printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild bamtools 2>&1 The package 'bamtools' will be built without being installed. Reading build dependency for bamtools-2.3.0-1... Reading dependency for bamtools-2.3.0-1... Reading build conflict for bamtools-2.3.0-1... The package 'cmake' will be installed. Reading dependency for cmake-2.8.12-2... Reading runtime dependency for cmake-2.8.12-2... The package 'libidn-shlibs' will be installed. Reading dependency for libidn-shlibs-1.22-6... Reading runtime dependency for libidn-shlibs-1.22-6... The following package will be rebuilt: bamtools The following 2 additional packages will be installed: cmake libidn-shlibs Do you want to continue? [Y/n] (assuming default) curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/v2.3.0.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 526k 0 1206 0 0 929 0 0:09:40 0:00:01 0:09:39 928 100 526k 100 526k 0 0 263k 0 0:00:01 0:00:01 --:--:-- 263k Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libidn-shlibs_1.22-6_darwin-x86_64.deb Selecting previously deselected package libidn-shlibs. (Reading database ... 4296 files and directories currently installed.) Unpacking libidn-shlibs (from .../libidn-shlibs_1.22-6_darwin-x86_64.deb) ... Setting up libidn-shlibs (1.22-6) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/cmake_2.8.12-2_darwin-x86_64.deb Selecting previously deselected package cmake. (Reading database ... 4297 files and directories currently installed.) Unpacking cmake (from .../cmake_2.8.12-2_darwin-x86_64.deb) ... Setting up cmake (2.8.12-2) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-bamtools-2.3.0-1 /sw/build.build dpkg-deb: building package `fink-buildlock-bamtools-2.3.0-1' in `/sw/build.build/fink-buildlock-bamtools-2.3.0-1_2014.07.31-07.16.09_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-bamtools-2.3.0-1_2014.07.31-07.16.09_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-bamtools-2.3.0-1. (Reading database ... 5027 files and directories currently installed.) Unpacking fink-buildlock-bamtools-2.3.0-1 (from .../fink-buildlock-bamtools-2.3.0-1_2014.07.31-07.16.09_darwin-x86_64.deb) ... Setting up fink-buildlock-bamtools-2.3.0-1 (2014.07.31-07.16.09) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.vvG1A env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/v2.3.0.tar.gz bamtools-2.3.0/ bamtools-2.3.0/CMakeLists.txt bamtools-2.3.0/LICENSE bamtools-2.3.0/README bamtools-2.3.0/docs/ bamtools-2.3.0/docs/Doxyfile bamtools-2.3.0/src/ bamtools-2.3.0/src/CMakeLists.txt bamtools-2.3.0/src/ExportHeader.cmake bamtools-2.3.0/src/api/ bamtools-2.3.0/src/api/BamAlgorithms.h bamtools-2.3.0/src/api/BamAlignment.cpp bamtools-2.3.0/src/api/BamAlignment.h bamtools-2.3.0/src/api/BamAux.h bamtools-2.3.0/src/api/BamConstants.h bamtools-2.3.0/src/api/BamIndex.h bamtools-2.3.0/src/api/BamMultiReader.cpp bamtools-2.3.0/src/api/BamMultiReader.h bamtools-2.3.0/src/api/BamReader.cpp bamtools-2.3.0/src/api/BamReader.h bamtools-2.3.0/src/api/BamWriter.cpp bamtools-2.3.0/src/api/BamWriter.h bamtools-2.3.0/src/api/CMakeLists.txt bamtools-2.3.0/src/api/IBamIODevice.h bamtools-2.3.0/src/api/SamConstants.h bamtools-2.3.0/src/api/SamHeader.cpp bamtools-2.3.0/src/api/SamHeader.h bamtools-2.3.0/src/api/SamProgram.cpp bamtools-2.3.0/src/api/SamProgram.h bamtools-2.3.0/src/api/SamProgramChain.cpp bamtools-2.3.0/src/api/SamProgramChain.h bamtools-2.3.0/src/api/SamReadGroup.cpp bamtools-2.3.0/src/api/SamReadGroup.h bamtools-2.3.0/src/api/SamReadGroupDictionary.cpp bamtools-2.3.0/src/api/SamReadGroupDictionary.h bamtools-2.3.0/src/api/SamSequence.cpp bamtools-2.3.0/src/api/SamSequence.h bamtools-2.3.0/src/api/SamSequenceDictionary.cpp bamtools-2.3.0/src/api/SamSequenceDictionary.h bamtools-2.3.0/src/api/algorithms/ bamtools-2.3.0/src/api/algorithms/Sort.h bamtools-2.3.0/src/api/api_global.h bamtools-2.3.0/src/api/internal/ bamtools-2.3.0/src/api/internal/CMakeLists.txt bamtools-2.3.0/src/api/internal/bam/ bamtools-2.3.0/src/api/internal/bam/BamHeader_p.cpp bamtools-2.3.0/src/api/internal/bam/BamHeader_p.h bamtools-2.3.0/src/api/internal/bam/BamMultiMerger_p.h bamtools-2.3.0/src/api/internal/bam/BamMultiReader_p.cpp bamtools-2.3.0/src/api/internal/bam/BamMultiReader_p.h bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.cpp bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.h bamtools-2.3.0/src/api/internal/bam/BamReader_p.cpp bamtools-2.3.0/src/api/internal/bam/BamReader_p.h bamtools-2.3.0/src/api/internal/bam/BamWriter_p.cpp bamtools-2.3.0/src/api/internal/bam/BamWriter_p.h bamtools-2.3.0/src/api/internal/bam/CMakeLists.txt bamtools-2.3.0/src/api/internal/index/ bamtools-2.3.0/src/api/internal/index/BamIndexFactory_p.cpp bamtools-2.3.0/src/api/internal/index/BamIndexFactory_p.h bamtools-2.3.0/src/api/internal/index/BamStandardIndex_p.cpp bamtools-2.3.0/src/api/internal/index/BamStandardIndex_p.h bamtools-2.3.0/src/api/internal/index/BamToolsIndex_p.cpp bamtools-2.3.0/src/api/internal/index/BamToolsIndex_p.h bamtools-2.3.0/src/api/internal/index/CMakeLists.txt bamtools-2.3.0/src/api/internal/io/ bamtools-2.3.0/src/api/internal/io/BamDeviceFactory_p.cpp bamtools-2.3.0/src/api/internal/io/BamDeviceFactory_p.h bamtools-2.3.0/src/api/internal/io/BamFile_p.cpp bamtools-2.3.0/src/api/internal/io/BamFile_p.h bamtools-2.3.0/src/api/internal/io/BamFtp_p.cpp bamtools-2.3.0/src/api/internal/io/BamFtp_p.h bamtools-2.3.0/src/api/internal/io/BamHttp_p.cpp bamtools-2.3.0/src/api/internal/io/BamHttp_p.h bamtools-2.3.0/src/api/internal/io/BamPipe_p.cpp bamtools-2.3.0/src/api/internal/io/BamPipe_p.h bamtools-2.3.0/src/api/internal/io/BgzfStream_p.cpp bamtools-2.3.0/src/api/internal/io/BgzfStream_p.h bamtools-2.3.0/src/api/internal/io/ByteArray_p.cpp bamtools-2.3.0/src/api/internal/io/ByteArray_p.h bamtools-2.3.0/src/api/internal/io/CMakeLists.txt bamtools-2.3.0/src/api/internal/io/HostAddress_p.cpp bamtools-2.3.0/src/api/internal/io/HostAddress_p.h bamtools-2.3.0/src/api/internal/io/HostInfo_p.cpp bamtools-2.3.0/src/api/internal/io/HostInfo_p.h bamtools-2.3.0/src/api/internal/io/HttpHeader_p.cpp bamtools-2.3.0/src/api/internal/io/HttpHeader_p.h bamtools-2.3.0/src/api/internal/io/ILocalIODevice_p.cpp bamtools-2.3.0/src/api/internal/io/ILocalIODevice_p.h bamtools-2.3.0/src/api/internal/io/NetUnix_p.h bamtools-2.3.0/src/api/internal/io/NetWin_p.h bamtools-2.3.0/src/api/internal/io/RollingBuffer_p.cpp bamtools-2.3.0/src/api/internal/io/RollingBuffer_p.h bamtools-2.3.0/src/api/internal/io/TcpSocketEngine_p.cpp bamtools-2.3.0/src/api/internal/io/TcpSocketEngine_p.h bamtools-2.3.0/src/api/internal/io/TcpSocketEngine_unix_p.cpp bamtools-2.3.0/src/api/internal/io/TcpSocketEngine_win_p.cpp bamtools-2.3.0/src/api/internal/io/TcpSocket_p.cpp bamtools-2.3.0/src/api/internal/io/TcpSocket_p.h bamtools-2.3.0/src/api/internal/sam/ bamtools-2.3.0/src/api/internal/sam/CMakeLists.txt bamtools-2.3.0/src/api/internal/sam/SamFormatParser_p.cpp bamtools-2.3.0/src/api/internal/sam/SamFormatParser_p.h bamtools-2.3.0/src/api/internal/sam/SamFormatPrinter_p.cpp bamtools-2.3.0/src/api/internal/sam/SamFormatPrinter_p.h bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.cpp bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.h bamtools-2.3.0/src/api/internal/sam/SamHeaderVersion_p.h bamtools-2.3.0/src/api/internal/utils/ bamtools-2.3.0/src/api/internal/utils/BamException_p.cpp bamtools-2.3.0/src/api/internal/utils/BamException_p.h bamtools-2.3.0/src/api/internal/utils/CMakeLists.txt bamtools-2.3.0/src/shared/ bamtools-2.3.0/src/shared/bamtools_global.h bamtools-2.3.0/src/third_party/ bamtools-2.3.0/src/third_party/CMakeLists.txt bamtools-2.3.0/src/third_party/gtest-1.6.0/ bamtools-2.3.0/src/third_party/gtest-1.6.0/CHANGES bamtools-2.3.0/src/third_party/gtest-1.6.0/CMakeLists.txt bamtools-2.3.0/src/third_party/gtest-1.6.0/CONTRIBUTORS bamtools-2.3.0/src/third_party/gtest-1.6.0/COPYING bamtools-2.3.0/src/third_party/gtest-1.6.0/README bamtools-2.3.0/src/third_party/gtest-1.6.0/cmake/ bamtools-2.3.0/src/third_party/gtest-1.6.0/cmake/internal_utils.cmake bamtools-2.3.0/src/third_party/gtest-1.6.0/fused-src/ bamtools-2.3.0/src/third_party/gtest-1.6.0/fused-src/gtest/ bamtools-2.3.0/src/third_party/gtest-1.6.0/fused-src/gtest/gtest-all.cc bamtools-2.3.0/src/third_party/gtest-1.6.0/fused-src/gtest/gtest.h bamtools-2.3.0/src/third_party/gtest-1.6.0/fused-src/gtest/gtest_main.cc bamtools-2.3.0/src/third_party/gtest-1.6.0/src/ bamtools-2.3.0/src/third_party/gtest-1.6.0/src/gtest-all.cc bamtools-2.3.0/src/third_party/gtest-1.6.0/src/gtest-death-test.cc bamtools-2.3.0/src/third_party/gtest-1.6.0/src/gtest-filepath.cc bamtools-2.3.0/src/third_party/gtest-1.6.0/src/gtest-internal-inl.h bamtools-2.3.0/src/third_party/gtest-1.6.0/src/gtest-port.cc bamtools-2.3.0/src/third_party/gtest-1.6.0/src/gtest-printers.cc bamtools-2.3.0/src/third_party/gtest-1.6.0/src/gtest-test-part.cc bamtools-2.3.0/src/third_party/gtest-1.6.0/src/gtest-typed-test.cc bamtools-2.3.0/src/third_party/gtest-1.6.0/src/gtest.cc bamtools-2.3.0/src/third_party/gtest-1.6.0/src/gtest_main.cc bamtools-2.3.0/src/third_party/jsoncpp/ bamtools-2.3.0/src/third_party/jsoncpp/CMakeLists.txt bamtools-2.3.0/src/third_party/jsoncpp/LICENSE bamtools-2.3.0/src/third_party/jsoncpp/json.h bamtools-2.3.0/src/third_party/jsoncpp/json_batchallocator.h bamtools-2.3.0/src/third_party/jsoncpp/json_config.h bamtools-2.3.0/src/third_party/jsoncpp/json_features.h bamtools-2.3.0/src/third_party/jsoncpp/json_forwards.h bamtools-2.3.0/src/third_party/jsoncpp/json_internalarray.inl bamtools-2.3.0/src/third_party/jsoncpp/json_internalmap.inl bamtools-2.3.0/src/third_party/jsoncpp/json_reader.cpp bamtools-2.3.0/src/third_party/jsoncpp/json_reader.h bamtools-2.3.0/src/third_party/jsoncpp/json_tool.h bamtools-2.3.0/src/third_party/jsoncpp/json_value.cpp bamtools-2.3.0/src/third_party/jsoncpp/json_value.h bamtools-2.3.0/src/third_party/jsoncpp/json_valueiterator.inl bamtools-2.3.0/src/third_party/jsoncpp/json_writer.cpp bamtools-2.3.0/src/third_party/jsoncpp/json_writer.h bamtools-2.3.0/src/toolkit/ bamtools-2.3.0/src/toolkit/CMakeLists.txt bamtools-2.3.0/src/toolkit/bamtools.cpp bamtools-2.3.0/src/toolkit/bamtools_convert.cpp bamtools-2.3.0/src/toolkit/bamtools_convert.h bamtools-2.3.0/src/toolkit/bamtools_count.cpp bamtools-2.3.0/src/toolkit/bamtools_count.h bamtools-2.3.0/src/toolkit/bamtools_coverage.cpp bamtools-2.3.0/src/toolkit/bamtools_coverage.h bamtools-2.3.0/src/toolkit/bamtools_filter.cpp bamtools-2.3.0/src/toolkit/bamtools_filter.h bamtools-2.3.0/src/toolkit/bamtools_header.cpp bamtools-2.3.0/src/toolkit/bamtools_header.h bamtools-2.3.0/src/toolkit/bamtools_index.cpp bamtools-2.3.0/src/toolkit/bamtools_index.h bamtools-2.3.0/src/toolkit/bamtools_merge.cpp bamtools-2.3.0/src/toolkit/bamtools_merge.h bamtools-2.3.0/src/toolkit/bamtools_random.cpp bamtools-2.3.0/src/toolkit/bamtools_random.h bamtools-2.3.0/src/toolkit/bamtools_resolve.cpp bamtools-2.3.0/src/toolkit/bamtools_resolve.h bamtools-2.3.0/src/toolkit/bamtools_revert.cpp bamtools-2.3.0/src/toolkit/bamtools_revert.h bamtools-2.3.0/src/toolkit/bamtools_sort.cpp bamtools-2.3.0/src/toolkit/bamtools_sort.h bamtools-2.3.0/src/toolkit/bamtools_split.cpp bamtools-2.3.0/src/toolkit/bamtools_split.h bamtools-2.3.0/src/toolkit/bamtools_stats.cpp bamtools-2.3.0/src/toolkit/bamtools_stats.h bamtools-2.3.0/src/toolkit/bamtools_tool.h bamtools-2.3.0/src/toolkit/bamtools_version.h.in bamtools-2.3.0/src/utils/ bamtools-2.3.0/src/utils/CMakeLists.txt bamtools-2.3.0/src/utils/bamtools_fasta.cpp bamtools-2.3.0/src/utils/bamtools_fasta.h bamtools-2.3.0/src/utils/bamtools_filter_engine.h bamtools-2.3.0/src/utils/bamtools_filter_properties.h bamtools-2.3.0/src/utils/bamtools_filter_ruleparser.h bamtools-2.3.0/src/utils/bamtools_options.cpp bamtools-2.3.0/src/utils/bamtools_options.h bamtools-2.3.0/src/utils/bamtools_pileup_engine.cpp bamtools-2.3.0/src/utils/bamtools_pileup_engine.h bamtools-2.3.0/src/utils/bamtools_utilities.cpp bamtools-2.3.0/src/utils/bamtools_utilities.h bamtools-2.3.0/src/utils/bamtools_variant.h bamtools-2.3.0/src/utils/utils_global.h sudo -u fink-bld [ENV] sh -c /tmp/fink.EJ2LT /tmp/fink.z7Gqv #!/bin/sh -ev mkdir finkbuild pushd finkbuild /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0 cmake \ -DCMAKE_INSTALL_PREFIX:PATH=/sw \ -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE \ -DCMAKE_INSTALL_NAME_DIR:PATH=/sw/lib/bamtools \ .. -- The C compiler identification is Clang 5.1.0 -- The CXX compiler identification is Clang 5.1.0 -- Check for working C compiler: /sw/var/lib/fink/path-prefix-clang/cc -- Check for working C compiler: /sw/var/lib/fink/path-prefix-clang/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /sw/var/lib/fink/path-prefix-clang/c++ -- Check for working CXX compiler: /sw/var/lib/fink/path-prefix-clang/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Configuring done -- Generating done -- Build files have been written to: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild popd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0 /bin/rm -rf /sw/build.build/root-bamtools-2.3.0-1 /bin/mkdir -p /sw/build.build/root-bamtools-2.3.0-1/sw /bin/mkdir -p /sw/build.build/root-bamtools-2.3.0-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-bamtools-2.3.0-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.N3tnA /tmp/fink.F_S_S #!/bin/sh -ev pushd finkbuild /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0 make install DESTDIR=/sw/build.build/root-bamtools-2.3.0-1 /sw/bin/cmake -H/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0 -B/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild --check-build-system CMakeFiles/Makefile.cmake 0 /sw/bin/cmake -E cmake_progress_start /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles/progress.marks /Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/Makefile2 all /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/CMakeFiles/SharedHeaders.dir/build.make src/CMakeFiles/SharedHeaders.dir/depend cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild && /sw/bin/cmake -E cmake_depends "Unix Makefiles" /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0 /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/CMakeFiles/SharedHeaders.dir/DependInfo.cmake --color= Scanning dependencies of target SharedHeaders /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/CMakeFiles/SharedHeaders.dir/build.make src/CMakeFiles/SharedHeaders.dir/build /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 83 [ 1%] Exporting SharedHeaders cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src && /sw/bin/cmake -E copy_if_different /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/shared/bamtools_global.h /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/include/shared/bamtools_global.h /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 83 [ 1%] Built target SharedHeaders /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/api/CMakeFiles/APIHeaders.dir/build.make src/api/CMakeFiles/APIHeaders.dir/depend cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild && /sw/bin/cmake -E cmake_depends "Unix Makefiles" /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0 /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api/CMakeFiles/APIHeaders.dir/DependInfo.cmake --color= Scanning dependencies of target APIHeaders /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/api/CMakeFiles/APIHeaders.dir/build.make src/api/CMakeFiles/APIHeaders.dir/build /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 1 [ 2%] Exporting APIHeaders cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -E copy_if_different /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/api_global.h /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/include/api/api_global.h cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -E copy_if_different /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlgorithms.h /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/include/api/BamAlgorithms.h cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -E copy_if_different /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlignment.h /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/include/api/BamAlignment.h cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -E copy_if_different /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAux.h /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/include/api/BamAux.h cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -E copy_if_different /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamConstants.h /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/include/api/BamConstants.h cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -E copy_if_different /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamIndex.h /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/include/api/BamIndex.h cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -E copy_if_different /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamMultiReader.h /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/include/api/BamMultiReader.h cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -E copy_if_different /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamReader.h /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/include/api/BamReader.h cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -E copy_if_different /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/include/api/BamWriter.h cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -E copy_if_different /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/IBamIODevice.h /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/include/api/IBamIODevice.h cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -E copy_if_different /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamConstants.h /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/include/api/SamConstants.h cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -E copy_if_different /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamHeader.h /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/include/api/SamHeader.h cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -E copy_if_different /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamProgram.h /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/include/api/SamProgram.h cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -E copy_if_different /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamProgramChain.h /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/include/api/SamProgramChain.h cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -E copy_if_different /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamReadGroup.h /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/include/api/SamReadGroup.h cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -E copy_if_different /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamReadGroupDictionary.h /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/include/api/SamReadGroupDictionary.h cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -E copy_if_different /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamSequence.h /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/include/api/SamSequence.h cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -E copy_if_different /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamSequenceDictionary.h /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/include/api/SamSequenceDictionary.h /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 1 [ 2%] Built target APIHeaders /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/api/CMakeFiles/AlgorithmsHeaders.dir/build.make src/api/CMakeFiles/AlgorithmsHeaders.dir/depend cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild && /sw/bin/cmake -E cmake_depends "Unix Makefiles" /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0 /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api/CMakeFiles/AlgorithmsHeaders.dir/DependInfo.cmake --color= Scanning dependencies of target AlgorithmsHeaders /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/api/CMakeFiles/AlgorithmsHeaders.dir/build.make src/api/CMakeFiles/AlgorithmsHeaders.dir/build /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 2 [ 3%] Exporting AlgorithmsHeaders cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -E copy_if_different /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/algorithms/Sort.h /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/include/api/algorithms/Sort.h /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 2 [ 3%] Built target AlgorithmsHeaders /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/api/CMakeFiles/BamTools.dir/build.make src/api/CMakeFiles/BamTools.dir/depend cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild && /sw/bin/cmake -E cmake_depends "Unix Makefiles" /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0 /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api/CMakeFiles/BamTools.dir/DependInfo.cmake --color= Scanning dependencies of target BamTools /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/api/CMakeFiles/BamTools.dir/build.make src/api/CMakeFiles/BamTools.dir/build /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 3 [ 4%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/BamAlignment.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlignment.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 4 [ 5%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamMultiReader.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 5 [ 6%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/BamReader.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamReader.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamReader.cpp:11: In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamReader_p.h:28: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] class BamAlignment; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlignment.h:32:19: note: previous use is here struct API_EXPORT BamAlignment { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here? class BamAlignment; ^~~~~ struct 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 6 [ 7%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/BamWriter.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.cpp:11: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] class BamAlignment; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlignment.h:32:19: note: previous use is here struct API_EXPORT BamAlignment { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:19:1: note: did you mean struct here? class BamAlignment; ^~~~~ struct In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.cpp:12: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/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 { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:20:1: note: did you mean struct here? class SamHeader; ^~~~~ struct 2 warnings generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 7 [ 8%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/SamHeader.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamHeader.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamHeader.cpp:13: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamFormatParser_p.h:28:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] class SamHeader; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamHeader.h:22:19: note: previous use is here struct API_EXPORT SamHeader { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamFormatParser_p.h:28:1: note: did you mean struct here? class SamHeader; ^~~~~ struct In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamHeader.cpp:15: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.h:30:1: warning: class 'SamReadGroup' was previously declared as a struct [-Wmismatched-tags] class SamReadGroup; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamReadGroup.h:18:19: note: previous use is here struct API_EXPORT SamReadGroup { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.h:30:1: note: did you mean struct here? class SamReadGroup; ^~~~~ struct /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.h:31:1: warning: class 'SamSequence' was previously declared as a struct [-Wmismatched-tags] class SamSequence; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamSequence.h:18:19: note: previous use is here struct API_EXPORT SamSequence { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.h:31:1: note: did you mean struct here? class SamSequence; ^~~~~ struct 3 warnings generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 8 [ 9%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/SamProgram.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamProgram.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 9 [ 10%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamProgramChain.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 10 [ 11%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamReadGroup.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 11 [ 12%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamReadGroupDictionary.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 12 [ 13%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/SamSequence.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamSequence.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 13 [ 14%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamSequenceDictionary.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 14 [ 15%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamHeader_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 15 [ 16%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamMultiReader_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 16 [ 17%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.cpp:12: In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamReader_p.h:23: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/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 { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here? class BamAlignment; ^~~~~ struct 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 17 [ 18%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamReader_p.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamReader_p.cpp:14: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] class BamAlignment; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlignment.h:32:19: note: previous use is here struct API_EXPORT BamAlignment { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here? class BamAlignment; ^~~~~ struct 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 18 [ 19%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamWriter_p.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamWriter_p.cpp:13: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamWriter_p.h:30:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] class BamAlignment; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlignment.h:32:19: note: previous use is here struct API_EXPORT BamAlignment { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamWriter_p.h:30:1: note: did you mean struct here? class BamAlignment; ^~~~~ struct 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 19 [ 20%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/index/BamIndexFactory_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 20 [ 21%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/index/BamStandardIndex_p.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/index/BamStandardIndex_p.cpp:11: In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamReader_p.h:28: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] class BamAlignment; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlignment.h:32:19: note: previous use is here struct API_EXPORT BamAlignment { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here? class BamAlignment; ^~~~~ struct 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 21 [ 22%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/index/BamToolsIndex_p.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/index/BamToolsIndex_p.cpp:11: In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamReader_p.h:28: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] class BamAlignment; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlignment.h:32:19: note: previous use is here struct API_EXPORT BamAlignment { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here? class BamAlignment; ^~~~~ struct 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 22 [ 23%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/BamDeviceFactory_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 23 [ 24%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/BamFile_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 24 [ 25%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/BamFtp_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 25 [ 26%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/BamHttp_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 26 [ 27%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/BamPipe_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 27 [ 28%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/BgzfStream_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 28 [ 29%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/ByteArray_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 29 [ 30%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/HostAddress_p.cpp /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/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. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 30 [ 31%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/HostInfo_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 31 [ 32%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/HttpHeader_p.cpp /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/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. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 32 [ 33%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/ILocalIODevice_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 33 [ 34%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/RollingBuffer_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 34 [ 35%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/TcpSocket_p.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/TcpSocket_p.cpp:12: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/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 { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here? class TcpSocketEngine; ^~~~~ struct 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 35 [ 36%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/TcpSocketEngine_p.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/TcpSocketEngine_p.cpp:15: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/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 { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here? class TcpSocketEngine; ^~~~~ struct 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 36 [ 37%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/TcpSocketEngine_unix_p.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/TcpSocketEngine_unix_p.cpp:10: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/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 { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here? class TcpSocketEngine; ^~~~~ struct 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 37 [ 38%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamFormatParser_p.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamFormatParser_p.cpp:12: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamFormatParser_p.h:28:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] class SamHeader; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamHeader.h:22:19: note: previous use is here struct API_EXPORT SamHeader { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamFormatParser_p.h:28:1: note: did you mean struct here? class SamHeader; ^~~~~ struct 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 38 [ 39%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamFormatPrinter_p.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamFormatPrinter_p.cpp:12: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamFormatPrinter_p.h:28:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] class SamHeader; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamHeader.h:22:19: note: previous use is here struct API_EXPORT SamHeader { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamFormatPrinter_p.h:28:1: note: did you mean struct here? class SamHeader; ^~~~~ struct 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 39 [ 40%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.cpp:12: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.h:29:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] class SamHeader; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamHeader.h:22:19: note: previous use is here struct API_EXPORT SamHeader { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.h:29:1: note: did you mean struct here? class SamHeader; ^~~~~ struct /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.h:30:1: warning: class 'SamReadGroup' was previously declared as a struct [-Wmismatched-tags] class SamReadGroup; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamReadGroup.h:18:19: note: previous use is here struct API_EXPORT SamReadGroup { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.h:30:1: note: did you mean struct here? class SamReadGroup; ^~~~~ struct /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.h:31:1: warning: class 'SamSequence' was previously declared as a struct [-Wmismatched-tags] class SamSequence; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamSequence.h:18:19: note: previous use is here struct API_EXPORT SamSequence { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.h:31:1: note: did you mean struct here? class SamSequence; ^~~~~ struct 3 warnings generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 40 [ 41%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -fPIC -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/utils/BamException_p.cpp Linking CXX shared library ../../../lib/libbamtools.dylib cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -E cmake_link_script CMakeFiles/BamTools.dir/link.txt --verbose=1 /sw/var/lib/fink/path-prefix-clang/c++ -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -dynamiclib -Wl,-headerpad_max_install_names -L/sw/lib -compatibility_version 2.3.0 -o ../../../lib/libbamtools.2.3.0.dylib -install_name /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/lib/libbamtools.2.3.0.dylib CMakeFiles/BamTools.dir/BamAlignment.cpp.o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o CMakeFiles/BamTools.dir/BamReader.cpp.o CMakeFiles/BamTools.dir/BamWriter.cpp.o CMakeFiles/BamTools.dir/SamHeader.cpp.o CMakeFiles/BamTools.dir/SamProgram.cpp.o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o CMakeFiles/BamTools.dir/SamSequence.cpp.o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -lz cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -E cmake_symlink_library ../../../lib/libbamtools.2.3.0.dylib ../../../lib/libbamtools.2.3.0.dylib ../../../lib/libbamtools.dylib /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 [ 41%] Built target BamTools /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/api/CMakeFiles/BamTools-static.dir/build.make src/api/CMakeFiles/BamTools-static.dir/depend cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild && /sw/bin/cmake -E cmake_depends "Unix Makefiles" /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0 /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api/CMakeFiles/BamTools-static.dir/DependInfo.cmake --color= Scanning dependencies of target BamTools-static /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/api/CMakeFiles/BamTools-static.dir/build.make src/api/CMakeFiles/BamTools-static.dir/build /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 41 [ 42%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlignment.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 42 [ 43%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamMultiReader.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 43 [ 44%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamReader.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/BamReader.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamReader.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamReader.cpp:11: In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamReader_p.h:28: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] class BamAlignment; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlignment.h:32:19: note: previous use is here struct API_EXPORT BamAlignment { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here? class BamAlignment; ^~~~~ struct 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 44 [ 45%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamWriter.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/BamWriter.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.cpp:11: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] class BamAlignment; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlignment.h:32:19: note: previous use is here struct API_EXPORT BamAlignment { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:19:1: note: did you mean struct here? class BamAlignment; ^~~~~ struct In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.cpp:12: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/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 { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:20:1: note: did you mean struct here? class SamHeader; ^~~~~ struct 2 warnings generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 45 [ 46%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamHeader.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/SamHeader.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamHeader.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamHeader.cpp:13: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamFormatParser_p.h:28:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] class SamHeader; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamHeader.h:22:19: note: previous use is here struct API_EXPORT SamHeader { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamFormatParser_p.h:28:1: note: did you mean struct here? class SamHeader; ^~~~~ struct In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamHeader.cpp:15: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.h:30:1: warning: class 'SamReadGroup' was previously declared as a struct [-Wmismatched-tags] class SamReadGroup; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamReadGroup.h:18:19: note: previous use is here struct API_EXPORT SamReadGroup { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.h:30:1: note: did you mean struct here? class SamReadGroup; ^~~~~ struct /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.h:31:1: warning: class 'SamSequence' was previously declared as a struct [-Wmismatched-tags] class SamSequence; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamSequence.h:18:19: note: previous use is here struct API_EXPORT SamSequence { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.h:31:1: note: did you mean struct here? class SamSequence; ^~~~~ struct 3 warnings generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 46 [ 47%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgram.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/SamProgram.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamProgram.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 47 [ 48%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamProgramChain.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 48 [ 49%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamReadGroup.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 49 [ 50%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamReadGroupDictionary.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 50 [ 51%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequence.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/SamSequence.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamSequence.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 51 [ 52%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamSequenceDictionary.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 52 [ 53%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamHeader_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/bam/BamHeader_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamHeader_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 53 [ 54%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamMultiReader_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/bam/BamMultiReader_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamMultiReader_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 54 [ 55%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamRandomAccessController_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/bam/BamRandomAccessController_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.cpp:12: In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamReader_p.h:23: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/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 { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here? class BamAlignment; ^~~~~ struct 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 55 [ 56%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamReader_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/bam/BamReader_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamReader_p.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamReader_p.cpp:14: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] class BamAlignment; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlignment.h:32:19: note: previous use is here struct API_EXPORT BamAlignment { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here? class BamAlignment; ^~~~~ struct 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 56 [ 57%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamWriter_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/bam/BamWriter_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamWriter_p.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamWriter_p.cpp:13: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamWriter_p.h:30:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] class BamAlignment; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlignment.h:32:19: note: previous use is here struct API_EXPORT BamAlignment { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamWriter_p.h:30:1: note: did you mean struct here? class BamAlignment; ^~~~~ struct 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 57 [ 58%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamIndexFactory_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/index/BamIndexFactory_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/index/BamIndexFactory_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 58 [ 59%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamStandardIndex_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/index/BamStandardIndex_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/index/BamStandardIndex_p.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/index/BamStandardIndex_p.cpp:11: In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamReader_p.h:28: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] class BamAlignment; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlignment.h:32:19: note: previous use is here struct API_EXPORT BamAlignment { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here? class BamAlignment; ^~~~~ struct 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 59 [ 60%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamToolsIndex_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/index/BamToolsIndex_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/index/BamToolsIndex_p.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/index/BamToolsIndex_p.cpp:11: In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamReader_p.h:28: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] class BamAlignment; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlignment.h:32:19: note: previous use is here struct API_EXPORT BamAlignment { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here? class BamAlignment; ^~~~~ struct 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 60 [ 61%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamDeviceFactory_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/BamDeviceFactory_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/BamDeviceFactory_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 61 [ 62%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFile_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/BamFile_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/BamFile_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 62 [ 63%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFtp_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/BamFtp_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/BamFtp_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 63 [ 64%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamHttp_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/BamHttp_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/BamHttp_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 64 [ 65%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/BamPipe_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 65 [ 66%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BgzfStream_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/BgzfStream_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/BgzfStream_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 66 [ 67%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ByteArray_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/ByteArray_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/ByteArray_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 67 [ 68%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/HostAddress_p.cpp /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/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. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 68 [ 69%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/HostInfo_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 69 [ 70%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/HttpHeader_p.cpp /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/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. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 70 [ 71%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/ILocalIODevice_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 71 [ 72%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/RollingBuffer_p.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 72 [ 73%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/TcpSocket_p.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/TcpSocket_p.cpp:12: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/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 { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here? class TcpSocketEngine; ^~~~~ struct 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 73 [ 74%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/TcpSocketEngine_p.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/TcpSocketEngine_p.cpp:15: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/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 { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here? class TcpSocketEngine; ^~~~~ struct 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 74 [ 75%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/TcpSocketEngine_unix_p.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/TcpSocketEngine_unix_p.cpp:10: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/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 { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here? class TcpSocketEngine; ^~~~~ struct 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 75 [ 76%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamFormatParser_p.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamFormatParser_p.cpp:12: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamFormatParser_p.h:28:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] class SamHeader; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamHeader.h:22:19: note: previous use is here struct API_EXPORT SamHeader { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamFormatParser_p.h:28:1: note: did you mean struct here? class SamHeader; ^~~~~ struct 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 76 [ 77%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamFormatPrinter_p.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamFormatPrinter_p.cpp:12: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamFormatPrinter_p.h:28:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] class SamHeader; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamHeader.h:22:19: note: previous use is here struct API_EXPORT SamHeader { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamFormatPrinter_p.h:28:1: note: did you mean struct here? class SamHeader; ^~~~~ struct 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 77 [ 78%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.cpp:12: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.h:29:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] class SamHeader; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamHeader.h:22:19: note: previous use is here struct API_EXPORT SamHeader { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.h:29:1: note: did you mean struct here? class SamHeader; ^~~~~ struct /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.h:30:1: warning: class 'SamReadGroup' was previously declared as a struct [-Wmismatched-tags] class SamReadGroup; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamReadGroup.h:18:19: note: previous use is here struct API_EXPORT SamReadGroup { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.h:30:1: note: did you mean struct here? class SamReadGroup; ^~~~~ struct /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.h:31:1: warning: class 'SamSequence' was previously declared as a struct [-Wmismatched-tags] class SamSequence; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamSequence.h:18:19: note: previous use is here struct API_EXPORT SamSequence { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/sam/SamHeaderValidator_p.h:31:1: note: did you mean struct here? class SamSequence; ^~~~~ struct 3 warnings generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 78 [ 79%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/internal/utils/BamException_p.cpp Linking CXX static library ../../../lib/libbamtools.a cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -P CMakeFiles/BamTools-static.dir/cmake_clean_target.cmake cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/api && /sw/bin/cmake -E cmake_link_script CMakeFiles/BamTools-static.dir/link.txt --verbose=1 /usr/bin/ar cr ../../../lib/libbamtools.a CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o CMakeFiles/BamTools-static.dir/BamReader.cpp.o CMakeFiles/BamTools-static.dir/BamWriter.cpp.o CMakeFiles/BamTools-static.dir/SamHeader.cpp.o CMakeFiles/BamTools-static.dir/SamProgram.cpp.o CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o CMakeFiles/BamTools-static.dir/SamSequence.cpp.o CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o CMakeFiles/BamTools-static.dir/internal/bam/BamHeader_p.cpp.o CMakeFiles/BamTools-static.dir/internal/bam/BamMultiReader_p.cpp.o CMakeFiles/BamTools-static.dir/internal/bam/BamRandomAccessController_p.cpp.o CMakeFiles/BamTools-static.dir/internal/bam/BamReader_p.cpp.o CMakeFiles/BamTools-static.dir/internal/bam/BamWriter_p.cpp.o CMakeFiles/BamTools-static.dir/internal/index/BamIndexFactory_p.cpp.o CMakeFiles/BamTools-static.dir/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools-static.dir/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/BamFtp_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/BamHttp_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o /usr/bin/ranlib ../../../lib/libbamtools.a /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 [ 79%] Built target BamTools-static /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/build.make src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/depend cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild && /sw/bin/cmake -E cmake_depends "Unix Makefiles" /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0 /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/third_party/jsoncpp /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/third_party/jsoncpp /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/DependInfo.cmake --color= Scanning dependencies of target jsoncpp /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/build.make src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/build /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 98 [ 80%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_reader.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/third_party/jsoncpp && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_JSONCPP_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/jsoncpp.dir/json_reader.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/third_party/jsoncpp/json_reader.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 99 [ 81%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_value.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/third_party/jsoncpp && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_JSONCPP_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/jsoncpp.dir/json_value.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/third_party/jsoncpp/json_value.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 100 [ 82%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_writer.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/third_party/jsoncpp && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_JSONCPP_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -Wall -fPIC -o CMakeFiles/jsoncpp.dir/json_writer.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/third_party/jsoncpp/json_writer.cpp Linking CXX static library ../../../../lib/libjsoncpp.a cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/third_party/jsoncpp && /sw/bin/cmake -P CMakeFiles/jsoncpp.dir/cmake_clean_target.cmake cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/third_party/jsoncpp && /sw/bin/cmake -E cmake_link_script CMakeFiles/jsoncpp.dir/link.txt --verbose=1 /usr/bin/ar cr ../../../../lib/libjsoncpp.a CMakeFiles/jsoncpp.dir/json_reader.cpp.o CMakeFiles/jsoncpp.dir/json_value.cpp.o CMakeFiles/jsoncpp.dir/json_writer.cpp.o /usr/bin/ranlib ../../../../lib/libjsoncpp.a /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 98 99 100 [ 82%] Built target jsoncpp /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/depend cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild && /sw/bin/cmake -E cmake_depends "Unix Makefiles" /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0 /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/utils /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/utils /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/utils/CMakeFiles/BamTools-utils.dir/DependInfo.cmake --color= Scanning dependencies of target BamTools-utils /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/build /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 79 [ 83%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/utils && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_UTILS_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api -Wall -fPIC -o CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/utils/bamtools_fasta.cpp /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/utils/bamtools_fasta.cpp:90:23: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if (seqLength < 0) ~~~~~~~~~ ^ ~ 1 warning generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 80 [ 84%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/utils && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_UTILS_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api -Wall -fPIC -o CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/utils/bamtools_options.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 81 [ 85%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/utils && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_UTILS_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api -Wall -fPIC -o CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/utils/bamtools_pileup_engine.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 82 [ 86%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/utils && /sw/var/lib/fink/path-prefix-clang/c++ -DBAMTOOLS_UTILS_LIBRARY -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api -Wall -fPIC -o CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/utils/bamtools_utilities.cpp Linking CXX static library ../../../lib/libbamtools-utils.a cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/utils && /sw/bin/cmake -P CMakeFiles/BamTools-utils.dir/cmake_clean_target.cmake cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/utils && /sw/bin/cmake -E cmake_link_script CMakeFiles/BamTools-utils.dir/link.txt --verbose=1 /usr/bin/ar cr ../../../lib/libbamtools-utils.a CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o /usr/bin/ranlib ../../../lib/libbamtools-utils.a /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 79 80 81 82 [ 86%] Built target BamTools-utils /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make src/toolkit/CMakeFiles/bamtools_cmd.dir/depend cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild && /sw/bin/cmake -E cmake_depends "Unix Makefiles" /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0 /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/toolkit /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/toolkit/CMakeFiles/bamtools_cmd.dir/DependInfo.cmake --color= Scanning dependencies of target bamtools_cmd /Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make src/toolkit/CMakeFiles/bamtools_cmd.dir/build /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 84 [ 87%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/toolkit && /sw/var/lib/fink/path-prefix-clang/c++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/utils -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_convert.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 85 [ 88%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/toolkit && /sw/var/lib/fink/path-prefix-clang/c++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/utils -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_count.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 86 [ 89%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/toolkit && /sw/var/lib/fink/path-prefix-clang/c++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/utils -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_coverage.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 87 [ 90%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/toolkit && /sw/var/lib/fink/path-prefix-clang/c++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/utils -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_filter.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_filter.cpp:13: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] class BamAlignment; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlignment.h:32:19: note: previous use is here struct API_EXPORT BamAlignment { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:19:1: note: did you mean struct here? class BamAlignment; ^~~~~ struct /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] class SamHeader; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamHeader.h:22:19: note: previous use is here struct API_EXPORT SamHeader { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:20:1: note: did you mean struct here? class SamHeader; ^~~~~ struct /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/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 { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_filter.h:31:9: note: did you mean class here? struct FilterToolPrivate; ^~~~~~ class 3 warnings generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 88 [ 91%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/toolkit && /sw/var/lib/fink/path-prefix-clang/c++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/utils -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_header.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 89 [ 92%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/toolkit && /sw/var/lib/fink/path-prefix-clang/c++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/utils -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_index.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 90 [ 93%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/toolkit && /sw/var/lib/fink/path-prefix-clang/c++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/utils -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_merge.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_merge.cpp:13: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] class BamAlignment; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlignment.h:32:19: note: previous use is here struct API_EXPORT BamAlignment { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:19:1: note: did you mean struct here? class BamAlignment; ^~~~~ struct /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] class SamHeader; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamHeader.h:22:19: note: previous use is here struct API_EXPORT SamHeader { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:20:1: note: did you mean struct here? class SamHeader; ^~~~~ struct 2 warnings generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 91 [ 94%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/toolkit && /sw/var/lib/fink/path-prefix-clang/c++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/utils -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_random.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_random.cpp:13: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] class BamAlignment; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlignment.h:32:19: note: previous use is here struct API_EXPORT BamAlignment { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:19:1: note: did you mean struct here? class BamAlignment; ^~~~~ struct /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] class SamHeader; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamHeader.h:22:19: note: previous use is here struct API_EXPORT SamHeader { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:20:1: note: did you mean struct here? class SamHeader; ^~~~~ struct 2 warnings generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 92 [ 95%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/toolkit && /sw/var/lib/fink/path-prefix-clang/c++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/utils -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_resolve.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_resolve.cpp:13: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] class BamAlignment; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlignment.h:32:19: note: previous use is here struct API_EXPORT BamAlignment { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:19:1: note: did you mean struct here? class BamAlignment; ^~~~~ struct /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] class SamHeader; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamHeader.h:22:19: note: previous use is here struct API_EXPORT SamHeader { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:20:1: note: did you mean struct here? class SamHeader; ^~~~~ struct /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_resolve.cpp:48:19: warning: unused variable 'OPEN_BRACE_CHAR' [-Wunused-const-variable] static const char OPEN_BRACE_CHAR = '['; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/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. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 93 [ 96%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/toolkit && /sw/var/lib/fink/path-prefix-clang/c++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/utils -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_revert.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_revert.cpp:13: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] class BamAlignment; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlignment.h:32:19: note: previous use is here struct API_EXPORT BamAlignment { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:19:1: note: did you mean struct here? class BamAlignment; ^~~~~ struct /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] class SamHeader; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamHeader.h:22:19: note: previous use is here struct API_EXPORT SamHeader { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:20:1: note: did you mean struct here? class SamHeader; ^~~~~ struct 2 warnings generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 94 [ 97%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/toolkit && /sw/var/lib/fink/path-prefix-clang/c++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/utils -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_sort.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_sort.cpp:14: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] class BamAlignment; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlignment.h:32:19: note: previous use is here struct API_EXPORT BamAlignment { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:19:1: note: did you mean struct here? class BamAlignment; ^~~~~ struct /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] class SamHeader; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamHeader.h:22:19: note: previous use is here struct API_EXPORT SamHeader { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:20:1: note: did you mean struct here? class SamHeader; ^~~~~ struct /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/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 { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_sort.h:31:9: note: did you mean class here? struct SortToolPrivate; ^~~~~~ class 3 warnings generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 95 [ 98%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/toolkit && /sw/var/lib/fink/path-prefix-clang/c++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/utils -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_split.cpp In file included from /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_split.cpp:15: /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] class BamAlignment; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamAlignment.h:32:19: note: previous use is here struct API_EXPORT BamAlignment { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:19:1: note: did you mean struct here? class BamAlignment; ^~~~~ struct /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] class SamHeader; ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/SamHeader.h:22:19: note: previous use is here struct API_EXPORT SamHeader { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api/BamWriter.h:20:1: note: did you mean struct here? class SamHeader; ^~~~~ struct /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/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 { ^ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_split.h:32:9: note: did you mean class here? struct SplitToolPrivate; ^~~~~~ class 3 warnings generated. /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 96 [ 99%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/toolkit && /sw/var/lib/fink/path-prefix-clang/c++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/utils -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools_stats.cpp /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 97 [100%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/toolkit && /sw/var/lib/fink/path-prefix-clang/c++ -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/api -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/utils -I/sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/third_party -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o -c /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools.cpp /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools.cpp:149:16: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] if ( (argc == 1) ) return Help(argc, argv); ~~~~~^~~~ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/src/toolkit/bamtools.cpp:149:16: note: remove extraneous parentheses around the comparison to silence this warning if ( (argc == 1) ) return Help(argc, argv); ~ ^ ~ /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/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 cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/toolkit && /sw/bin/cmake -E cmake_link_script CMakeFiles/bamtools_cmd.dir/link.txt --verbose=1 /sw/var/lib/fink/path-prefix-clang/c++ -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -Wl,-search_paths_first -Wl,-headerpad_max_install_names -L/sw/lib CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o -o ../../../bin/bamtools-2.3.0 ../../../lib/libbamtools.2.3.0.dylib ../../../lib/libbamtools-utils.a ../../../lib/libjsoncpp.a ../../../lib/libbamtools.2.3.0.dylib -lz cd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/src/toolkit && /sw/bin/cmake -E cmake_symlink_executable ../../../bin/bamtools-2.3.0 ../../../bin/bamtools /sw/bin/cmake -E cmake_progress_report /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 84 85 86 87 88 89 90 91 92 93 94 95 96 97 [100%] Built target bamtools_cmd /sw/bin/cmake -E cmake_progress_start /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0/finkbuild/CMakeFiles 0 /Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/Makefile2 preinstall make[1]: Nothing to be done for `preinstall'. Install the project... /sw/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/include/bamtools/shared/bamtools_global.h -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/lib/bamtools/libbamtools.2.3.0.dylib -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/lib/bamtools/libbamtools.dylib -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/lib/bamtools/libbamtools.a -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/include/bamtools/api/api_global.h -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/include/bamtools/api/BamAlgorithms.h -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/include/bamtools/api/BamAlignment.h -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/include/bamtools/api/BamAux.h -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/include/bamtools/api/BamConstants.h -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/include/bamtools/api/BamIndex.h -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/include/bamtools/api/BamMultiReader.h -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/include/bamtools/api/BamReader.h -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/include/bamtools/api/BamWriter.h -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/include/bamtools/api/IBamIODevice.h -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/include/bamtools/api/SamConstants.h -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/include/bamtools/api/SamHeader.h -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/include/bamtools/api/SamProgram.h -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/include/bamtools/api/SamProgramChain.h -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/include/bamtools/api/SamReadGroup.h -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/include/bamtools/api/SamReadGroupDictionary.h -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/include/bamtools/api/SamSequence.h -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/include/bamtools/api/SamSequenceDictionary.h -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/include/bamtools/api/algorithms/Sort.h -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/bin/bamtools-2.3.0 -- Installing: /sw/build.build/root-bamtools-2.3.0-1/sw/bin/bamtools popd /sw/build.build/bamtools-2.3.0-1/bamtools-2.3.0 rm -r /sw/build.build/root-bamtools-2.3.0-1/sw/include /sw/build.build/root-bamtools-2.3.0-1/sw/lib/bamtools/libbamtools.{a,dylib} sudo -u fink-bld [ENV] sh -c /tmp/fink.DMlrj /usr/bin/install -d -m 700 /sw/build.build/root-bamtools-2.3.0-1/sw/share/doc/bamtools /bin/cp -r LICENSE /sw/build.build/root-bamtools-2.3.0-1/sw/share/doc/bamtools/ /bin/cp -r README /sw/build.build/root-bamtools-2.3.0-1/sw/share/doc/bamtools/ /bin/chmod -R go=u-w /sw/build.build/root-bamtools-2.3.0-1/sw/share/doc/bamtools /bin/rm -f /sw/build.build/root-bamtools-2.3.0-1/sw/info/dir /sw/build.build/root-bamtools-2.3.0-1/sw/info/dir.old /sw/build.build/root-bamtools-2.3.0-1/sw/share/info/dir /sw/build.build/root-bamtools-2.3.0-1/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Creating shlibs files... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-bamtools-2.3.0-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `bamtools' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/bamtools_2.3.0-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-bamtools-2.3.0-1 (Reading database ... 5028 files and directories currently installed.) Removing fink-buildlock-bamtools-2.3.0-1 ...