o Contamination.o SegfaultHandler.o ../vcflib/tabixpp/tabix.o ../vcflib/tabixpp/bgzf.o ../vcflib/smithwaterman/SmithWatermanGotoh.o ../vcflib/smithwaterman/disorder.c ../vcflib/smithwaterman/LeftAlign.o ../vcflib/smithwaterman/Repeats.o ../vcflib/smithwaterman/IndelAllele.o Variant.o ../bamtools/lib/libbamtools.a -o ../bin/freebayes -L./ -L../vcflib/tabixpp/ -L../bamtools/lib -ltabix -lz -lm
    clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated
    g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c bamleftalign.cpp
    g++ -O3 -D_FILE_OFFSET_BITS=64 -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o ../bamtools/lib/libbamtools.a -o ../bin/bamleftalign -L./ -L../vcflib/tabixpp/ -L../bamtools/lib -ltabix -lz -lm
    bash-3.2$ =

@chapmanb
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chapmanb commented Dec 4, 2014

Rodrigo;
Thanks for testing and sorry this doesn't fix it. I'm out of ideas now as it seems like the patch was applied and I'm not sure why you see compile differences inside and outside of homebrew. From reading Stackoverflow answers related to this error it seems like there might be library incompatibilities related to g++/c++ although I have no knowledge of OSX so don't know how to proceed. @roryk, do you have any idea? Re-opening and sorry about to be stuck.

@chapmanb chapmanb reopened this Dec 4, 2014
@ekg
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ekg commented Dec 11, 2014

I'm equally confused... any ideas?

@roryk
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roryk commented Dec 11, 2014

Hi Rodrigo,

Not too sure either; freebayes seems to install fine for me under 10.10.1; our brew config output looks almost identical.

@roryk
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roryk commented Mar 10, 2015

Closing this, @RodrigoGM. Feel free to reopen if it still isn't working for you. Hope everything is all set.

@roryk roryk closed this as completed Mar 10, 2015
@RodrigoGM
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OK. I have freebayes installed manually, but have not continued to try installing with brew lately.

Thanks for all the help

On 10 Mar 2015, at 16:42, Rory Kirchner notifications@github.com wrote:

Closing this, @RodrigoGM https://github.com/RodrigoGM. Feel free to reopen if it still isn't working for you. Hope everything is all set.

—
Reply to this email directly or view it on GitHub #14 (comment).

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@chapmanb @ekg @roryk @RodrigoGM