printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild cufflinks 2>&1 WARNING: your info file index has not been updated for 22 days. You should run 'fink selfupdate' to get the latest package descriptions. The package 'cufflinks' will be built without being installed. Reading build dependency for cufflinks-2.2.1-2... Reading dependency for cufflinks-2.2.1-2... Reading build conflict for cufflinks-2.2.1-2... The package 'boost1.55-nopython' will be installed. Reading dependency for boost1.55-nopython-1.55.0-4... Reading runtime dependency for boost1.55-nopython-1.55.0-4... The package 'eigen3' will be installed. Reading dependency for eigen3-3.2.1-1... Reading runtime dependency for eigen3-3.2.1-1... The package 'fink-package-precedence' will be installed. Reading dependency for fink-package-precedence-0.18-1... Reading runtime dependency for fink-package-precedence-0.18-1... The package 'libbam0-dev' will be installed. Reading dependency for libbam0-dev-0.1.19-2... Reading runtime dependency for libbam0-dev-0.1.19-2... The package 'boost1.55-nopython-shlibs' will be installed. Reading dependency for boost1.55-nopython-shlibs-1.55.0-4... Reading runtime dependency for boost1.55-nopython-shlibs-1.55.0-4... The package 'openmpi-shlibs' will be installed. Reading dependency for openmpi-shlibs-1.8.1-3... Reading runtime dependency for openmpi-shlibs-1.8.1-3... The package 'gcc49-shlibs' will be installed. Reading dependency for gcc49-shlibs-4.9.1-1000... Reading runtime dependency for gcc49-shlibs-4.9.1-1000... The package 'hwloc-shlibs' will be installed. Reading dependency for hwloc-shlibs-1.9-1... Reading runtime dependency for hwloc-shlibs-1.9-1... The following package will be rebuilt: cufflinks The following 8 additional packages will be installed: boost1.55-nopython boost1.55-nopython-shlibs eigen3 fink-package-precedence gcc49-shlibs hwloc-shlibs libbam0-dev openmpi-shlibs Do you want to continue? [Y/n] (assuming default) Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/eigen3_3.2.1-1_darwin-x86_64.deb Selecting previously deselected package eigen3. (Reading database ... 4405 files and directories currently installed.) Unpacking eigen3 (from .../eigen3_3.2.1-1_darwin-x86_64.deb) ... Setting up eigen3 (3.2.1-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/fink-package-precedence_0.18-1_darwin-x86_64.deb Selecting previously deselected package fink-package-precedence. (Reading database ... 4823 files and directories currently installed.) Unpacking fink-package-precedence (from .../fink-package-precedence_0.18-1_darwin-x86_64.deb) ... Setting up fink-package-precedence (0.18-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/gcc49-shlibs_4.9.1-1000_darwin-x86_64.deb Selecting previously deselected package gcc49-shlibs. (Reading database ... 4824 files and directories currently installed.) Unpacking gcc49-shlibs (from .../gcc49-shlibs_4.9.1-1000_darwin-x86_64.deb) ... Setting up gcc49-shlibs (4.9.1-1000) ... Clearing dependency_libs of .la files being installed Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/devel/hwloc-shlibs_1.9-1_darwin-x86_64.deb Selecting previously deselected package hwloc-shlibs. (Reading database ... 4869 files and directories currently installed.) Unpacking hwloc-shlibs (from .../hwloc-shlibs_1.9-1_darwin-x86_64.deb) ... Setting up hwloc-shlibs (1.9-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/libbam0-dev_0.1.19-2_darwin-x86_64.deb Selecting previously deselected package libbam0-dev. (Reading database ... 4875 files and directories currently installed.) Unpacking libbam0-dev (from .../libbam0-dev_0.1.19-2_darwin-x86_64.deb) ... Setting up libbam0-dev (0.1.19-2) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/devel/openmpi-shlibs_1.8.1-3_darwin-x86_64.deb Selecting previously deselected package openmpi-shlibs. (Reading database ... 4900 files and directories currently installed.) Unpacking openmpi-shlibs (from .../openmpi-shlibs_1.8.1-3_darwin-x86_64.deb) ... Setting up openmpi-shlibs (1.8.1-3) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/boost1.55-nopython_1.55.0-4_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/boost1.55-nopython-shlibs_1.55.0-4_darwin-x86_64.deb Selecting previously deselected package boost1.55-nopython. (Reading database ... 4923 files and directories currently installed.) Unpacking boost1.55-nopython (from .../boost1.55-nopython_1.55.0-4_darwin-x86_64.deb) ... Selecting previously deselected package boost1.55-nopython-shlibs. Unpacking boost1.55-nopython-shlibs (from .../boost1.55-nopython-shlibs_1.55.0-4_darwin-x86_64.deb) ... Setting up boost1.55-nopython-shlibs (1.55.0-4) ... Setting up boost1.55-nopython (1.55.0-4) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-cufflinks-2.2.1-2 /sw/build.build dpkg-deb: building package `fink-buildlock-cufflinks-2.2.1-2' in `/sw/build.build/fink-buildlock-cufflinks-2.2.1-2_2014.08.16-11.13.46_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-cufflinks-2.2.1-2_2014.08.16-11.13.46_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-cufflinks-2.2.1-2. (Reading database ... 52040 files and directories currently installed.) Unpacking fink-buildlock-cufflinks-2.2.1-2 (from .../fink-buildlock-cufflinks-2.2.1-2_2014.08.16-11.13.46_darwin-x86_64.deb) ... Setting up fink-buildlock-cufflinks-2.2.1-2 (2014.08.16-11.13.46) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.WO4it env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/cufflinks-2.2.1.tar.gz cufflinks-2.2.1/ cufflinks-2.2.1/ax_boost_system.m4 cufflinks-2.2.1/config.h.in cufflinks-2.2.1/LICENSE cufflinks-2.2.1/configure cufflinks-2.2.1/configure.ac cufflinks-2.2.1/build-aux/ cufflinks-2.2.1/build-aux/install-sh cufflinks-2.2.1/build-aux/config.sub cufflinks-2.2.1/build-aux/config.guess cufflinks-2.2.1/build-aux/missing cufflinks-2.2.1/build-aux/depcomp cufflinks-2.2.1/README cufflinks-2.2.1/Makefile.in cufflinks-2.2.1/ax_bam.m4 cufflinks-2.2.1/aclocal.m4 cufflinks-2.2.1/src/ cufflinks-2.2.1/src/codons.h cufflinks-2.2.1/src/GFaSeqGet.cpp cufflinks-2.2.1/src/gff_utils.h cufflinks-2.2.1/src/graph_optimize.h cufflinks-2.2.1/src/tokenize.h cufflinks-2.2.1/src/cuffnorm.cpp cufflinks-2.2.1/src/GStr.h cufflinks-2.2.1/src/GVec.hh cufflinks-2.2.1/src/matching_merge.cpp cufflinks-2.2.1/src/GHash.hh cufflinks-2.2.1/src/tokenize.cpp cufflinks-2.2.1/src/assemble.h cufflinks-2.2.1/src/tracking.h cufflinks-2.2.1/src/biascorrection.h cufflinks-2.2.1/src/gff.h cufflinks-2.2.1/src/gffread.cpp cufflinks-2.2.1/src/update_check.h cufflinks-2.2.1/src/GBase.cpp cufflinks-2.2.1/src/sampling.h cufflinks-2.2.1/src/gff_utils.cpp cufflinks-2.2.1/src/cuffmerge cufflinks-2.2.1/src/matching_merge.h cufflinks-2.2.1/src/biascorrection.cpp cufflinks-2.2.1/src/gtf_to_sam.cpp cufflinks-2.2.1/src/hits.h cufflinks-2.2.1/src/common.cpp cufflinks-2.2.1/src/clustering.h cufflinks-2.2.1/src/GBase.h cufflinks-2.2.1/src/differential.cpp cufflinks-2.2.1/src/bundles.cpp cufflinks-2.2.1/src/compress_gtf.cpp cufflinks-2.2.1/src/cuffdiff.cpp cufflinks-2.2.1/src/scaffolds.cpp cufflinks-2.2.1/src/sampling.cpp cufflinks-2.2.1/src/common.h cufflinks-2.2.1/src/codons.cpp cufflinks-2.2.1/src/tracking.cpp cufflinks-2.2.1/src/cuffcompare.cpp cufflinks-2.2.1/src/filters.cpp cufflinks-2.2.1/src/GStr.cpp cufflinks-2.2.1/src/Makefile.in cufflinks-2.2.1/src/transitive_reduction.h cufflinks-2.2.1/src/gtf_tracking.h cufflinks-2.2.1/src/gdna.h cufflinks-2.2.1/src/differential.h cufflinks-2.2.1/src/multireads.cpp cufflinks-2.2.1/src/gdna.cpp cufflinks-2.2.1/src/scaffold_graph.h cufflinks-2.2.1/src/scaffold_graph.cpp cufflinks-2.2.1/src/genes.h cufflinks-2.2.1/src/jensen_shannon.cpp cufflinks-2.2.1/src/transitive_closure.h cufflinks-2.2.1/src/genes.cpp cufflinks-2.2.1/src/GArgs.cpp cufflinks-2.2.1/src/multireads.h cufflinks-2.2.1/src/scaffolds.h cufflinks-2.2.1/src/graph_optimize.cpp cufflinks-2.2.1/src/gtf_tracking.cpp cufflinks-2.2.1/src/rounding.h cufflinks-2.2.1/src/Makefile.am cufflinks-2.2.1/src/hits.cpp cufflinks-2.2.1/src/clustering.cpp cufflinks-2.2.1/src/gff.cpp cufflinks-2.2.1/src/GList.hh cufflinks-2.2.1/src/replicates.cpp cufflinks-2.2.1/src/bundles.h cufflinks-2.2.1/src/cufflinks.cpp cufflinks-2.2.1/src/GFaSeqGet.h cufflinks-2.2.1/src/GFastaIndex.cpp cufflinks-2.2.1/src/negative_binomial_distribution.h cufflinks-2.2.1/src/progressbar.h cufflinks-2.2.1/src/abundances.h cufflinks-2.2.1/src/cuffquant.cpp cufflinks-2.2.1/src/filters.h cufflinks-2.2.1/src/abundances.cpp cufflinks-2.2.1/src/GFastaIndex.h cufflinks-2.2.1/src/lemon/ cufflinks-2.2.1/src/lemon/bipartite_matching.h cufflinks-2.2.1/src/lemon/fib_heap.h cufflinks-2.2.1/src/lemon/list_graph.h cufflinks-2.2.1/src/lemon/maps.h cufflinks-2.2.1/src/lemon/bfs.h cufflinks-2.2.1/src/lemon/error.h cufflinks-2.2.1/src/lemon/topology.h cufflinks-2.2.1/src/lemon/tolerance.h cufflinks-2.2.1/src/lemon/graph_utils.h cufflinks-2.2.1/src/lemon/bin_heap.h cufflinks-2.2.1/src/lemon/smart_graph.h cufflinks-2.2.1/src/lemon/graph_adaptor.h cufflinks-2.2.1/src/lemon/bits/ cufflinks-2.2.1/src/lemon/bits/map_extender.h cufflinks-2.2.1/src/lemon/bits/utility.h cufflinks-2.2.1/src/lemon/bits/graph_adaptor_extender.h cufflinks-2.2.1/src/lemon/bits/array_map.h cufflinks-2.2.1/src/lemon/bits/invalid.h cufflinks-2.2.1/src/lemon/bits/alteration_notifier.h cufflinks-2.2.1/src/lemon/bits/default_map.h cufflinks-2.2.1/src/lemon/bits/path_dump.h cufflinks-2.2.1/src/lemon/bits/variant.h cufflinks-2.2.1/src/lemon/bits/vector_map.h cufflinks-2.2.1/src/lemon/bits/traits.h cufflinks-2.2.1/src/lemon/bits/graph_extender.h cufflinks-2.2.1/src/lemon/bits/debug_map.h cufflinks-2.2.1/src/lemon/bits/base_extender.h cufflinks-2.2.1/src/lemon/dfs.h cufflinks-2.2.1/src/lemon/bucket_heap.h cufflinks-2.2.1/src/lemon/concept_check.h cufflinks-2.2.1/src/lemon/math.h cufflinks-2.2.1/src/lemon/concepts/ cufflinks-2.2.1/src/lemon/concepts/bpugraph.h cufflinks-2.2.1/src/lemon/concepts/maps.h cufflinks-2.2.1/src/lemon/concepts/matrix_maps.h cufflinks-2.2.1/src/lemon/concepts/heap.h cufflinks-2.2.1/src/lemon/concepts/graph_components.h cufflinks-2.2.1/src/lemon/concepts/graph.h cufflinks-2.2.1/src/lemon/concepts/ugraph.h cufflinks-2.2.1/src/lemon/concepts/path.h cufflinks-2.2.1/src/replicates.h cufflinks-2.2.1/src/jensen_shannon.h cufflinks-2.2.1/src/locfit/ cufflinks-2.2.1/src/locfit/m_eigen.c cufflinks-2.2.1/src/locfit/simul.c cufflinks-2.2.1/src/locfit/density.c cufflinks-2.2.1/src/locfit/lf_vari.c cufflinks-2.2.1/src/locfit/pout.c cufflinks-2.2.1/src/locfit/readfile.c cufflinks-2.2.1/src/locfit/ar_funs.c cufflinks-2.2.1/src/locfit/lf_robust.c cufflinks-2.2.1/src/locfit/lfd.c cufflinks-2.2.1/src/locfit/design.h cufflinks-2.2.1/src/locfit/m_jacob.c cufflinks-2.2.1/src/locfit/scb.c cufflinks-2.2.1/src/locfit/startlf.c cufflinks-2.2.1/src/locfit/minmax.c cufflinks-2.2.1/src/locfit/locfit.c cufflinks-2.2.1/src/locfit/lfstr.c cufflinks-2.2.1/src/locfit/math.c cufflinks-2.2.1/src/locfit/family.c cufflinks-2.2.1/src/locfit/dens_int.c cufflinks-2.2.1/src/locfit/pcomp.c cufflinks-2.2.1/src/locfit/linalg.c cufflinks-2.2.1/src/locfit/lfstruc.h cufflinks-2.2.1/src/locfit/mutil.h cufflinks-2.2.1/src/locfit/ev_kdtre.c cufflinks-2.2.1/src/locfit/ev_trian.c cufflinks-2.2.1/src/locfit/solve.c cufflinks-2.2.1/src/locfit/lf_dercor.c cufflinks-2.2.1/src/locfit/ev_main.c cufflinks-2.2.1/src/locfit/fitted.c cufflinks-2.2.1/src/locfit/ev_atree.c cufflinks-2.2.1/src/locfit/band.c cufflinks-2.2.1/src/locfit/arith.c cufflinks-2.2.1/src/locfit/weight.c cufflinks-2.2.1/src/locfit/dens_odi.c cufflinks-2.2.1/src/locfit/preplot.c cufflinks-2.2.1/src/locfit/ev_interp.c cufflinks-2.2.1/src/locfit/wdiag.c cufflinks-2.2.1/src/locfit/scb_cons.c cufflinks-2.2.1/src/locfit/frend.c cufflinks-2.2.1/src/locfit/nbhd.c cufflinks-2.2.1/src/locfit/lfcons.h cufflinks-2.2.1/src/locfit/makecmd.c cufflinks-2.2.1/src/locfit/lf_fitfun.c cufflinks-2.2.1/src/locfit/c_args.c cufflinks-2.2.1/src/locfit/help.c cufflinks-2.2.1/src/locfit/vari.cpp cufflinks-2.2.1/src/locfit/lfwin.h cufflinks-2.2.1/src/locfit/dens_haz.c cufflinks-2.2.1/src/locfit/imatlb.h cufflinks-2.2.1/src/locfit/lffuns.h cufflinks-2.2.1/src/locfit/strings.c cufflinks-2.2.1/src/locfit/local.h cufflinks-2.2.1/src/locfit/c_plot.c cufflinks-2.2.1/src/locfit/m_chol.c cufflinks-2.2.1/src/locfit/random.c cufflinks-2.2.1/src/locfit/vari.hpp cufflinks-2.2.1/src/locfit/cmd.c cufflinks-2.2.1/src/locfit/adap.c cufflinks-2.2.1/src/locfit/dist.c cufflinks-2.2.1/src/locfit/m_max.c cufflinks-2.2.1/src/GArgs.h cufflinks-2.2.1/src/assemble.cpp cufflinks-2.2.1/ax_boost_base.m4 cufflinks-2.2.1/ax_check_eigen.m4 cufflinks-2.2.1/ax_check_zlib.m4 cufflinks-2.2.1/ax_boost_thread.m4 cufflinks-2.2.1/make_bin.sh cufflinks-2.2.1/Makefile.am cufflinks-2.2.1/ax_boost_serialization.m4 cufflinks-2.2.1/AUTHORS sudo -u fink-bld [ENV] sh -c /tmp/fink.koa72 /tmp/fink.ZjGut #!/bin/sh -ev export PYTHON=/usr/bin/python2.7 ./configure --prefix=/sw --enable-dependency-tracking \ --enable-intel64 \ --with-boost=/sw/opt/boost-1_55 \ --with-boost-system=-lboost_system-mt \ --with-boost-serialization=-lboost_serialization-mt \ --with-boost-thread=-lboost_thread-mt \ --with-eigen 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(cached) yes checking for ranlib... ranlib checking for a BSD-compatible install... /usr/bin/install -c checking whether /usr/bin/python2.7 version >= 2.4... yes checking for /usr/bin/python2.7 version... 2.7 checking for /usr/bin/python2.7 platform... darwin checking for /usr/bin/python2.7 script directory... ${prefix}/lib/python2.7/site-packages checking for /usr/bin/python2.7 extension module directory... ${exec_prefix}/lib/python2.7/site-packages checking for boostlib >= 1.47.0... yes checking for bamlib... yes checking build system type... i686-apple-darwin13.3.0 using -lboost_system-mt checking whether the Boost::System library is available... yes using -lboost_serialization-mt checking whether the Boost::Serialization library is available... yes using -lboost_thread-mt checking whether the Boost::Thread library is available... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking if zlib is wanted... yes checking for inflateEnd in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for inflateEnd in -lz... (cached) yes checking zlib in /usr... ok checking for eigenlib... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for inline... inline checking for pid_t... yes checking for size_t... yes checking for ptrdiff_t... yes checking host system type... i686-apple-darwin13.3.0 checking for struct sysinfo.totalram... no checking whether sysctl is declared... yes checking whether CTL_HW is declared... yes checking whether HW_PHYSMEM is declared... yes checking how to create a pax tar archive... gnutar checking dependency style of gcc... (cached) gcc3 checking dependency style of g++... (cached) gcc3 configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands -- cufflinks 2.2.1 Configuration Results -- C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -L/sw/lib GCC version: Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn) Host System type: i686-apple-darwin13.3.0 Install prefix: /sw Install eprefix: ${prefix} See config.h for further configuration information. Email with questions and bug reports. make /Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive Making all in src if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT clustering.o -MD -MP -MF ".deps/clustering.Tpo" -c -o clustering.o clustering.cpp; \ then mv -f ".deps/clustering.Tpo" ".deps/clustering.Po"; else rm -f ".deps/clustering.Tpo"; exit 1; fi In file included from clustering.cpp:10: In file included from ./clustering.h:38: In file included from ./abundances.h:23: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from clustering.cpp:10: In file included from ./clustering.h:38: In file included from ./abundances.h:25: In file included from ./bundles.h:22: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ In file included from clustering.cpp:10: In file included from ./clustering.h:38: In file included from ./abundances.h:18: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/matrix.hpp:16: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/vector.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/storage.hpp:26: /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:45:27: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned int boost_numeric_ublas_abs (const unsigned int& t) { ^ /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:49:28: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned long boost_numeric_ublas_abs (const unsigned long& t) { ^ 4 warnings generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT differential.o -MD -MP -MF ".deps/differential.Tpo" -c -o differential.o differential.cpp; \ then mv -f ".deps/differential.Tpo" ".deps/differential.Po"; else rm -f ".deps/differential.Tpo"; exit 1; fi In file included from differential.cpp:20: In file included from ./abundances.h:23: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from differential.cpp:20: In file included from ./abundances.h:25: In file included from ./bundles.h:22: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ In file included from differential.cpp:21: In file included from ./differential.h:29: ./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^ differential.cpp:131:31: warning: unused variable 's2' [-Wunused-variable] const AbundanceGroup& s2 = prev.transcripts; ^ differential.cpp:159:31: warning: unused variable 's2' [-Wunused-variable] const AbundanceGroup& s2 = prev.transcripts; ^ In file included from differential.cpp:13: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/vector.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/storage.hpp:26: /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:45:27: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned int boost_numeric_ublas_abs (const unsigned int& t) { ^ /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:49:28: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned long boost_numeric_ublas_abs (const unsigned long& t) { ^ 7 warnings generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT common.o -MD -MP -MF ".deps/common.Tpo" -c -o common.o common.cpp; \ then mv -f ".deps/common.Tpo" ".deps/common.Po"; else rm -f ".deps/common.Tpo"; exit 1; fi In file included from common.cpp:28: In file included from ./replicates.h:10: In file included from ./bundles.h:20: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from common.cpp:28: In file included from ./replicates.h:10: In file included from ./bundles.h:22: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ In file included from common.cpp:28: ./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^ In file included from common.cpp:27: In file included from ./common.h:21: In file included from /sw/opt/boost-1_55/include/boost/math/distributions/normal.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/math/special_functions/erf.hpp:15: In file included from /sw/opt/boost-1_55/include/boost/math/special_functions/gamma.hpp:21: In file included from /sw/opt/boost-1_55/include/boost/math/policies/error_handling.hpp:31: In file included from /sw/opt/boost-1_55/include/boost/format.hpp:38: In file included from /sw/opt/boost-1_55/include/boost/format/internals.hpp:23: In file included from /sw/opt/boost-1_55/include/boost/format/alt_sstream.hpp:21: In file included from /sw/opt/boost-1_55/include/boost/shared_ptr.hpp:17: In file included from /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:30: /sw/opt/boost-1_55/include/boost/checked_delete.hpp:34:5: warning: delete called on 'PoissonDispersionModel' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] delete x; ^ /sw/opt/boost-1_55/include/boost/smart_ptr/detail/shared_count.hpp:134:20: note: in instantiation of function template specialization 'boost::checked_delete' requested here boost::checked_delete( p ); ^ /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:276:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count' requested here boost::detail::shared_count( p ).swap( pn ); ^ /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:354:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ common.cpp:506:30: note: in instantiation of function template specialization 'boost::shared_ptr::shared_ptr' requested here _mass_dispersion_model = boost::shared_ptr(new PoissonDispersionModel("")); ^ 4 warnings generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT assemble.o -MD -MP -MF ".deps/assemble.Tpo" -c -o assemble.o assemble.cpp; \ then mv -f ".deps/assemble.Tpo" ".deps/assemble.Po"; else rm -f ".deps/assemble.Tpo"; exit 1; fi In file included from assemble.cpp:48: In file included from ./assemble.h:21: In file included from ./bundles.h:20: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from assemble.cpp:48: In file included from ./assemble.h:21: In file included from ./bundles.h:22: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ assemble.cpp:188:21: warning: unused variable 'a_for_b' [-Wunused-variable] ReachGraph::ANode a_for_b = b_to_a[b_id]; ^ assemble.cpp:123:17: warning: unused variable 'hits_for_node' [-Wunused-variable] HitsForNodeMap hits_for_node = get(vertex_name, dag); ^ assemble.cpp:262:21: warning: unused variable 'a_for_b' [-Wunused-variable] ReachGraph::ANode a_for_b = bp.nodeFromANodeId(a_id_for_b); ^ In file included from assemble.cpp:54: In file included from ./clustering.h:38: In file included from ./abundances.h:18: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/matrix.hpp:16: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/vector.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/storage.hpp:26: /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:45:27: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned int boost_numeric_ublas_abs (const unsigned int& t) { ^ /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:49:28: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned long boost_numeric_ublas_abs (const unsigned long& t) { ^ 7 warnings generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT tokenize.o -MD -MP -MF ".deps/tokenize.Tpo" -c -o tokenize.o tokenize.cpp; \ then mv -f ".deps/tokenize.Tpo" ".deps/tokenize.Po"; else rm -f ".deps/tokenize.Tpo"; exit 1; fi if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT abundances.o -MD -MP -MF ".deps/abundances.Tpo" -c -o abundances.o abundances.cpp; \ then mv -f ".deps/abundances.Tpo" ".deps/abundances.Po"; else rm -f ".deps/abundances.Tpo"; exit 1; fi In file included from abundances.cpp:16: In file included from ./abundances.h:23: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from abundances.cpp:16: In file included from ./abundances.h:25: In file included from ./bundles.h:22: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ In file included from abundances.cpp:43: ./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^ abundances.cpp:1043:20: warning: unused variable 'curr_mass' [-Wunused-variable] double curr_mass = inserted.first->second; ^ abundances.cpp:2070:58: warning: unused variable 'sc_ab' [-Wunused-variable] const vector >& sc_ab = itr->second->abundances(); ^ abundances.cpp:2796:24: warning: unused variable 'fpkm' [-Wunused-variable] double fpkm = _abundances[i]->FPKM(); ^ abundances.cpp:4066:94: warning: unused variable 'al_itr' [-Wunused-variable] map, vector >::const_iterator al_itr = ^ In file included from abundances.cpp:16: In file included from ./abundances.h:18: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/matrix.hpp:16: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/vector.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/storage.hpp:26: /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:45:27: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned int boost_numeric_ublas_abs (const unsigned int& t) { ^ /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:49:28: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned long boost_numeric_ublas_abs (const unsigned long& t) { ^ In file included from abundances.cpp:42: In file included from ./filters.h:18: ./genes.h:210:6: warning: private field '_id' is not used [-Wunused-private-field] int _id; ^ 10 warnings generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT scaffolds.o -MD -MP -MF ".deps/scaffolds.Tpo" -c -o scaffolds.o scaffolds.cpp; \ then mv -f ".deps/scaffolds.Tpo" ".deps/scaffolds.Po"; else rm -f ".deps/scaffolds.Tpo"; exit 1; fi In file included from scaffolds.cpp:14: In file included from ./scaffolds.h:20: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ 1 warning generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT hits.o -MD -MP -MF ".deps/hits.Tpo" -c -o hits.o hits.cpp; \ then mv -f ".deps/hits.Tpo" ".deps/hits.Po"; else rm -f ".deps/hits.Tpo"; exit 1; fi In file included from hits.cpp:22: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from hits.cpp:25: In file included from ./abundances.h:25: In file included from ./bundles.h:22: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ In file included from hits.cpp:25: In file included from ./abundances.h:18: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/matrix.hpp:16: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/vector.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/storage.hpp:26: /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:45:27: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned int boost_numeric_ublas_abs (const unsigned int& t) { ^ /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:49:28: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned long boost_numeric_ublas_abs (const unsigned long& t) { ^ hits.cpp:738:23: warning: unused variable 'MAX_HEADER_LEN' [-Wunused-const-variable] static const unsigned MAX_HEADER_LEN = 64 * 1024 * 1024; // 4 MB ^ 5 warnings generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT genes.o -MD -MP -MF ".deps/genes.Tpo" -c -o genes.o genes.cpp; \ then mv -f ".deps/genes.Tpo" ".deps/genes.Po"; else rm -f ".deps/genes.Tpo"; exit 1; fi In file included from genes.cpp:10: In file included from ./genes.h:17: In file included from ./scaffolds.h:20: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from genes.cpp:10: In file included from ./genes.h:18: In file included from ./abundances.h:25: In file included from ./bundles.h:22: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ In file included from genes.cpp:10: In file included from ./genes.h:18: In file included from ./abundances.h:18: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/matrix.hpp:16: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/vector.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/storage.hpp:26: /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:45:27: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned int boost_numeric_ublas_abs (const unsigned int& t) { ^ /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:49:28: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned long boost_numeric_ublas_abs (const unsigned long& t) { ^ In file included from genes.cpp:10: ./genes.h:210:6: warning: private field '_id' is not used [-Wunused-private-field] int _id; ^ 5 warnings generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT bundles.o -MD -MP -MF ".deps/bundles.Tpo" -c -o bundles.o bundles.cpp; \ then mv -f ".deps/bundles.Tpo" ".deps/bundles.Po"; else rm -f ".deps/bundles.Tpo"; exit 1; fi In file included from bundles.cpp:17: In file included from ./bundles.h:20: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from bundles.cpp:17: In file included from ./bundles.h:22: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ bundles.cpp:701:23: warning: integer constant is larger than the largest signed integer type if (tmp.ref_id() == 12638153115695167477) // corresponds to SAM "*" under FNV hash. unaligned read record ^ bundles.cpp:2065:212: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat] fprintf (stderr, "Error in file %s: reconstituted expression bundle %s (%d transcripts) does not match GTF (%d transcripts):\n", read_group_properties()->file_path().c_str(), bundle_label_buf, ab->abundances().size(), bundle.ref_scaffolds().size()); ~~ ^~~~~~~~~~~~~~~~~~~~~~~ %lu bundles.cpp:2065:237: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat] fprintf (stderr, "Error in file %s: reconstituted expression bundle %s (%d transcripts) does not match GTF (%d transcripts):\n", read_group_properties()->file_path().c_str(), bundle_label_buf, ab->abundances().size(), bundle.ref_scaffolds().size()); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %lu In file included from bundles.cpp:20: In file included from ./abundances.h:18: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/matrix.hpp:16: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/vector.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/storage.hpp:26: /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:45:27: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned int boost_numeric_ublas_abs (const unsigned int& t) { ^ /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:49:28: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned long boost_numeric_ublas_abs (const unsigned long& t) { ^ 7 warnings generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT filters.o -MD -MP -MF ".deps/filters.Tpo" -c -o filters.o filters.cpp; \ then mv -f ".deps/filters.Tpo" ".deps/filters.Po"; else rm -f ".deps/filters.Tpo"; exit 1; fi In file included from filters.cpp:10: In file included from ./filters.h:17: In file included from ./scaffolds.h:20: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from filters.cpp:10: In file included from ./filters.h:18: In file included from ./genes.h:18: In file included from ./abundances.h:25: In file included from ./bundles.h:22: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ In file included from filters.cpp:10: In file included from ./filters.h:18: In file included from ./genes.h:18: In file included from ./abundances.h:18: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/matrix.hpp:16: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/vector.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/storage.hpp:26: /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:45:27: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned int boost_numeric_ublas_abs (const unsigned int& t) { ^ /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:49:28: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned long boost_numeric_ublas_abs (const unsigned long& t) { ^ 4 warnings generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT scaffold_graph.o -MD -MP -MF ".deps/scaffold_graph.Tpo" -c -o scaffold_graph.o scaffold_graph.cpp; \ then mv -f ".deps/scaffold_graph.Tpo" ".deps/scaffold_graph.Po"; else rm -f ".deps/scaffold_graph.Tpo"; exit 1; fi In file included from scaffold_graph.cpp:12: In file included from ./scaffolds.h:20: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ 1 warning generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT matching_merge.o -MD -MP -MF ".deps/matching_merge.Tpo" -c -o matching_merge.o matching_merge.cpp; \ then mv -f ".deps/matching_merge.Tpo" ".deps/matching_merge.Po"; else rm -f ".deps/matching_merge.Tpo"; exit 1; fi In file included from matching_merge.cpp:10: In file included from ./matching_merge.h:20: In file included from ./scaffolds.h:20: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ 1 warning generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT graph_optimize.o -MD -MP -MF ".deps/graph_optimize.Tpo" -c -o graph_optimize.o graph_optimize.cpp; \ then mv -f ".deps/graph_optimize.Tpo" ".deps/graph_optimize.Po"; else rm -f ".deps/graph_optimize.Tpo"; exit 1; fi In file included from graph_optimize.cpp:13: In file included from ./graph_optimize.h:17: In file included from ./bundles.h:20: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from graph_optimize.cpp:13: In file included from ./graph_optimize.h:17: In file included from ./bundles.h:22: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ graph_optimize.cpp:264:30: warning: unused variable 'e' [-Wunused-variable] ContainmentGraph::UEdge e = containment.addEdge(nj.first, ^ In file included from graph_optimize.cpp:22: In file included from ./filters.h:18: In file included from ./genes.h:18: In file included from ./abundances.h:18: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/matrix.hpp:16: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/vector.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/storage.hpp:26: /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:45:27: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned int boost_numeric_ublas_abs (const unsigned int& t) { ^ /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:49:28: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned long boost_numeric_ublas_abs (const unsigned long& t) { ^ In file included from graph_optimize.cpp:22: In file included from ./filters.h:18: ./genes.h:210:6: warning: private field '_id' is not used [-Wunused-private-field] int _id; ^ 6 warnings generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT biascorrection.o -MD -MP -MF ".deps/biascorrection.Tpo" -c -o biascorrection.o biascorrection.cpp; \ then mv -f ".deps/biascorrection.Tpo" ".deps/biascorrection.Po"; else rm -f ".deps/biascorrection.Tpo"; exit 1; fi In file included from biascorrection.cpp:11: In file included from ./scaffolds.h:20: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from biascorrection.cpp:12: In file included from ./abundances.h:25: In file included from ./bundles.h:22: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ In file included from biascorrection.cpp:10: In file included from ./biascorrection.h:14: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/matrix.hpp:16: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/vector.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/storage.hpp:26: /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:45:27: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned int boost_numeric_ublas_abs (const unsigned int& t) { ^ /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:49:28: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned long boost_numeric_ublas_abs (const unsigned long& t) { ^ 4 warnings generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT sampling.o -MD -MP -MF ".deps/sampling.Tpo" -c -o sampling.o sampling.cpp; \ then mv -f ".deps/sampling.Tpo" ".deps/sampling.Po"; else rm -f ".deps/sampling.Tpo"; exit 1; fi In file included from sampling.cpp:9: In file included from ./sampling.h:20: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/matrix.hpp:16: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/vector.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/storage.hpp:26: /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:45:27: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned int boost_numeric_ublas_abs (const unsigned int& t) { ^ /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:49:28: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned long boost_numeric_ublas_abs (const unsigned long& t) { ^ 2 warnings generated. if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT adap.o -MD -MP -MF ".deps/adap.Tpo" -c -o adap.o `test -f 'locfit/adap.c' || echo './'`locfit/adap.c; \ then mv -f ".deps/adap.Tpo" ".deps/adap.Po"; else rm -f ".deps/adap.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT ar_funs.o -MD -MP -MF ".deps/ar_funs.Tpo" -c -o ar_funs.o `test -f 'locfit/ar_funs.c' || echo './'`locfit/ar_funs.c; \ then mv -f ".deps/ar_funs.Tpo" ".deps/ar_funs.Po"; else rm -f ".deps/ar_funs.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT arith.o -MD -MP -MF ".deps/arith.Tpo" -c -o arith.o `test -f 'locfit/arith.c' || echo './'`locfit/arith.c; \ then mv -f ".deps/arith.Tpo" ".deps/arith.Po"; else rm -f ".deps/arith.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT band.o -MD -MP -MF ".deps/band.Tpo" -c -o band.o `test -f 'locfit/band.c' || echo './'`locfit/band.c; \ then mv -f ".deps/band.Tpo" ".deps/band.Po"; else rm -f ".deps/band.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT c_args.o -MD -MP -MF ".deps/c_args.Tpo" -c -o c_args.o `test -f 'locfit/c_args.c' || echo './'`locfit/c_args.c; \ then mv -f ".deps/c_args.Tpo" ".deps/c_args.Po"; else rm -f ".deps/c_args.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT c_plot.o -MD -MP -MF ".deps/c_plot.Tpo" -c -o c_plot.o `test -f 'locfit/c_plot.c' || echo './'`locfit/c_plot.c; \ then mv -f ".deps/c_plot.Tpo" ".deps/c_plot.Po"; else rm -f ".deps/c_plot.Tpo"; exit 1; fi locfit/c_plot.c:470:14: warning: incompatible pointer types passing 'char *' to parameter of type 'vari *' [-Wincompatible-pointer-types] setvarname(curstr,tname); ^~~~~~ locfit/vari.hpp:23:27: note: passing argument to parameter 'v' here void setvarname(vari* v, varname name); ^ 1 warning generated. if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT cmd.o -MD -MP -MF ".deps/cmd.Tpo" -c -o cmd.o `test -f 'locfit/cmd.c' || echo './'`locfit/cmd.c; \ then mv -f ".deps/cmd.Tpo" ".deps/cmd.Po"; else rm -f ".deps/cmd.Tpo"; exit 1; fi locfit/cmd.c:353:29: warning: incompatible pointer types passing 'char *' to parameter of type 'varname *' (aka 'char (*)[64]') [-Wincompatible-pointer-types] { vr = knotsvar(argarg(v,k),n); ^~~~~~~~~~~ locfit/lffuns.h:168:21: note: expanded from macro 'argarg' #define argarg(v,i) (((carg *)viptr(v,i))->arg) ^~~~~~~~~~~~~~~~~~~~~~~~~~~ locfit/cmd.c:358:25: warning: incompatible pointer types passing 'char *' to parameter of type 'varname *' (aka 'char (*)[64]') [-Wincompatible-pointer-types] { vr = knotsvar(argarg(v,k),n); ^~~~~~~~~~~ locfit/lffuns.h:168:21: note: expanded from macro 'argarg' #define argarg(v,i) (((carg *)viptr(v,i))->arg) ^~~~~~~~~~~~~~~~~~~~~~~~~~~ locfit/cmd.c:363:25: warning: incompatible pointer types passing 'char *' to parameter of type 'varname *' (aka 'char (*)[64]') [-Wincompatible-pointer-types] { vr = knotsvar(argarg(v,k),n); ^~~~~~~~~~~ locfit/lffuns.h:168:21: note: expanded from macro 'argarg' #define argarg(v,i) (((carg *)viptr(v,i))->arg) ^~~~~~~~~~~~~~~~~~~~~~~~~~~ locfit/cmd.c:368:25: warning: incompatible pointer types passing 'char *' to parameter of type 'varname *' (aka 'char (*)[64]') [-Wincompatible-pointer-types] { vr = knotsvar(argarg(v,k),n); ^~~~~~~~~~~ locfit/lffuns.h:168:21: note: expanded from macro 'argarg' #define argarg(v,i) (((carg *)viptr(v,i))->arg) ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 4 warnings generated. if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT dens_haz.o -MD -MP -MF ".deps/dens_haz.Tpo" -c -o dens_haz.o `test -f 'locfit/dens_haz.c' || echo './'`locfit/dens_haz.c; \ then mv -f ".deps/dens_haz.Tpo" ".deps/dens_haz.Po"; else rm -f ".deps/dens_haz.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT dens_int.o -MD -MP -MF ".deps/dens_int.Tpo" -c -o dens_int.o `test -f 'locfit/dens_int.c' || echo './'`locfit/dens_int.c; \ then mv -f ".deps/dens_int.Tpo" ".deps/dens_int.Po"; else rm -f ".deps/dens_int.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT dens_odi.o -MD -MP -MF ".deps/dens_odi.Tpo" -c -o dens_odi.o `test -f 'locfit/dens_odi.c' || echo './'`locfit/dens_odi.c; \ then mv -f ".deps/dens_odi.Tpo" ".deps/dens_odi.Po"; else rm -f ".deps/dens_odi.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT density.o -MD -MP -MF ".deps/density.Tpo" -c -o density.o `test -f 'locfit/density.c' || echo './'`locfit/density.c; \ then mv -f ".deps/density.Tpo" ".deps/density.Po"; else rm -f ".deps/density.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT dist.o -MD -MP -MF ".deps/dist.Tpo" -c -o dist.o `test -f 'locfit/dist.c' || echo './'`locfit/dist.c; \ then mv -f ".deps/dist.Tpo" ".deps/dist.Po"; else rm -f ".deps/dist.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT ev_atree.o -MD -MP -MF ".deps/ev_atree.Tpo" -c -o ev_atree.o `test -f 'locfit/ev_atree.c' || echo './'`locfit/ev_atree.c; \ then mv -f ".deps/ev_atree.Tpo" ".deps/ev_atree.Po"; else rm -f ".deps/ev_atree.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT ev_interp.o -MD -MP -MF ".deps/ev_interp.Tpo" -c -o ev_interp.o `test -f 'locfit/ev_interp.c' || echo './'`locfit/ev_interp.c; \ then mv -f ".deps/ev_interp.Tpo" ".deps/ev_interp.Po"; else rm -f ".deps/ev_interp.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT ev_kdtre.o -MD -MP -MF ".deps/ev_kdtre.Tpo" -c -o ev_kdtre.o `test -f 'locfit/ev_kdtre.c' || echo './'`locfit/ev_kdtre.c; \ then mv -f ".deps/ev_kdtre.Tpo" ".deps/ev_kdtre.Po"; else rm -f ".deps/ev_kdtre.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT ev_main.o -MD -MP -MF ".deps/ev_main.Tpo" -c -o ev_main.o `test -f 'locfit/ev_main.c' || echo './'`locfit/ev_main.c; \ then mv -f ".deps/ev_main.Tpo" ".deps/ev_main.Po"; else rm -f ".deps/ev_main.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT ev_trian.o -MD -MP -MF ".deps/ev_trian.Tpo" -c -o ev_trian.o `test -f 'locfit/ev_trian.c' || echo './'`locfit/ev_trian.c; \ then mv -f ".deps/ev_trian.Tpo" ".deps/ev_trian.Po"; else rm -f ".deps/ev_trian.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT family.o -MD -MP -MF ".deps/family.Tpo" -c -o family.o `test -f 'locfit/family.c' || echo './'`locfit/family.c; \ then mv -f ".deps/family.Tpo" ".deps/family.Po"; else rm -f ".deps/family.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT fitted.o -MD -MP -MF ".deps/fitted.Tpo" -c -o fitted.o `test -f 'locfit/fitted.c' || echo './'`locfit/fitted.c; \ then mv -f ".deps/fitted.Tpo" ".deps/fitted.Po"; else rm -f ".deps/fitted.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT frend.o -MD -MP -MF ".deps/frend.Tpo" -c -o frend.o `test -f 'locfit/frend.c' || echo './'`locfit/frend.c; \ then mv -f ".deps/frend.Tpo" ".deps/frend.Po"; else rm -f ".deps/frend.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT help.o -MD -MP -MF ".deps/help.Tpo" -c -o help.o `test -f 'locfit/help.c' || echo './'`locfit/help.c; \ then mv -f ".deps/help.Tpo" ".deps/help.Po"; else rm -f ".deps/help.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT lf_dercor.o -MD -MP -MF ".deps/lf_dercor.Tpo" -c -o lf_dercor.o `test -f 'locfit/lf_dercor.c' || echo './'`locfit/lf_dercor.c; \ then mv -f ".deps/lf_dercor.Tpo" ".deps/lf_dercor.Po"; else rm -f ".deps/lf_dercor.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT lf_fitfun.o -MD -MP -MF ".deps/lf_fitfun.Tpo" -c -o lf_fitfun.o `test -f 'locfit/lf_fitfun.c' || echo './'`locfit/lf_fitfun.c; \ then mv -f ".deps/lf_fitfun.Tpo" ".deps/lf_fitfun.Po"; else rm -f ".deps/lf_fitfun.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT lf_robust.o -MD -MP -MF ".deps/lf_robust.Tpo" -c -o lf_robust.o `test -f 'locfit/lf_robust.c' || echo './'`locfit/lf_robust.c; \ then mv -f ".deps/lf_robust.Tpo" ".deps/lf_robust.Po"; else rm -f ".deps/lf_robust.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT lf_vari.o -MD -MP -MF ".deps/lf_vari.Tpo" -c -o lf_vari.o `test -f 'locfit/lf_vari.c' || echo './'`locfit/lf_vari.c; \ then mv -f ".deps/lf_vari.Tpo" ".deps/lf_vari.Po"; else rm -f ".deps/lf_vari.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT lfd.o -MD -MP -MF ".deps/lfd.Tpo" -c -o lfd.o `test -f 'locfit/lfd.c' || echo './'`locfit/lfd.c; \ then mv -f ".deps/lfd.Tpo" ".deps/lfd.Po"; else rm -f ".deps/lfd.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT lfstr.o -MD -MP -MF ".deps/lfstr.Tpo" -c -o lfstr.o `test -f 'locfit/lfstr.c' || echo './'`locfit/lfstr.c; \ then mv -f ".deps/lfstr.Tpo" ".deps/lfstr.Po"; else rm -f ".deps/lfstr.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT linalg.o -MD -MP -MF ".deps/linalg.Tpo" -c -o linalg.o `test -f 'locfit/linalg.c' || echo './'`locfit/linalg.c; \ then mv -f ".deps/linalg.Tpo" ".deps/linalg.Po"; else rm -f ".deps/linalg.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT locfit.o -MD -MP -MF ".deps/locfit.Tpo" -c -o locfit.o `test -f 'locfit/locfit.c' || echo './'`locfit/locfit.c; \ then mv -f ".deps/locfit.Tpo" ".deps/locfit.Po"; else rm -f ".deps/locfit.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT m_chol.o -MD -MP -MF ".deps/m_chol.Tpo" -c -o m_chol.o `test -f 'locfit/m_chol.c' || echo './'`locfit/m_chol.c; \ then mv -f ".deps/m_chol.Tpo" ".deps/m_chol.Po"; else rm -f ".deps/m_chol.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT m_eigen.o -MD -MP -MF ".deps/m_eigen.Tpo" -c -o m_eigen.o `test -f 'locfit/m_eigen.c' || echo './'`locfit/m_eigen.c; \ then mv -f ".deps/m_eigen.Tpo" ".deps/m_eigen.Po"; else rm -f ".deps/m_eigen.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT m_jacob.o -MD -MP -MF ".deps/m_jacob.Tpo" -c -o m_jacob.o `test -f 'locfit/m_jacob.c' || echo './'`locfit/m_jacob.c; \ then mv -f ".deps/m_jacob.Tpo" ".deps/m_jacob.Po"; else rm -f ".deps/m_jacob.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT m_max.o -MD -MP -MF ".deps/m_max.Tpo" -c -o m_max.o `test -f 'locfit/m_max.c' || echo './'`locfit/m_max.c; \ then mv -f ".deps/m_max.Tpo" ".deps/m_max.Po"; else rm -f ".deps/m_max.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT makecmd.o -MD -MP -MF ".deps/makecmd.Tpo" -c -o makecmd.o `test -f 'locfit/makecmd.c' || echo './'`locfit/makecmd.c; \ then mv -f ".deps/makecmd.Tpo" ".deps/makecmd.Po"; else rm -f ".deps/makecmd.Tpo"; exit 1; fi locfit/makecmd.c:88:36: warning: '&&' within '||' [-Wlogical-op-parentheses] } while ((instr) || (*z !=' ') && (!isterminator(*z))); ~~ ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ locfit/makecmd.c:88:36: note: place parentheses around the '&&' expression to silence this warning } while ((instr) || (*z !=' ') && (!isterminator(*z))); ^ ( ) locfit/makecmd.c:203:29: warning: format string is not a string literal (potentially insecure) [-Wformat-security] sprintf((char *)vdptr(vs),cmdline); ^~~~~~~ /usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^ 2 warnings generated. if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT math.o -MD -MP -MF ".deps/math.Tpo" -c -o math.o `test -f 'locfit/math.c' || echo './'`locfit/math.c; \ then mv -f ".deps/math.Tpo" ".deps/math.Po"; else rm -f ".deps/math.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT minmax.o -MD -MP -MF ".deps/minmax.Tpo" -c -o minmax.o `test -f 'locfit/minmax.c' || echo './'`locfit/minmax.c; \ then mv -f ".deps/minmax.Tpo" ".deps/minmax.Po"; else rm -f ".deps/minmax.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT nbhd.o -MD -MP -MF ".deps/nbhd.Tpo" -c -o nbhd.o `test -f 'locfit/nbhd.c' || echo './'`locfit/nbhd.c; \ then mv -f ".deps/nbhd.Tpo" ".deps/nbhd.Po"; else rm -f ".deps/nbhd.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT pcomp.o -MD -MP -MF ".deps/pcomp.Tpo" -c -o pcomp.o `test -f 'locfit/pcomp.c' || echo './'`locfit/pcomp.c; \ then mv -f ".deps/pcomp.Tpo" ".deps/pcomp.Po"; else rm -f ".deps/pcomp.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT pout.o -MD -MP -MF ".deps/pout.Tpo" -c -o pout.o `test -f 'locfit/pout.c' || echo './'`locfit/pout.c; \ then mv -f ".deps/pout.Tpo" ".deps/pout.Po"; else rm -f ".deps/pout.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT preplot.o -MD -MP -MF ".deps/preplot.Tpo" -c -o preplot.o `test -f 'locfit/preplot.c' || echo './'`locfit/preplot.c; \ then mv -f ".deps/preplot.Tpo" ".deps/preplot.Po"; else rm -f ".deps/preplot.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT random.o -MD -MP -MF ".deps/random.Tpo" -c -o random.o `test -f 'locfit/random.c' || echo './'`locfit/random.c; \ then mv -f ".deps/random.Tpo" ".deps/random.Po"; else rm -f ".deps/random.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT readfile.o -MD -MP -MF ".deps/readfile.Tpo" -c -o readfile.o `test -f 'locfit/readfile.c' || echo './'`locfit/readfile.c; \ then mv -f ".deps/readfile.Tpo" ".deps/readfile.Po"; else rm -f ".deps/readfile.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT scb.o -MD -MP -MF ".deps/scb.Tpo" -c -o scb.o `test -f 'locfit/scb.c' || echo './'`locfit/scb.c; \ then mv -f ".deps/scb.Tpo" ".deps/scb.Po"; else rm -f ".deps/scb.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT scb_cons.o -MD -MP -MF ".deps/scb_cons.Tpo" -c -o scb_cons.o `test -f 'locfit/scb_cons.c' || echo './'`locfit/scb_cons.c; \ then mv -f ".deps/scb_cons.Tpo" ".deps/scb_cons.Po"; else rm -f ".deps/scb_cons.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT simul.o -MD -MP -MF ".deps/simul.Tpo" -c -o simul.o `test -f 'locfit/simul.c' || echo './'`locfit/simul.c; \ then mv -f ".deps/simul.Tpo" ".deps/simul.Po"; else rm -f ".deps/simul.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT solve.o -MD -MP -MF ".deps/solve.Tpo" -c -o solve.o `test -f 'locfit/solve.c' || echo './'`locfit/solve.c; \ then mv -f ".deps/solve.Tpo" ".deps/solve.Po"; else rm -f ".deps/solve.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT startlf.o -MD -MP -MF ".deps/startlf.Tpo" -c -o startlf.o `test -f 'locfit/startlf.c' || echo './'`locfit/startlf.c; \ then mv -f ".deps/startlf.Tpo" ".deps/startlf.Po"; else rm -f ".deps/startlf.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT strings.o -MD -MP -MF ".deps/strings.Tpo" -c -o strings.o `test -f 'locfit/strings.c' || echo './'`locfit/strings.c; \ then mv -f ".deps/strings.Tpo" ".deps/strings.Po"; else rm -f ".deps/strings.Tpo"; exit 1; fi if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT vari.o -MD -MP -MF ".deps/vari.Tpo" -c -o vari.o `test -f 'locfit/vari.cpp' || echo './'`locfit/vari.cpp; \ then mv -f ".deps/vari.Tpo" ".deps/vari.Po"; else rm -f ".deps/vari.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT wdiag.o -MD -MP -MF ".deps/wdiag.Tpo" -c -o wdiag.o `test -f 'locfit/wdiag.c' || echo './'`locfit/wdiag.c; \ then mv -f ".deps/wdiag.Tpo" ".deps/wdiag.Po"; else rm -f ".deps/wdiag.Tpo"; exit 1; fi if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -MT weight.o -MD -MP -MF ".deps/weight.Tpo" -c -o weight.o `test -f 'locfit/weight.c' || echo './'`locfit/weight.c; \ then mv -f ".deps/weight.Tpo" ".deps/weight.Po"; else rm -f ".deps/weight.Tpo"; exit 1; fi if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT replicates.o -MD -MP -MF ".deps/replicates.Tpo" -c -o replicates.o replicates.cpp; \ then mv -f ".deps/replicates.Tpo" ".deps/replicates.Po"; else rm -f ".deps/replicates.Tpo"; exit 1; fi In file included from replicates.cpp:18: In file included from ./replicates.h:10: In file included from ./bundles.h:20: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from replicates.cpp:18: In file included from ./replicates.h:10: In file included from ./bundles.h:22: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ In file included from replicates.cpp:18: ./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^ In file included from replicates.cpp:9: In file included from /sw/opt/boost-1_55/include/boost/thread.hpp:13: In file included from /sw/opt/boost-1_55/include/boost/thread/thread.hpp:12: In file included from /sw/opt/boost-1_55/include/boost/thread/thread_only.hpp:17: In file included from /sw/opt/boost-1_55/include/boost/thread/pthread/thread_data.hpp:12: In file included from /sw/opt/boost-1_55/include/boost/thread/lock_types.hpp:18: In file included from /sw/opt/boost-1_55/include/boost/thread/thread_time.hpp:9: In file included from /sw/opt/boost-1_55/include/boost/date_time/time_clock.hpp:17: In file included from /sw/opt/boost-1_55/include/boost/shared_ptr.hpp:17: In file included from /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:30: /sw/opt/boost-1_55/include/boost/checked_delete.hpp:34:5: warning: delete called on 'PoissonDispersionModel' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] delete x; ^ /sw/opt/boost-1_55/include/boost/smart_ptr/detail/shared_count.hpp:134:20: note: in instantiation of function template specialization 'boost::checked_delete' requested here boost::checked_delete( p ); ^ /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:276:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count' requested here boost::detail::shared_count( p ).swap( pn ); ^ /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:354:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ replicates.cpp:793:21: note: in instantiation of function template specialization 'boost::shared_ptr::shared_ptr' requested here disperser = boost::shared_ptr(new PoissonDispersionModel(condition_name)); ^ In file included from replicates.cpp:9: In file included from /sw/opt/boost-1_55/include/boost/thread.hpp:13: In file included from /sw/opt/boost-1_55/include/boost/thread/thread.hpp:12: In file included from /sw/opt/boost-1_55/include/boost/thread/thread_only.hpp:17: In file included from /sw/opt/boost-1_55/include/boost/thread/pthread/thread_data.hpp:12: In file included from /sw/opt/boost-1_55/include/boost/thread/lock_types.hpp:18: In file included from /sw/opt/boost-1_55/include/boost/thread/thread_time.hpp:9: In file included from /sw/opt/boost-1_55/include/boost/date_time/time_clock.hpp:17: In file included from /sw/opt/boost-1_55/include/boost/shared_ptr.hpp:17: In file included from /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:30: /sw/opt/boost-1_55/include/boost/checked_delete.hpp:34:5: warning: delete called on 'MassDispersionModel' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] delete x; ^ /sw/opt/boost-1_55/include/boost/smart_ptr/detail/shared_count.hpp:134:20: note: in instantiation of function template specialization 'boost::checked_delete' requested here boost::checked_delete( p ); ^ /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:276:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count' requested here boost::detail::shared_count( p ).swap( pn ); ^ /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:354:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ replicates.cpp:871:17: note: in instantiation of function template specialization 'boost::shared_ptr::shared_ptr' requested here disperser = boost::shared_ptr(new MassDispersionModel(condition_name, compatible_count_means, raw_variances, fitted_values)); ^ 5 warnings generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT multireads.o -MD -MP -MF ".deps/multireads.Tpo" -c -o multireads.o multireads.cpp; \ then mv -f ".deps/multireads.Tpo" ".deps/multireads.Po"; else rm -f ".deps/multireads.Tpo"; exit 1; fi In file included from multireads.cpp:11: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ 1 warning generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT jensen_shannon.o -MD -MP -MF ".deps/jensen_shannon.Tpo" -c -o jensen_shannon.o jensen_shannon.cpp; \ then mv -f ".deps/jensen_shannon.Tpo" ".deps/jensen_shannon.Po"; else rm -f ".deps/jensen_shannon.Tpo"; exit 1; fi jensen_shannon.cpp:132:24: warning: unused variable 'curr_grad' [-Wunused-variable] double curr_grad = gradient(i*kappa_length + k); ^ In file included from jensen_shannon.cpp:12: In file included from ./jensen_shannon.h:10: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/matrix.hpp:16: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/vector.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/storage.hpp:26: /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:45:27: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned int boost_numeric_ublas_abs (const unsigned int& t) { ^ /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:49:28: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned long boost_numeric_ublas_abs (const unsigned long& t) { ^ 3 warnings generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT tracking.o -MD -MP -MF ".deps/tracking.Tpo" -c -o tracking.o tracking.cpp; \ then mv -f ".deps/tracking.Tpo" ".deps/tracking.Po"; else rm -f ".deps/tracking.Tpo"; exit 1; fi In file included from tracking.cpp:1: In file included from ./tracking.h:1: In file included from ./abundances.h:23: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from tracking.cpp:1: In file included from ./tracking.h:1: In file included from ./abundances.h:25: In file included from ./bundles.h:22: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ In file included from tracking.cpp:1: In file included from ./tracking.h:1: In file included from ./abundances.h:18: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/matrix.hpp:16: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/vector.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/storage.hpp:26: /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:45:27: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned int boost_numeric_ublas_abs (const unsigned int& t) { ^ /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:49:28: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned long boost_numeric_ublas_abs (const unsigned long& t) { ^ 4 warnings generated. rm -f libcufflinks.a ar cru libcufflinks.a clustering.o differential.o common.o assemble.o tokenize.o abundances.o scaffolds.o hits.o genes.o bundles.o filters.o scaffold_graph.o matching_merge.o graph_optimize.o biascorrection.o sampling.o adap.o ar_funs.o arith.o band.o c_args.o c_plot.o cmd.o dens_haz.o dens_int.o dens_odi.o density.o dist.o ev_atree.o ev_interp.o ev_kdtre.o ev_main.o ev_trian.o family.o fitted.o frend.o help.o lf_dercor.o lf_fitfun.o lf_robust.o lf_vari.o lfd.o lfstr.o linalg.o locfit.o m_chol.o m_eigen.o m_jacob.o m_max.o makecmd.o math.o minmax.o nbhd.o pcomp.o pout.o preplot.o random.o readfile.o scb.o scb_cons.o simul.o solve.o startlf.o strings.o vari.o wdiag.o weight.o replicates.o multireads.o jensen_shannon.o tracking.o ranlib libcufflinks.a if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT codons.o -MD -MP -MF ".deps/codons.Tpo" -c -o codons.o codons.cpp; \ then mv -f ".deps/codons.Tpo" ".deps/codons.Po"; else rm -f ".deps/codons.Tpo"; exit 1; fi if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT GArgs.o -MD -MP -MF ".deps/GArgs.Tpo" -c -o GArgs.o GArgs.cpp; \ then mv -f ".deps/GArgs.Tpo" ".deps/GArgs.Po"; else rm -f ".deps/GArgs.Tpo"; exit 1; fi if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT GBase.o -MD -MP -MF ".deps/GBase.Tpo" -c -o GBase.o GBase.cpp; \ then mv -f ".deps/GBase.Tpo" ".deps/GBase.Po"; else rm -f ".deps/GBase.Tpo"; exit 1; fi if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT gdna.o -MD -MP -MF ".deps/gdna.Tpo" -c -o gdna.o gdna.cpp; \ then mv -f ".deps/gdna.Tpo" ".deps/gdna.Po"; else rm -f ".deps/gdna.Tpo"; exit 1; fi if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT GStr.o -MD -MP -MF ".deps/GStr.Tpo" -c -o GStr.o GStr.cpp; \ then mv -f ".deps/GStr.Tpo" ".deps/GStr.Po"; else rm -f ".deps/GStr.Tpo"; exit 1; fi if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT GFaSeqGet.o -MD -MP -MF ".deps/GFaSeqGet.Tpo" -c -o GFaSeqGet.o GFaSeqGet.cpp; \ then mv -f ".deps/GFaSeqGet.Tpo" ".deps/GFaSeqGet.Po"; else rm -f ".deps/GFaSeqGet.Tpo"; exit 1; fi In file included from GFaSeqGet.cpp:1: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ 1 warning generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT GFastaIndex.o -MD -MP -MF ".deps/GFastaIndex.Tpo" -c -o GFastaIndex.o GFastaIndex.cpp; \ then mv -f ".deps/GFastaIndex.Tpo" ".deps/GFastaIndex.Po"; else rm -f ".deps/GFastaIndex.Tpo"; exit 1; fi In file included from GFastaIndex.cpp:8: In file included from ./GFastaIndex.h:12: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ 1 warning generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT gff.o -MD -MP -MF ".deps/gff.Tpo" -c -o gff.o gff.cpp; \ then mv -f ".deps/gff.Tpo" ".deps/gff.Po"; else rm -f ".deps/gff.Tpo"; exit 1; fi In file included from gff.cpp:1: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ 1 warning generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT gff_utils.o -MD -MP -MF ".deps/gff_utils.Tpo" -c -o gff_utils.o gff_utils.cpp; \ then mv -f ".deps/gff_utils.Tpo" ".deps/gff_utils.Po"; else rm -f ".deps/gff_utils.Tpo"; exit 1; fi In file included from gff_utils.cpp:1: In file included from ./gff_utils.h:3: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ 1 warning generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT gtf_tracking.o -MD -MP -MF ".deps/gtf_tracking.Tpo" -c -o gtf_tracking.o gtf_tracking.cpp; \ then mv -f ".deps/gtf_tracking.Tpo" ".deps/gtf_tracking.Po"; else rm -f ".deps/gtf_tracking.Tpo"; exit 1; fi In file included from gtf_tracking.cpp:10: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ 1 warning generated. rm -f libgc.a ar cru libgc.a codons.o GArgs.o GBase.o gdna.o GStr.o GFaSeqGet.o GFastaIndex.o gff.o gff_utils.o gtf_tracking.o ranlib libgc.a if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT cufflinks.o -MD -MP -MF ".deps/cufflinks.Tpo" -c -o cufflinks.o cufflinks.cpp; \ then mv -f ".deps/cufflinks.Tpo" ".deps/cufflinks.Po"; else rm -f ".deps/cufflinks.Tpo"; exit 1; fi In file included from cufflinks.cpp:21: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from cufflinks.cpp:26: In file included from ./clustering.h:38: In file included from ./abundances.h:25: In file included from ./bundles.h:22: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ In file included from cufflinks.cpp:34: ./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^ cufflinks.cpp:1182:17: warning: unused variable 'map_mass' [-Wunused-variable] long double map_mass = rg_props->normalized_map_mass(); ^ cufflinks.cpp:1353:22: warning: variable 'status' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (iso.status() == NUMERIC_FAIL) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ cufflinks.cpp:1373:21: note: uninitialized use occurs here status); ^~~~~~ cufflinks.cpp:1353:18: note: remove the 'if' if its condition is always true else if (iso.status() == NUMERIC_FAIL) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cufflinks.cpp:1346:22: note: initialize the variable 'status' to silence this warning const char* status; ^ = NULL In file included from cufflinks.cpp:20: In file included from ./common.h:21: In file included from /sw/opt/boost-1_55/include/boost/math/distributions/normal.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/math/special_functions/erf.hpp:15: In file included from /sw/opt/boost-1_55/include/boost/math/special_functions/gamma.hpp:21: In file included from /sw/opt/boost-1_55/include/boost/math/policies/error_handling.hpp:31: In file included from /sw/opt/boost-1_55/include/boost/format.hpp:38: In file included from /sw/opt/boost-1_55/include/boost/format/internals.hpp:23: In file included from /sw/opt/boost-1_55/include/boost/format/alt_sstream.hpp:21: In file included from /sw/opt/boost-1_55/include/boost/shared_ptr.hpp:17: In file included from /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:30: /sw/opt/boost-1_55/include/boost/checked_delete.hpp:34:5: warning: delete called on 'BundleFactory' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] delete x; ^ /sw/opt/boost-1_55/include/boost/smart_ptr/detail/shared_count.hpp:134:20: note: in instantiation of function template specialization 'boost::checked_delete' requested here boost::checked_delete( p ); ^ /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:276:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count' requested here boost::detail::shared_count( p ).swap( pn ); ^ /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:354:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ cufflinks.cpp:1613:52: note: in instantiation of function template specialization 'boost::shared_ptr::shared_ptr' requested here boost::shared_ptr bundle_factory = boost::shared_ptr(new BundleFactory(hit_factory, bundle_mode)); ^ In file included from cufflinks.cpp:26: In file included from ./clustering.h:38: In file included from ./abundances.h:18: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/matrix.hpp:16: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/vector.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/storage.hpp:26: /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:45:27: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned int boost_numeric_ublas_abs (const unsigned int& t) { ^ /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:49:28: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned long boost_numeric_ublas_abs (const unsigned long& t) { ^ 8 warnings generated. g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -L/sw/lib -o cufflinks -L/sw/lib -L/sw/opt/boost-1_55/lib cufflinks.o libcufflinks.a libgc.a -lboost_thread-mt -lboost_system-mt -lboost_serialization-mt -lbam -lz clang: warning: argument unused during compilation: '-pthread' if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT cuffcompare.o -MD -MP -MF ".deps/cuffcompare.Tpo" -c -o cuffcompare.o cuffcompare.cpp; \ then mv -f ".deps/cuffcompare.Tpo" ".deps/cuffcompare.Po"; else rm -f ".deps/cuffcompare.Tpo"; exit 1; fi In file included from cuffcompare.cpp:11: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ cuffcompare.cpp:1596:12: warning: unused variable 'pre_mrna_threshold' [-Wunused-const-variable] const uint pre_mrna_threshold = 100; ^ 2 warnings generated. g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -L/sw/lib -o cuffcompare cuffcompare.o libgc.a -lz clang: warning: argument unused during compilation: '-pthread' if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT cuffdiff.o -MD -MP -MF ".deps/cuffdiff.Tpo" -c -o cuffdiff.o cuffdiff.cpp; \ then mv -f ".deps/cuffdiff.Tpo" ".deps/cuffdiff.Po"; else rm -f ".deps/cuffdiff.Tpo"; exit 1; fi In file included from cuffdiff.cpp:26: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from cuffdiff.cpp:27: In file included from ./bundles.h:22: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ In file included from cuffdiff.cpp:44: In file included from ./differential.h:29: ./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^ In file included from cuffdiff.cpp:25: In file included from ./common.h:21: In file included from /sw/opt/boost-1_55/include/boost/math/distributions/normal.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/math/special_functions/erf.hpp:15: In file included from /sw/opt/boost-1_55/include/boost/math/special_functions/gamma.hpp:21: In file included from /sw/opt/boost-1_55/include/boost/math/policies/error_handling.hpp:31: In file included from /sw/opt/boost-1_55/include/boost/format.hpp:38: In file included from /sw/opt/boost-1_55/include/boost/format/internals.hpp:23: In file included from /sw/opt/boost-1_55/include/boost/format/alt_sstream.hpp:21: In file included from /sw/opt/boost-1_55/include/boost/shared_ptr.hpp:17: In file included from /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:30: /sw/opt/boost-1_55/include/boost/checked_delete.hpp:34:5: warning: delete called on 'MassDispersionModel' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] delete x; ^ /sw/opt/boost-1_55/include/boost/smart_ptr/detail/shared_count.hpp:134:20: note: in instantiation of function template specialization 'boost::checked_delete' requested here boost::checked_delete( p ); ^ /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:276:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count' requested here boost::detail::shared_count( p ).swap( pn ); ^ /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:354:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ cuffdiff.cpp:1544:28: note: in instantiation of function template specialization 'boost::shared_ptr::shared_ptr' requested here pooled_model = boost::shared_ptr(new MassDispersionModel("pooled", compatible_mass, compatible_variances, est_fitted_var)); ^ In file included from cuffdiff.cpp:25: In file included from ./common.h:21: In file included from /sw/opt/boost-1_55/include/boost/math/distributions/normal.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/math/special_functions/erf.hpp:15: In file included from /sw/opt/boost-1_55/include/boost/math/special_functions/gamma.hpp:21: In file included from /sw/opt/boost-1_55/include/boost/math/policies/error_handling.hpp:31: In file included from /sw/opt/boost-1_55/include/boost/format.hpp:38: In file included from /sw/opt/boost-1_55/include/boost/format/internals.hpp:23: In file included from /sw/opt/boost-1_55/include/boost/format/alt_sstream.hpp:21: In file included from /sw/opt/boost-1_55/include/boost/shared_ptr.hpp:17: In file included from /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:30: /sw/opt/boost-1_55/include/boost/checked_delete.hpp:34:5: warning: delete called on 'PoissonDispersionModel' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] delete x; ^ /sw/opt/boost-1_55/include/boost/smart_ptr/detail/shared_count.hpp:134:20: note: in instantiation of function template specialization 'boost::checked_delete' requested here boost::checked_delete( p ); ^ /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:276:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count' requested here boost::detail::shared_count( p ).swap( pn ); ^ /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:354:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ cuffdiff.cpp:1571:60: note: in instantiation of function template specialization 'boost::shared_ptr::shared_ptr' requested here boost::shared_ptr disperser = boost::shared_ptr(new PoissonDispersionModel("")); ^ In file included from cuffdiff.cpp:25: In file included from ./common.h:21: In file included from /sw/opt/boost-1_55/include/boost/math/distributions/normal.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/math/special_functions/erf.hpp:15: In file included from /sw/opt/boost-1_55/include/boost/math/special_functions/gamma.hpp:21: In file included from /sw/opt/boost-1_55/include/boost/math/policies/error_handling.hpp:31: In file included from /sw/opt/boost-1_55/include/boost/format.hpp:38: In file included from /sw/opt/boost-1_55/include/boost/format/internals.hpp:23: In file included from /sw/opt/boost-1_55/include/boost/format/alt_sstream.hpp:21: In file included from /sw/opt/boost-1_55/include/boost/shared_ptr.hpp:17: In file included from /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:30: /sw/opt/boost-1_55/include/boost/checked_delete.hpp:34:5: warning: delete called on 'PrecomputedExpressionBundleFactory' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] delete x; ^ /sw/opt/boost-1_55/include/boost/smart_ptr/detail/shared_count.hpp:134:20: note: in instantiation of function template specialization 'boost::checked_delete' requested here boost::checked_delete( p ); ^ /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:276:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count' requested here boost::detail::shared_count( p ).swap( pn ); ^ /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:354:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ cuffdiff.cpp:1611:22: note: in instantiation of function template specialization 'boost::shared_ptr::shared_ptr' requested here hf = boost::shared_ptr(new PrecomputedExpressionBundleFactory(static_pointer_cast(hs))); ^ In file included from cuffdiff.cpp:25: In file included from ./common.h:21: In file included from /sw/opt/boost-1_55/include/boost/math/distributions/normal.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/math/special_functions/erf.hpp:15: In file included from /sw/opt/boost-1_55/include/boost/math/special_functions/gamma.hpp:21: In file included from /sw/opt/boost-1_55/include/boost/math/policies/error_handling.hpp:31: In file included from /sw/opt/boost-1_55/include/boost/format.hpp:38: In file included from /sw/opt/boost-1_55/include/boost/format/internals.hpp:23: In file included from /sw/opt/boost-1_55/include/boost/format/alt_sstream.hpp:21: In file included from /sw/opt/boost-1_55/include/boost/shared_ptr.hpp:17: In file included from /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:30: /sw/opt/boost-1_55/include/boost/checked_delete.hpp:34:5: warning: delete called on 'BundleFactory' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] delete x; ^ /sw/opt/boost-1_55/include/boost/smart_ptr/detail/shared_count.hpp:134:20: note: in instantiation of function template specialization 'boost::checked_delete' requested here boost::checked_delete( p ); ^ /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:276:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count' requested here boost::detail::shared_count( p ).swap( pn ); ^ /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:354:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ cuffdiff.cpp:1635:22: note: in instantiation of function template specialization 'boost::shared_ptr::shared_ptr' requested here hf = boost::shared_ptr(new BundleFactory(hs, REF_DRIVEN)); ^ In file included from cuffdiff.cpp:28: In file included from ./abundances.h:18: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/matrix.hpp:16: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/vector.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/storage.hpp:26: /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:45:27: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned int boost_numeric_ublas_abs (const unsigned int& t) { ^ /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:49:28: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned long boost_numeric_ublas_abs (const unsigned long& t) { ^ 9 warnings generated. g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -L/sw/lib -o cuffdiff -L/sw/lib -L/sw/opt/boost-1_55/lib cuffdiff.o libcufflinks.a libgc.a -lboost_thread-mt -lboost_system-mt -lboost_serialization-mt -lbam -lz clang: warning: argument unused during compilation: '-pthread' if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT gtf_to_sam.o -MD -MP -MF ".deps/gtf_to_sam.Tpo" -c -o gtf_to_sam.o gtf_to_sam.cpp; \ then mv -f ".deps/gtf_to_sam.Tpo" ".deps/gtf_to_sam.Po"; else rm -f ".deps/gtf_to_sam.Tpo"; exit 1; fi In file included from gtf_to_sam.cpp:28: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from gtf_to_sam.cpp:29: In file included from ./bundles.h:22: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ gtf_to_sam.cpp:148:86: warning: format specifies type 'int' but the argument has type 'RefID' (aka 'unsigned long long') [-Wformat] fprintf(stderr, "Warning: Could not find contig name for ID %d, skipping\n", scaff.ref_id()); ~~ ^~~~~~~~~~~~~~ %llu 3 warnings generated. g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -L/sw/lib -o gtf_to_sam -L/sw/lib -L/sw/opt/boost-1_55/lib gtf_to_sam.o libcufflinks.a libgc.a -lboost_thread-mt -lboost_system-mt -lboost_serialization-mt -lbam -lz clang: warning: argument unused during compilation: '-pthread' if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT compress_gtf.o -MD -MP -MF ".deps/compress_gtf.Tpo" -c -o compress_gtf.o compress_gtf.cpp; \ then mv -f ".deps/compress_gtf.Tpo" ".deps/compress_gtf.Po"; else rm -f ".deps/compress_gtf.Tpo"; exit 1; fi In file included from compress_gtf.cpp:29: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from compress_gtf.cpp:30: In file included from ./bundles.h:22: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ In file included from compress_gtf.cpp:35: In file included from ./genes.h:18: In file included from ./abundances.h:18: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/matrix.hpp:16: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/vector.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/storage.hpp:26: /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:45:27: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned int boost_numeric_ublas_abs (const unsigned int& t) { ^ /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:49:28: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned long boost_numeric_ublas_abs (const unsigned long& t) { ^ In file included from compress_gtf.cpp:35: ./genes.h:210:6: warning: private field '_id' is not used [-Wunused-private-field] int _id; ^ 5 warnings generated. g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -L/sw/lib -o compress_gtf -L/sw/lib -L/sw/opt/boost-1_55/lib compress_gtf.o libcufflinks.a libgc.a -lboost_thread-mt -lboost_system-mt -lboost_serialization-mt -lbam -lz clang: warning: argument unused during compilation: '-pthread' if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT gffread.o -MD -MP -MF ".deps/gffread.Tpo" -c -o gffread.o gffread.cpp; \ then mv -f ".deps/gffread.Tpo" ".deps/gffread.Po"; else rm -f ".deps/gffread.Tpo"; exit 1; fi In file included from gffread.cpp:2: In file included from ./gff_utils.h:3: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ 1 warning generated. g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -L/sw/lib -o gffread gffread.o libgc.a -lz clang: warning: argument unused during compilation: '-pthread' if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT cuffquant.o -MD -MP -MF ".deps/cuffquant.Tpo" -c -o cuffquant.o cuffquant.cpp; \ then mv -f ".deps/cuffquant.Tpo" ".deps/cuffquant.Po"; else rm -f ".deps/cuffquant.Tpo"; exit 1; fi In file included from cuffquant.cpp:27: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from cuffquant.cpp:28: In file included from ./bundles.h:22: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ In file included from cuffquant.cpp:45: ./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^ cuffquant.cpp:754:31: warning: unused variable 's2' [-Wunused-variable] const AbundanceGroup& s2 = prev.transcripts; ^ cuffquant.cpp:772:25: warning: unused variable 'ab_group' [-Wunused-variable] const AbundanceGroup& ab_group = abundances[i]->transcripts; ^ In file included from cuffquant.cpp:26: In file included from ./common.h:21: In file included from /sw/opt/boost-1_55/include/boost/math/distributions/normal.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/math/special_functions/erf.hpp:15: In file included from /sw/opt/boost-1_55/include/boost/math/special_functions/gamma.hpp:21: In file included from /sw/opt/boost-1_55/include/boost/math/policies/error_handling.hpp:31: In file included from /sw/opt/boost-1_55/include/boost/format.hpp:38: In file included from /sw/opt/boost-1_55/include/boost/format/internals.hpp:23: In file included from /sw/opt/boost-1_55/include/boost/format/alt_sstream.hpp:21: In file included from /sw/opt/boost-1_55/include/boost/shared_ptr.hpp:17: In file included from /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:30: /sw/opt/boost-1_55/include/boost/checked_delete.hpp:34:5: warning: delete called on 'BundleFactory' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] delete x; ^ /sw/opt/boost-1_55/include/boost/smart_ptr/detail/shared_count.hpp:134:20: note: in instantiation of function template specialization 'boost::checked_delete' requested here boost::checked_delete( p ); ^ /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:276:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count' requested here boost::detail::shared_count( p ).swap( pn ); ^ /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:354:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ cuffquant.cpp:1091:46: note: in instantiation of function template specialization 'boost::shared_ptr::shared_ptr' requested here boost::shared_ptr hf(new BundleFactory(hs, REF_DRIVEN)); ^ In file included from cuffquant.cpp:29: In file included from ./abundances.h:18: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/matrix.hpp:16: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/vector.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/storage.hpp:26: /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:45:27: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned int boost_numeric_ublas_abs (const unsigned int& t) { ^ /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:49:28: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned long boost_numeric_ublas_abs (const unsigned long& t) { ^ 8 warnings generated. g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -L/sw/lib -o cuffquant -L/sw/lib -L/sw/opt/boost-1_55/lib cuffquant.o libcufflinks.a libgc.a -lboost_thread-mt -lboost_system-mt -lboost_serialization-mt -lbam -lz clang: warning: argument unused during compilation: '-pthread' if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/sw/include/eigen3 -I/sw/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -MT cuffnorm.o -MD -MP -MF ".deps/cuffnorm.Tpo" -c -o cuffnorm.o cuffnorm.cpp; \ then mv -f ".deps/cuffnorm.Tpo" ".deps/cuffnorm.Po"; else rm -f ".deps/cuffnorm.Tpo"; exit 1; fi In file included from cuffnorm.cpp:26: ./hits.h:817:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^ In file included from cuffnorm.cpp:27: In file included from ./bundles.h:22: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:10: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ In file included from cuffnorm.cpp:44: In file included from ./differential.h:29: ./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^ cuffnorm.cpp:502:43: warning: unused variable 'first_itr' [-Wunused-variable] FPKMTrackingTable::const_iterator first_itr = tracking.begin(); ^ cuffnorm.cpp:545:43: warning: unused variable 'first_itr' [-Wunused-variable] FPKMTrackingTable::const_iterator first_itr = tracking.begin(); ^ In file included from cuffnorm.cpp:25: In file included from ./common.h:21: In file included from /sw/opt/boost-1_55/include/boost/math/distributions/normal.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/math/special_functions/erf.hpp:15: In file included from /sw/opt/boost-1_55/include/boost/math/special_functions/gamma.hpp:21: In file included from /sw/opt/boost-1_55/include/boost/math/policies/error_handling.hpp:31: In file included from /sw/opt/boost-1_55/include/boost/format.hpp:38: In file included from /sw/opt/boost-1_55/include/boost/format/internals.hpp:23: In file included from /sw/opt/boost-1_55/include/boost/format/alt_sstream.hpp:21: In file included from /sw/opt/boost-1_55/include/boost/shared_ptr.hpp:17: In file included from /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:30: /sw/opt/boost-1_55/include/boost/checked_delete.hpp:34:5: warning: delete called on 'PrecomputedExpressionBundleFactory' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] delete x; ^ /sw/opt/boost-1_55/include/boost/smart_ptr/detail/shared_count.hpp:134:20: note: in instantiation of function template specialization 'boost::checked_delete' requested here boost::checked_delete( p ); ^ /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:276:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count' requested here boost::detail::shared_count( p ).swap( pn ); ^ /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:354:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ cuffnorm.cpp:1160:22: note: in instantiation of function template specialization 'boost::shared_ptr::shared_ptr' requested here hf = boost::shared_ptr(new PrecomputedExpressionBundleFactory(static_pointer_cast(hs))); ^ In file included from cuffnorm.cpp:25: In file included from ./common.h:21: In file included from /sw/opt/boost-1_55/include/boost/math/distributions/normal.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/math/special_functions/erf.hpp:15: In file included from /sw/opt/boost-1_55/include/boost/math/special_functions/gamma.hpp:21: In file included from /sw/opt/boost-1_55/include/boost/math/policies/error_handling.hpp:31: In file included from /sw/opt/boost-1_55/include/boost/format.hpp:38: In file included from /sw/opt/boost-1_55/include/boost/format/internals.hpp:23: In file included from /sw/opt/boost-1_55/include/boost/format/alt_sstream.hpp:21: In file included from /sw/opt/boost-1_55/include/boost/shared_ptr.hpp:17: In file included from /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:30: /sw/opt/boost-1_55/include/boost/checked_delete.hpp:34:5: warning: delete called on 'BundleFactory' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] delete x; ^ /sw/opt/boost-1_55/include/boost/smart_ptr/detail/shared_count.hpp:134:20: note: in instantiation of function template specialization 'boost::checked_delete' requested here boost::checked_delete( p ); ^ /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:276:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count' requested here boost::detail::shared_count( p ).swap( pn ); ^ /sw/opt/boost-1_55/include/boost/smart_ptr/shared_ptr.hpp:354:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ cuffnorm.cpp:1184:22: note: in instantiation of function template specialization 'boost::shared_ptr::shared_ptr' requested here hf = boost::shared_ptr(new BundleFactory(hs, REF_DRIVEN)); ^ In file included from cuffnorm.cpp:28: In file included from ./abundances.h:18: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/matrix.hpp:16: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/vector.hpp:19: In file included from /sw/opt/boost-1_55/include/boost/numeric/ublas/storage.hpp:26: /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:45:27: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned int boost_numeric_ublas_abs (const unsigned int& t) { ^ /sw/opt/boost-1_55/include/boost/numeric/ublas/traits.hpp:49:28: warning: unused function 'boost_numeric_ublas_abs' [-Wunused-function] template<> unsigned long boost_numeric_ublas_abs (const unsigned long& t) { ^ 9 warnings generated. g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -arch x86_64 -march=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -L/sw/lib -o cuffnorm -L/sw/lib -L/sw/opt/boost-1_55/lib cuffnorm.o libcufflinks.a libgc.a -lboost_thread-mt -lboost_system-mt -lboost_serialization-mt -lbam -lz clang: warning: argument unused during compilation: '-pthread' make[2]: Nothing to be done for `all-am'. fink-package-precedence . Scanning /\.Plo,\.Po$/ dependency files... ./src/.deps/abundances.Po ./src/.deps/adap.Po ./src/.deps/ar_funs.Po ./src/.deps/arith.Po ./src/.deps/assemble.Po ./src/.deps/band.Po ./src/.deps/biascorrection.Po ./src/.deps/bundles.Po ./src/.deps/c_args.Po ./src/.deps/c_plot.Po ./src/.deps/clustering.Po ./src/.deps/cmd.Po ./src/.deps/codons.Po ./src/.deps/common.Po ./src/.deps/compress_gtf.Po ./src/.deps/cuffcompare.Po ./src/.deps/cuffdiff.Po ./src/.deps/cufflinks.Po ./src/.deps/cuffnorm.Po ./src/.deps/cuffquant.Po ./src/.deps/dens_haz.Po ./src/.deps/dens_int.Po ./src/.deps/dens_odi.Po ./src/.deps/density.Po ./src/.deps/differential.Po ./src/.deps/dist.Po ./src/.deps/ev_atree.Po ./src/.deps/ev_interp.Po ./src/.deps/ev_kdtre.Po ./src/.deps/ev_main.Po ./src/.deps/ev_trian.Po ./src/.deps/family.Po ./src/.deps/filters.Po ./src/.deps/fitted.Po ./src/.deps/frend.Po ./src/.deps/GArgs.Po ./src/.deps/GBase.Po ./src/.deps/gdna.Po ./src/.deps/genes.Po ./src/.deps/GFaSeqGet.Po ./src/.deps/GFastaIndex.Po ./src/.deps/gff.Po ./src/.deps/gff_utils.Po ./src/.deps/gffread.Po ./src/.deps/graph_optimize.Po ./src/.deps/GStr.Po ./src/.deps/gtf_to_sam.Po ./src/.deps/gtf_tracking.Po ./src/.deps/help.Po ./src/.deps/hits.Po ./src/.deps/jensen_shannon.Po ./src/.deps/lf_dercor.Po ./src/.deps/lf_fitfun.Po ./src/.deps/lf_robust.Po ./src/.deps/lf_vari.Po ./src/.deps/lfd.Po ./src/.deps/lfstr.Po ./src/.deps/linalg.Po ./src/.deps/locfit.Po ./src/.deps/m_chol.Po ./src/.deps/m_eigen.Po ./src/.deps/m_jacob.Po ./src/.deps/m_max.Po ./src/.deps/makecmd.Po ./src/.deps/matching_merge.Po ./src/.deps/math.Po ./src/.deps/minmax.Po ./src/.deps/multireads.Po ./src/.deps/nbhd.Po ./src/.deps/pcomp.Po ./src/.deps/pout.Po ./src/.deps/preplot.Po ./src/.deps/random.Po ./src/.deps/readfile.Po ./src/.deps/replicates.Po ./src/.deps/sampling.Po ./src/.deps/scaffold_graph.Po ./src/.deps/scaffolds.Po ./src/.deps/scb.Po ./src/.deps/scb_cons.Po ./src/.deps/simul.Po ./src/.deps/solve.Po ./src/.deps/startlf.Po ./src/.deps/strings.Po ./src/.deps/tokenize.Po ./src/.deps/tracking.Po ./src/.deps/vari.Po ./src/.deps/wdiag.Po ./src/.deps/weight.Po Looking for incorrect headers in 89 dependency files... Determining fink providers of 1874 headers... 1 - 100 101 - 200 201 - 300 301 - 400 401 - 500 501 - 600 601 - 700 701 - 800 801 - 900 901 - 1000 1001 - 1100 1101 - 1200 1201 - 1300 1301 - 1400 1401 - 1500 1501 - 1600 1601 - 1700 1701 - 1800 1801 - 1874 Found use of headers from 3 fink packages: boost1.55-nopython eigen3 libbam0-dev Scanning binaries for incorrect dyld linking... /bin/rm -rf /sw/build.build/root-cufflinks-2.2.1-2 /bin/mkdir -p /sw/build.build/root-cufflinks-2.2.1-2/sw /bin/mkdir -p /sw/build.build/root-cufflinks-2.2.1-2/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-cufflinks-2.2.1-2 sudo -u fink-bld [ENV] sh -c /tmp/fink.bJXW9 /tmp/fink.SaOgU #!/bin/sh -ev make install PREFIX=/sw DESTDIR=/sw/build.build/root-cufflinks-2.2.1-2 Making install in src test -z "/sw/bin" || /sw/build.build/cufflinks-2.2.1-2/cufflinks-2.2.1/build-aux/install-sh -d "/sw/build.build/root-cufflinks-2.2.1-2/sw/bin" /usr/bin/install -c 'cufflinks' '/sw/build.build/root-cufflinks-2.2.1-2/sw/bin/cufflinks' /usr/bin/install -c 'cuffcompare' '/sw/build.build/root-cufflinks-2.2.1-2/sw/bin/cuffcompare' /usr/bin/install -c 'cuffdiff' '/sw/build.build/root-cufflinks-2.2.1-2/sw/bin/cuffdiff' /usr/bin/install -c 'gtf_to_sam' '/sw/build.build/root-cufflinks-2.2.1-2/sw/bin/gtf_to_sam' /usr/bin/install -c 'compress_gtf' '/sw/build.build/root-cufflinks-2.2.1-2/sw/bin/compress_gtf' /usr/bin/install -c 'gffread' '/sw/build.build/root-cufflinks-2.2.1-2/sw/bin/gffread' /usr/bin/install -c 'cuffquant' '/sw/build.build/root-cufflinks-2.2.1-2/sw/bin/cuffquant' /usr/bin/install -c 'cuffnorm' '/sw/build.build/root-cufflinks-2.2.1-2/sw/bin/cuffnorm' test -z "/sw/bin" || /sw/build.build/cufflinks-2.2.1-2/cufflinks-2.2.1/build-aux/install-sh -d "/sw/build.build/root-cufflinks-2.2.1-2/sw/bin" /usr/bin/install -c 'cuffmerge' '/sw/build.build/root-cufflinks-2.2.1-2/sw/bin/cuffmerge' make[2]: Nothing to be done for `install-data-am'. make[2]: Nothing to be done for `install-exec-am'. make[2]: Nothing to be done for `install-data-am'. sudo -u fink-bld [ENV] sh -c /tmp/fink.ak3Rw /usr/bin/install -d -m 700 /sw/build.build/root-cufflinks-2.2.1-2/sw/share/doc/cufflinks /bin/cp -r AUTHORS /sw/build.build/root-cufflinks-2.2.1-2/sw/share/doc/cufflinks/ /bin/cp -r LICENSE /sw/build.build/root-cufflinks-2.2.1-2/sw/share/doc/cufflinks/ /bin/cp -r README /sw/build.build/root-cufflinks-2.2.1-2/sw/share/doc/cufflinks/ /bin/chmod -R go=u-w /sw/build.build/root-cufflinks-2.2.1-2/sw/share/doc/cufflinks /bin/rm -f /sw/build.build/root-cufflinks-2.2.1-2/sw/info/dir /sw/build.build/root-cufflinks-2.2.1-2/sw/info/dir.old /sw/build.build/root-cufflinks-2.2.1-2/sw/share/info/dir /sw/build.build/root-cufflinks-2.2.1-2/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-cufflinks-2.2.1-2 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `cufflinks' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/cufflinks_2.2.1-2_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-cufflinks-2.2.1-2 (Reading database ... 52041 files and directories currently installed.) Removing fink-buildlock-cufflinks-2.2.1-2 ...