[Debian-med-packaging] Bug#797280: cufflinks ftbfs in unstable
Matthias Klose
doko at debian.org
Sat Aug 29 08:27:38 UTC 2015
Package: src:cufflinks
Version: 2.2.1-1
Severity: serious
Tags: sid stretch
cufflinks ftbfs in unstable, log attached.
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dpkg-buildpackage: source package cufflinks
dpkg-buildpackage: source version 2.2.1-1
dpkg-buildpackage: source distribution unstable
dpkg-buildpackage: source changed by Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
dpkg-source --before-build cufflinks-2.2.1
dpkg-buildpackage: host architecture amd64
fakeroot debian/rules clean
dh clean --with autoreconf --parallel
dh_testdir -O--parallel
debian/rules override_dh_auto_clean
make[1]: Entering directory '/scratch/packages/tmp/cufflinks-2.2.1'
dh_auto_clean
rm -rf autom4te.cache
make[1]: Leaving directory '/scratch/packages/tmp/cufflinks-2.2.1'
dh_autoreconf_clean -O--parallel
dh_clean -O--parallel
debian/rules build
dh build --with autoreconf --parallel
dh_testdir -O--parallel
dh_autoreconf -O--parallel
sh: 1: svnversion: not found
configure.ac:39: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from...
../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from...
ax_boost_system.m4:33: AX_BOOST_SYSTEM is expanded from...
configure.ac:39: the top level
configure.ac:40: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from...
../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from...
ax_boost_serialization.m4:33: AX_BOOST_SERIALIZATION is expanded from...
configure.ac:40: the top level
configure.ac:41: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from...
../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from...
ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from...
configure.ac:41: the top level
sh: 1: svnversion: not found
configure.ac:39: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from...
../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from...
ax_boost_system.m4:33: AX_BOOST_SYSTEM is expanded from...
configure.ac:39: the top level
configure.ac:40: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from...
../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from...
ax_boost_serialization.m4:33: AX_BOOST_SERIALIZATION is expanded from...
configure.ac:40: the top level
configure.ac:41: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from...
../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from...
ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from...
configure.ac:41: the top level
sh: 1: svnversion: not found
configure.ac:39: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from...
../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from...
ax_boost_system.m4:33: AX_BOOST_SYSTEM is expanded from...
configure.ac:39: the top level
configure.ac:40: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from...
../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from...
ax_boost_serialization.m4:33: AX_BOOST_SERIALIZATION is expanded from...
configure.ac:40: the top level
configure.ac:41: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from...
../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from...
ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from...
configure.ac:41: the top level
sh: 1: svnversion: not found
configure.ac:39: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from...
../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from...
ax_boost_system.m4:33: AX_BOOST_SYSTEM is expanded from...
configure.ac:39: the top level
configure.ac:40: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from...
../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from...
ax_boost_serialization.m4:33: AX_BOOST_SERIALIZATION is expanded from...
configure.ac:40: the top level
configure.ac:41: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from...
../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from...
ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from...
configure.ac:41: the top level
sh: 1: svnversion: not found
configure.ac:39: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from...
../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from...
ax_boost_system.m4:33: AX_BOOST_SYSTEM is expanded from...
configure.ac:39: the top level
configure.ac:40: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from...
../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from...
ax_boost_serialization.m4:33: AX_BOOST_SERIALIZATION is expanded from...
configure.ac:40: the top level
configure.ac:41: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from...
../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from...
ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from...
configure.ac:41: the top level
configure.ac:35: installing 'build-aux/ar-lib'
configure.ac:31: installing 'build-aux/compile'
src/Makefile.am:113: warning: source file 'locfit/adap.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
automake: warning: possible forward-incompatibility.
automake: At least a source file is in a subdirectory, but the 'subdir-objects'
automake: automake option hasn't been enabled. For now, the corresponding output
automake: object file(s) will be placed in the top-level directory. However,
automake: this behaviour will change in future Automake versions: they will
automake: unconditionally cause object files to be placed in the same subdirectory
automake: of the corresponding sources.
automake: You are advised to start using 'subdir-objects' option throughout your
automake: project, to avoid future incompatibilities.
src/Makefile.am:113: warning: source file 'locfit/ar_funs.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/arith.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/band.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/c_args.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/c_plot.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/cmd.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/dens_haz.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/dens_int.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/dens_odi.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/density.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/dist.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/ev_atree.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/ev_interp.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/ev_kdtre.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/ev_main.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/ev_trian.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/family.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/fitted.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/frend.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/help.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/lf_dercor.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/lf_fitfun.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/lf_robust.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/lf_vari.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/lfd.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/lfstr.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/linalg.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/locfit.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/m_chol.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/m_eigen.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/m_jacob.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/m_max.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/makecmd.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/math.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/minmax.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/nbhd.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/pcomp.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/pout.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/preplot.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/random.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/readfile.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/scb.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/scb_cons.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/simul.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/solve.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/startlf.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/strings.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/vari.cpp' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/wdiag.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
src/Makefile.am:113: warning: source file 'locfit/weight.c' is in a subdirectory,
src/Makefile.am:113: but option 'subdir-objects' is disabled
debian/rules override_dh_auto_configure
make[1]: Entering directory '/scratch/packages/tmp/cufflinks-2.2.1'
dh_auto_configure -- LIBS="-lboost_system -lboost_thread -lboost_serialization"
./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking "LIBS=-lboost_system -lboost_thread -lboost_serialization"
configure: WARNING: unrecognized options: --disable-maintainer-mode
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gawk... (cached) gawk
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... none
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking whether make sets $(MAKE)... (cached) yes
checking for ranlib... ranlib
checking for ar... ar
checking the archiver (ar) interface... ar
checking for a Python interpreter with version >= 2.4... python
checking for python... /usr/bin/python
checking for python version... 2.7
checking for python platform... linux2
checking for python script directory... ${prefix}/lib/python2.7/dist-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.7/dist-packages
checking for boostlib >= 1.47.0... yes
checking for bamlib... yes
checking build system type... x86_64-pc-linux-gnu
checking whether the Boost::System library is available... yes
checking whether the Boost::Serialization library is available... yes
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... /bin/grep
checking for egrep... /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... x86_64-pc-linux-gnu
checking for struct sysinfo.totalram... yes
checking whether sysctl is declared... yes
checking whether CTL_HW is declared... no
checking whether HW_PHYSMEM is declared... no
checking how to create a pax tar archive... gnutar
checking dependency style of gcc... (cached) none
checking dependency style of g++... (cached) none
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
-- cufflinks 2.2.1 Configuration Results --
C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -Wl,-z,relro
GCC version: gcc (Debian 5.2.1-15) 5.2.1 20150808
Host System type: x86_64-pc-linux-gnu
Install prefix: /usr
Install eprefix: ${prefix}
See config.h for further configuration information.
Email <cole at cs.umd.edu> with questions and bug reports.
make[1]: Leaving directory '/scratch/packages/tmp/cufflinks-2.2.1'
dh_auto_build -O--parallel
make -j12
make[1]: Entering directory '/scratch/packages/tmp/cufflinks-2.2.1'
make all-recursive
make[2]: Entering directory '/scratch/packages/tmp/cufflinks-2.2.1'
Making all in src
make[3]: Entering directory '/scratch/packages/tmp/cufflinks-2.2.1/src'
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o clustering.o clustering.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o differential.o differential.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o common.o common.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o assemble.o assemble.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o tokenize.o tokenize.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o abundances.o abundances.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o scaffolds.o scaffolds.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o hits.o hits.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o genes.o genes.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o bundles.o bundles.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o filters.o filters.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o scaffold_graph.o scaffold_graph.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o matching_merge.o matching_merge.cpp
bundles.cpp:701:23: warning: integer constant is so large that it is unsigned
if (tmp.ref_id() == 12638153115695167477) // corresponds to SAM "*" under FNV hash. unaligned read record
^
bundles.cpp:701:3: warning: this decimal constant is unsigned only in ISO C90
if (tmp.ref_id() == 12638153115695167477) // corresponds to SAM "*" under FNV hash. unaligned read record
^
In file included from assemble.cpp:19:0:
./lemon/topology.h: In function 'bool lemon::stronglyConnected(const Graph&)':
./lemon/topology.h:249:34: warning: typedef 'Node' locally defined but not used [-Wunused-local-typedefs]
typedef typename Graph::Node Node;
^
./lemon/topology.h: In function 'int lemon::countStronglyConnectedComponents(const Graph&)':
./lemon/topology.h:311:34: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef typename Graph::Edge Edge;
^
./lemon/topology.h:313:36: warning: typedef 'EdgeIt' locally defined but not used [-Wunused-local-typedefs]
typedef typename Graph::EdgeIt EdgeIt;
^
./lemon/topology.h: In function 'void lemon::topologicalSort(const Graph&, NodeMap&)':
./lemon/topology.h:1213:34: warning: typedef 'Node' locally defined but not used [-Wunused-local-typedefs]
typedef typename Graph::Node Node;
^
./lemon/topology.h:1215:34: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
typedef typename Graph::Edge Edge;
^
./lemon/topology.h: In function 'bool lemon::bipartite(const UGraph&)':
./lemon/topology.h:1470:37: warning: typedef 'EdgeIt' locally defined but not used [-Wunused-local-typedefs]
typedef typename UGraph::EdgeIt EdgeIt;
^
./lemon/topology.h: In function 'bool lemon::bipartitePartitions(const UGraph&, NodeMap&)':
./lemon/topology.h:1514:35: warning: typedef 'Node' locally defined but not used [-Wunused-local-typedefs]
typedef typename UGraph::Node Node;
^
./lemon/topology.h:1516:37: warning: typedef 'EdgeIt' locally defined but not used [-Wunused-local-typedefs]
typedef typename UGraph::EdgeIt EdgeIt;
^
In file included from scaffolds.h:20:0,
from scaffolds.cpp:14:
hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)':
hits.h:928:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder]
string _expression_file_name;
^
hits.h:927:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder]
std::ifstream _ifs;
^
In file included from scaffolds.h:20:0,
from scaffolds.cpp:14:
hits.h:814:5: warning: when initialized here [-Wreorder]
PrecomputedExpressionHitFactory(const string& expression_file_name,
^
In file included from scaffolds.h:20:0,
from genes.h:17,
from genes.cpp:10:
hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)':
hits.h:928:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder]
string _expression_file_name;
^
hits.h:927:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder]
std::ifstream _ifs;
^
In file included from scaffolds.h:20:0,
from genes.h:17,
from genes.cpp:10:
hits.h:814:5: warning: when initialized here [-Wreorder]
PrecomputedExpressionHitFactory(const string& expression_file_name,
^
In file included from bundles.h:20:0,
from replicates.h:10,
from common.cpp:28:
hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)':
hits.h:928:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder]
string _expression_file_name;
^
hits.h:927:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder]
std::ifstream _ifs;
^
In file included from bundles.h:20:0,
from replicates.h:10,
from common.cpp:28:
hits.h:814:5: warning: when initialized here [-Wreorder]
PrecomputedExpressionHitFactory(const string& expression_file_name,
^
In file included from hits.cpp:22:0:
hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)':
hits.h:928:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder]
string _expression_file_name;
^
hits.h:927:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder]
std::ifstream _ifs;
^
In file included from hits.cpp:22:0:
hits.h:814:5: warning: when initialized here [-Wreorder]
PrecomputedExpressionHitFactory(const string& expression_file_name,
^
In file included from bundles.h:20:0,
from bundles.cpp:17:
hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)':
hits.h:928:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder]
string _expression_file_name;
^
hits.h:927:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder]
std::ifstream _ifs;
^
In file included from bundles.h:20:0,
from bundles.cpp:17:
hits.h:814:5: warning: when initialized here [-Wreorder]
PrecomputedExpressionHitFactory(const string& expression_file_name,
^
In file included from common.cpp:28:0:
replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&)':
replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable]
const vector<boost::shared_ptr<Scaffold> >& s2 = bundles[i-1]->ref_scaffolds();
^
In file included from scaffolds.h:20:0,
from filters.h:17,
from filters.cpp:10:
hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)':
hits.h:928:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder]
string _expression_file_name;
^
hits.h:927:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder]
std::ifstream _ifs;
^
In file included from scaffolds.h:20:0,
from filters.h:17,
from filters.cpp:10:
hits.h:814:5: warning: when initialized here [-Wreorder]
PrecomputedExpressionHitFactory(const string& expression_file_name,
^
In file included from scaffolds.h:20:0,
from scaffold_graph.cpp:12:
hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)':
hits.h:928:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder]
string _expression_file_name;
^
hits.h:927:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder]
std::ifstream _ifs;
^
In file included from scaffolds.h:20:0,
from scaffold_graph.cpp:12:
hits.h:814:5: warning: when initialized here [-Wreorder]
PrecomputedExpressionHitFactory(const string& expression_file_name,
^
In file included from assemble.cpp:44:0:
transitive_closure.h: In function 'void transitive_closure(const Graph&, GraphTC&, G_to_TC_VertexMap, VertexIndexMap)':
transitive_closure.h:85:62: warning: typedef 'edge' locally defined but not used [-Wunused-local-typedefs]
typedef typename graph_traits < Graph >::edge_descriptor edge;
^
transitive_closure.h:226:66: warning: typedef 'tc_vertex' locally defined but not used [-Wunused-local-typedefs]
typedef typename graph_traits < GraphTC >::vertex_descriptor tc_vertex;
^
transitive_closure.h: In function 'void warshall_transitive_closure(G&)':
transitive_closure.h:323:60: warning: typedef 'vertex' locally defined but not used [-Wunused-local-typedefs]
typedef typename graph_traits < G >::vertex_descriptor vertex;
^
transitive_closure.h: In function 'void warren_transitive_closure(G&)':
transitive_closure.h:349:60: warning: typedef 'vertex' locally defined but not used [-Wunused-local-typedefs]
typedef typename graph_traits < G >::vertex_descriptor vertex;
^
In file included from assemble.cpp:45:0:
transitive_reduction.h: In function 'boost::ccheck_aux::unaryfunptr_arg_type<void (*)()>::type boost::transitive_reduction(const Graph&, GraphTR&, G_to_TR_VertexMap, VertexIndexMap)':
transitive_reduction.h:53:63: warning: typedef 'VertexIterator' locally defined but not used [-Wunused-local-typedefs]
typedef typename graph_traits<Graph>::vertex_iterator VertexIterator;
^
In file included from scaffolds.h:20:0,
from matching_merge.h:20,
from matching_merge.cpp:10:
hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)':
hits.h:928:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder]
string _expression_file_name;
^
hits.h:927:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder]
std::ifstream _ifs;
^
In file included from scaffolds.h:20:0,
from matching_merge.h:20,
from matching_merge.cpp:10:
hits.h:814:5: warning: when initialized here [-Wreorder]
PrecomputedExpressionHitFactory(const string& expression_file_name,
^
hits.cpp: In member function 'void ReadHit::trim(int)':
hits.cpp:40:9: warning: variable 'new_left' set but not used [-Wunused-but-set-variable]
int new_left = 0;
^
In file included from abundances.h:23:0,
from abundances.cpp:16:
hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)':
hits.h:928:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder]
string _expression_file_name;
^
hits.h:927:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder]
std::ifstream _ifs;
^
In file included from abundances.h:23:0,
from abundances.cpp:16:
hits.h:814:5: warning: when initialized here [-Wreorder]
PrecomputedExpressionHitFactory(const string& expression_file_name,
^
bundles.cpp: In member function 'bool HitBundle::add_open_hit(boost::shared_ptr<const ReadGroupProperties>, const ReadHit*, bool)':
bundles.cpp:300:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (m.right() - m.left() > max_gene_length)
^
bundles.cpp: In member function 'double BundleFactory::next_valid_alignment(const ReadHit*&)':
bundles.cpp:741:18: warning: variable 'found_scaff' set but not used [-Wunused-but-set-variable]
bool found_scaff = false;
^
bundles.cpp: In member function 'bool BundleFactory::next_bundle_hit_driven(HitBundle&)':
bundles.cpp:817:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (bundle.hits().size() >= max_frags_per_bundle)
^
bundles.cpp: In member function 'bool BundleFactory::next_bundle_ref_driven(HitBundle&)':
bundles.cpp:859:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (bundle.hits().size() < max_frags_per_bundle)
^
bundles.cpp:900:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (bundle.hits().size() >= max_frags_per_bundle)
^
bundles.cpp:889:8: warning: variable 'last_hit_ref_id_seen' set but not used [-Wunused-but-set-variable]
RefID last_hit_ref_id_seen = 0;
^
bundles.cpp:890:6: warning: variable 'last_hit_pos_seen' set but not used [-Wunused-but-set-variable]
int last_hit_pos_seen = 0;
^
bundles.cpp: In member function 'virtual bool PrecomputedExpressionBundleFactory::next_bundle(HitBundle&)':
bundles.cpp:2065:266: warning: format '%d' expects argument of type 'int', but argument 5 has type 'std::vector<boost::shared_ptr<Abundance> >::size_type {aka long unsigned int}' [-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());
^
bundles.cpp:2065:266: warning: format '%d' expects argument of type 'int', but argument 6 has type 'std::vector<boost::shared_ptr<Scaffold> >::size_type {aka long unsigned int}' [-Wformat=]
In file included from abundances.h:23:0,
from differential.cpp:20:
hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)':
hits.h:928:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder]
string _expression_file_name;
^
hits.h:927:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder]
std::ifstream _ifs;
^
In file included from abundances.h:23:0,
from differential.cpp:20:
hits.h:814:5: warning: when initialized here [-Wreorder]
PrecomputedExpressionHitFactory(const string& expression_file_name,
^
In file included from bundles.h:20:0,
from assemble.h:21,
from assemble.cpp:48:
hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)':
hits.h:928:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder]
string _expression_file_name;
^
hits.h:927:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder]
std::ifstream _ifs;
^
In file included from bundles.h:20:0,
from assemble.h:21,
from assemble.cpp:48:
hits.h:814:5: warning: when initialized here [-Wreorder]
PrecomputedExpressionHitFactory(const string& expression_file_name,
^
In file included from abundances.cpp:43:0:
replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&)':
replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable]
const vector<boost::shared_ptr<Scaffold> >& s2 = bundles[i-1]->ref_scaffolds();
^
In file included from abundances.cpp:44:0:
sampling.h: In function 'double boost::numeric::ublas::cholesky_factorize(M&)':
sampling.h:50:13: warning: typedef 'matrix_type' locally defined but not used [-Wunused-local-typedefs]
typedef M matrix_type;
^
In file included from abundances.cpp:44:0:
sampling.h: In function 'void boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::vector_expression<E2>&)':
sampling.h:113:19: warning: typedef 'const_matrix_type' locally defined but not used [-Wunused-local-typedefs]
typedef const M const_matrix_type;
^
sampling.h:114:42: warning: typedef 'vector_type' locally defined but not used [-Wunused-local-typedefs]
typedef vector<typename E::value_type> vector_type;
^
sampling.h: In function 'void boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::matrix_expression<E2>&)':
sampling.h:120:19: warning: typedef 'const_matrix_type' locally defined but not used [-Wunused-local-typedefs]
typedef const M const_matrix_type;
^
sampling.h:121:42: warning: typedef 'matrix_type' locally defined but not used [-Wunused-local-typedefs]
typedef matrix<typename E::value_type> matrix_type;
^
sampling.h: In function 'void boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::vector_expression<E>&, const M&)':
sampling.h:127:19: warning: typedef 'const_matrix_type' locally defined but not used [-Wunused-local-typedefs]
typedef const M const_matrix_type;
^
sampling.h:128:42: warning: typedef 'vector_type' locally defined but not used [-Wunused-local-typedefs]
typedef vector<typename E::value_type> vector_type;
^
sampling.h: In function 'void boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::matrix_expression<E>&, const M&)':
sampling.h:134:19: warning: typedef 'const_matrix_type' locally defined but not used [-Wunused-local-typedefs]
typedef const M const_matrix_type;
^
sampling.h:135:42: warning: typedef 'matrix_type' locally defined but not used [-Wunused-local-typedefs]
typedef matrix<typename E::value_type> matrix_type;
^
In file included from abundances.h:23:0,
from clustering.h:38,
from clustering.cpp:10:
hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)':
hits.h:928:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder]
string _expression_file_name;
^
hits.h:927:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder]
std::ifstream _ifs;
^
In file included from abundances.h:23:0,
from clustering.h:38,
from clustering.cpp:10:
hits.h:814:5: warning: when initialized here [-Wreorder]
PrecomputedExpressionHitFactory(const string& expression_file_name,
^
In file included from differential.h:29:0,
from differential.cpp:21:
replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&)':
replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable]
const vector<boost::shared_ptr<Scaffold> >& s2 = bundles[i-1]->ref_scaffolds();
^
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/bits/char_traits.h:39,
from /usr/include/c++/5/ios:40,
from /usr/include/c++/5/ostream:38,
from /usr/include/c++/5/iostream:39,
from hits.cpp:17:
/usr/include/c++/5/bits/stl_pair.h: In instantiation of 'std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const void*; _U2 = boost::shared_ptr<const ReadGroupProperties>; _T1 = const void* const; _T2 = boost::shared_ptr<void>]':
/usr/include/boost/serialization/shared_ptr_helper.hpp:182:20: required from 'void boost::serialization::shared_ptr_helper<SPT>::reset(SPT<T>&, T*) [with T = const ReadGroupProperties; SPT = boost::shared_ptr]'
/usr/include/boost/serialization/shared_ptr.hpp:171:5: required from 'void boost::serialization::load(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]'
/usr/include/boost/serialization/split_free.hpp:58:13: required from 'static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const ReadGroupProperties>]'
/usr/include/boost/serialization/split_free.hpp:74:18: required from 'void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const ReadGroupProperties>]'
/usr/include/boost/serialization/shared_ptr.hpp:187:37: required from 'void boost::serialization::serialize(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]'
/usr/include/boost/serialization/serialization.hpp:128:18: [ skipping 80 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/boost/archive/detail/iserializer.hpp:618:18: required from 'void boost::archive::load(Archive&, T&) [with Archive = boost::archive::binary_iarchive; T = std::pair<int, AbundanceGroup>]'
/usr/include/boost/archive/detail/common_iarchive.hpp:66:22: required from 'void boost::archive::detail::common_iarchive<Archive>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
/usr/include/boost/archive/basic_binary_iarchive.hpp:76:7: required from 'void boost::archive::basic_binary_iarchive<Archive>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
/usr/include/boost/archive/binary_iarchive_impl.hpp:62:9: required from 'void boost::archive::binary_iarchive_impl<Archive, Elem, Tr>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive; Elem = char; Tr = std::char_traits<char>]'
/usr/include/boost/archive/detail/interface_iarchive.hpp:60:9: required from 'Archive& boost::archive::detail::interface_iarchive<Archive>::operator>>(T&) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
hits.cpp:1125:15: required from here
/usr/include/c++/5/bits/stl_pair.h:119:39: error: no matching function for call to 'boost::shared_ptr<void>::shared_ptr(const boost::shared_ptr<const ReadGroupProperties>&)'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from /usr/include/boost/format/alt_sstream.hpp:21,
from /usr/include/boost/format/internals.hpp:23,
from /usr/include/boost/format.hpp:38,
from /usr/include/boost/math/policies/error_handling.hpp:31,
from /usr/include/boost/math/special_functions/gamma.hpp:23,
from /usr/include/boost/math/special_functions/erf.hpp:15,
from /usr/include/boost/math/distributions/normal.hpp:19,
from common.h:21,
from hits.cpp:21:
/usr/include/boost/smart_ptr/shared_ptr.hpp:467:14: note: candidate: template<class Ap> boost::shared_ptr<T>::shared_ptr(Ap, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type)
explicit shared_ptr( Ap r, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type = 0 ): px( r.get() ), pn()
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:467:14: note: template argument deduction/substitution failed:
/usr/include/boost/smart_ptr/shared_ptr.hpp: In substitution of 'template<class Ap> boost::shared_ptr<T>::shared_ptr(Ap, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type) [with Ap = boost::shared_ptr<const ReadGroupProperties>]':
/usr/include/c++/5/bits/stl_pair.h:119:39: required from 'std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const void*; _U2 = boost::shared_ptr<const ReadGroupProperties>; _T1 = const void* const; _T2 = boost::shared_ptr<void>]'
/usr/include/boost/serialization/shared_ptr_helper.hpp:182:20: required from 'void boost::serialization::shared_ptr_helper<SPT>::reset(SPT<T>&, T*) [with T = const ReadGroupProperties; SPT = boost::shared_ptr]'
/usr/include/boost/serialization/shared_ptr.hpp:171:5: required from 'void boost::serialization::load(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]'
/usr/include/boost/serialization/split_free.hpp:58:13: required from 'static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const ReadGroupProperties>]'
/usr/include/boost/serialization/split_free.hpp:74:18: required from 'void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const ReadGroupProperties>]'
/usr/include/boost/serialization/shared_ptr.hpp:187:37: [ skipping 81 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/boost/archive/detail/iserializer.hpp:618:18: required from 'void boost::archive::load(Archive&, T&) [with Archive = boost::archive::binary_iarchive; T = std::pair<int, AbundanceGroup>]'
/usr/include/boost/archive/detail/common_iarchive.hpp:66:22: required from 'void boost::archive::detail::common_iarchive<Archive>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
/usr/include/boost/archive/basic_binary_iarchive.hpp:76:7: required from 'void boost::archive::basic_binary_iarchive<Archive>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
/usr/include/boost/archive/binary_iarchive_impl.hpp:62:9: required from 'void boost::archive::binary_iarchive_impl<Archive, Elem, Tr>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive; Elem = char; Tr = std::char_traits<char>]'
/usr/include/boost/archive/detail/interface_iarchive.hpp:60:9: required from 'Archive& boost::archive::detail::interface_iarchive<Archive>::operator>>(T&) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
hits.cpp:1125:15: required from here
/usr/include/boost/smart_ptr/shared_ptr.hpp:467:14: error: no type named 'type' in 'struct boost::detail::sp_enable_if_auto_ptr<boost::shared_ptr<const ReadGroupProperties>, int>'
/usr/include/c++/5/bits/stl_pair.h: In instantiation of 'std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const void*; _U2 = boost::shared_ptr<const ReadGroupProperties>; _T1 = const void* const; _T2 = boost::shared_ptr<void>]':
/usr/include/boost/serialization/shared_ptr_helper.hpp:182:20: required from 'void boost::serialization::shared_ptr_helper<SPT>::reset(SPT<T>&, T*) [with T = const ReadGroupProperties; SPT = boost::shared_ptr]'
/usr/include/boost/serialization/shared_ptr.hpp:171:5: required from 'void boost::serialization::load(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]'
/usr/include/boost/serialization/split_free.hpp:58:13: required from 'static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const ReadGroupProperties>]'
/usr/include/boost/serialization/split_free.hpp:74:18: required from 'void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const ReadGroupProperties>]'
/usr/include/boost/serialization/shared_ptr.hpp:187:37: required from 'void boost::serialization::serialize(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]'
/usr/include/boost/serialization/serialization.hpp:128:18: [ skipping 80 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/boost/archive/detail/iserializer.hpp:618:18: required from 'void boost::archive::load(Archive&, T&) [with Archive = boost::archive::binary_iarchive; T = std::pair<int, AbundanceGroup>]'
/usr/include/boost/archive/detail/common_iarchive.hpp:66:22: required from 'void boost::archive::detail::common_iarchive<Archive>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
/usr/include/boost/archive/basic_binary_iarchive.hpp:76:7: required from 'void boost::archive::basic_binary_iarchive<Archive>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
/usr/include/boost/archive/binary_iarchive_impl.hpp:62:9: required from 'void boost::archive::binary_iarchive_impl<Archive, Elem, Tr>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive; Elem = char; Tr = std::char_traits<char>]'
/usr/include/boost/archive/detail/interface_iarchive.hpp:60:9: required from 'Archive& boost::archive::detail::interface_iarchive<Archive>::operator>>(T&) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
hits.cpp:1125:15: required from here
/usr/include/boost/smart_ptr/shared_ptr.hpp:441:14: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(std::auto_ptr<_Tp1>&)
explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:441:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/bits/char_traits.h:39,
from /usr/include/c++/5/ios:40,
from /usr/include/c++/5/ostream:38,
from /usr/include/c++/5/iostream:39,
from hits.cpp:17:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: types 'std::auto_ptr<Y>' and 'const boost::shared_ptr<const ReadGroupProperties>' have incompatible cv-qualifiers
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from /usr/include/boost/format/alt_sstream.hpp:21,
from /usr/include/boost/format/internals.hpp:23,
from /usr/include/boost/format.hpp:38,
from /usr/include/boost/math/policies/error_handling.hpp:31,
from /usr/include/boost/math/special_functions/gamma.hpp:23,
from /usr/include/boost/math/special_functions/erf.hpp:15,
from /usr/include/boost/math/distributions/normal.hpp:19,
from common.h:21,
from hits.cpp:21:
/usr/include/boost/smart_ptr/shared_ptr.hpp:434:5: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(const boost::shared_ptr<Y>&, boost::shared_ptr<T>::element_type*)
shared_ptr( shared_ptr<Y> const & r, element_type * p ) BOOST_NOEXCEPT : px( p ), pn( r.pn )
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:434:5: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/bits/char_traits.h:39,
from /usr/include/c++/5/ios:40,
from /usr/include/c++/5/ostream:38,
from /usr/include/c++/5/iostream:39,
from hits.cpp:17:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: candidate expects 2 arguments, 1 provided
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from /usr/include/boost/format/alt_sstream.hpp:21,
from /usr/include/boost/format/internals.hpp:23,
from /usr/include/boost/format.hpp:38,
from /usr/include/boost/math/policies/error_handling.hpp:31,
from /usr/include/boost/math/special_functions/gamma.hpp:23,
from /usr/include/boost/math/special_functions/erf.hpp:15,
from /usr/include/boost/math/distributions/normal.hpp:19,
from common.h:21,
from hits.cpp:21:
/usr/include/boost/smart_ptr/shared_ptr.hpp:420:5: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(const boost::shared_ptr<Y>&, typename boost::detail::sp_enable_if_convertible<Y, T>::type)
shared_ptr( shared_ptr<Y> const & r, typename boost::detail::sp_enable_if_convertible<Y,T>::type = boost::detail::sp_empty() )
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:420:5: note: template argument deduction/substitution failed:
/usr/include/boost/smart_ptr/shared_ptr.hpp: In substitution of 'template<class Y> boost::shared_ptr<T>::shared_ptr(const boost::shared_ptr<Y>&, typename boost::detail::sp_enable_if_convertible<Y, T>::type) [with Y = const ReadGroupProperties]':
/usr/include/c++/5/bits/stl_pair.h:119:39: required from 'std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const void*; _U2 = boost::shared_ptr<const ReadGroupProperties>; _T1 = const void* const; _T2 = boost::shared_ptr<void>]'
/usr/include/boost/serialization/shared_ptr_helper.hpp:182:20: required from 'void boost::serialization::shared_ptr_helper<SPT>::reset(SPT<T>&, T*) [with T = const ReadGroupProperties; SPT = boost::shared_ptr]'
/usr/include/boost/serialization/shared_ptr.hpp:171:5: required from 'void boost::serialization::load(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]'
/usr/include/boost/serialization/split_free.hpp:58:13: required from 'static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const ReadGroupProperties>]'
/usr/include/boost/serialization/split_free.hpp:74:18: required from 'void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const ReadGroupProperties>]'
/usr/include/boost/serialization/shared_ptr.hpp:187:37: [ skipping 81 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/boost/archive/detail/iserializer.hpp:618:18: required from 'void boost::archive::load(Archive&, T&) [with Archive = boost::archive::binary_iarchive; T = std::pair<int, AbundanceGroup>]'
/usr/include/boost/archive/detail/common_iarchive.hpp:66:22: required from 'void boost::archive::detail::common_iarchive<Archive>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
/usr/include/boost/archive/basic_binary_iarchive.hpp:76:7: required from 'void boost::archive::basic_binary_iarchive<Archive>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
/usr/include/boost/archive/binary_iarchive_impl.hpp:62:9: required from 'void boost::archive::binary_iarchive_impl<Archive, Elem, Tr>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive; Elem = char; Tr = std::char_traits<char>]'
/usr/include/boost/archive/detail/interface_iarchive.hpp:60:9: required from 'Archive& boost::archive::detail::interface_iarchive<Archive>::operator>>(T&) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
hits.cpp:1125:15: required from here
/usr/include/boost/smart_ptr/shared_ptr.hpp:420:5: error: no type named 'type' in 'struct boost::detail::sp_enable_if_convertible<const ReadGroupProperties, void>'
/usr/include/c++/5/bits/stl_pair.h: In instantiation of 'std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const void*; _U2 = boost::shared_ptr<const ReadGroupProperties>; _T1 = const void* const; _T2 = boost::shared_ptr<void>]':
/usr/include/boost/serialization/shared_ptr_helper.hpp:182:20: required from 'void boost::serialization::shared_ptr_helper<SPT>::reset(SPT<T>&, T*) [with T = const ReadGroupProperties; SPT = boost::shared_ptr]'
/usr/include/boost/serialization/shared_ptr.hpp:171:5: required from 'void boost::serialization::load(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]'
/usr/include/boost/serialization/split_free.hpp:58:13: required from 'static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const ReadGroupProperties>]'
/usr/include/boost/serialization/split_free.hpp:74:18: required from 'void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const ReadGroupProperties>]'
/usr/include/boost/serialization/shared_ptr.hpp:187:37: required from 'void boost::serialization::serialize(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]'
/usr/include/boost/serialization/serialization.hpp:128:18: [ skipping 80 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/boost/archive/detail/iserializer.hpp:618:18: required from 'void boost::archive::load(Archive&, T&) [with Archive = boost::archive::binary_iarchive; T = std::pair<int, AbundanceGroup>]'
/usr/include/boost/archive/detail/common_iarchive.hpp:66:22: required from 'void boost::archive::detail::common_iarchive<Archive>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
/usr/include/boost/archive/basic_binary_iarchive.hpp:76:7: required from 'void boost::archive::basic_binary_iarchive<Archive>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
/usr/include/boost/archive/binary_iarchive_impl.hpp:62:9: required from 'void boost::archive::binary_iarchive_impl<Archive, Elem, Tr>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive; Elem = char; Tr = std::char_traits<char>]'
/usr/include/boost/archive/detail/interface_iarchive.hpp:60:9: required from 'Archive& boost::archive::detail::interface_iarchive<Archive>::operator>>(T&) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
hits.cpp:1125:15: required from here
/usr/include/boost/smart_ptr/shared_ptr.hpp:408:5: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(const boost::weak_ptr<Y>&, boost::detail::sp_nothrow_tag)
shared_ptr( weak_ptr<Y> const & r, boost::detail::sp_nothrow_tag )
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:408:5: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/bits/char_traits.h:39,
from /usr/include/c++/5/ios:40,
from /usr/include/c++/5/ostream:38,
from /usr/include/c++/5/iostream:39,
from hits.cpp:17:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: 'const boost::shared_ptr<const ReadGroupProperties>' is not derived from 'const boost::weak_ptr<Y>'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from /usr/include/boost/format/alt_sstream.hpp:21,
from /usr/include/boost/format/internals.hpp:23,
from /usr/include/boost/format.hpp:38,
from /usr/include/boost/math/policies/error_handling.hpp:31,
from /usr/include/boost/math/special_functions/gamma.hpp:23,
from /usr/include/boost/math/special_functions/erf.hpp:15,
from /usr/include/boost/math/distributions/normal.hpp:19,
from common.h:21,
from hits.cpp:21:
/usr/include/boost/smart_ptr/shared_ptr.hpp:399:14: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(const boost::weak_ptr<Y>&)
explicit shared_ptr( weak_ptr<Y> const & r ): pn( r.pn ) // may throw
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:399:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/bits/char_traits.h:39,
from /usr/include/c++/5/ios:40,
from /usr/include/c++/5/ostream:38,
from /usr/include/c++/5/iostream:39,
from hits.cpp:17:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: 'const boost::shared_ptr<const ReadGroupProperties>' is not derived from 'const boost::weak_ptr<Y>'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from /usr/include/boost/format/alt_sstream.hpp:21,
from /usr/include/boost/format/internals.hpp:23,
from /usr/include/boost/format.hpp:38,
from /usr/include/boost/math/policies/error_handling.hpp:31,
from /usr/include/boost/math/special_functions/gamma.hpp:23,
from /usr/include/boost/math/special_functions/erf.hpp:15,
from /usr/include/boost/math/distributions/normal.hpp:19,
from common.h:21,
from hits.cpp:21:
/usr/include/boost/smart_ptr/shared_ptr.hpp:373:41: note: candidate: template<class Y, class D, class A> boost::shared_ptr<T>::shared_ptr(Y*, D, A)
template<class Y, class D, class A> shared_ptr( Y * p, D d, A a ): px( p ), pn( p, d, a )
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:373:41: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/bits/char_traits.h:39,
from /usr/include/c++/5/ios:40,
from /usr/include/c++/5/ostream:38,
from /usr/include/c++/5/iostream:39,
from hits.cpp:17:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: mismatched types 'Y*' and 'boost::shared_ptr<const ReadGroupProperties>'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from /usr/include/boost/format/alt_sstream.hpp:21,
from /usr/include/boost/format/internals.hpp:23,
from /usr/include/boost/format.hpp:38,
from /usr/include/boost/math/policies/error_handling.hpp:31,
from /usr/include/boost/math/special_functions/gamma.hpp:23,
from /usr/include/boost/math/special_functions/erf.hpp:15,
from /usr/include/boost/math/distributions/normal.hpp:19,
from common.h:21,
from hits.cpp:21:
/usr/include/boost/smart_ptr/shared_ptr.hpp:358:32: note: candidate: template<class Y, class D> boost::shared_ptr<T>::shared_ptr(Y*, D)
template<class Y, class D> shared_ptr( Y * p, D d ): px( p ), pn( p, d )
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:358:32: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/bits/char_traits.h:39,
from /usr/include/c++/5/ios:40,
from /usr/include/c++/5/ostream:38,
from /usr/include/c++/5/iostream:39,
from hits.cpp:17:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: mismatched types 'Y*' and 'boost::shared_ptr<const ReadGroupProperties>'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from /usr/include/boost/format/alt_sstream.hpp:21,
from /usr/include/boost/format/internals.hpp:23,
from /usr/include/boost/format.hpp:38,
from /usr/include/boost/math/policies/error_handling.hpp:31,
from /usr/include/boost/math/special_functions/gamma.hpp:23,
from /usr/include/boost/math/special_functions/erf.hpp:15,
from /usr/include/boost/math/distributions/normal.hpp:19,
from common.h:21,
from hits.cpp:21:
/usr/include/boost/smart_ptr/shared_ptr.hpp:347:14: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(Y*)
explicit shared_ptr( Y * p ): px( p ), pn() // Y must be complete
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:347:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/bits/char_traits.h:39,
from /usr/include/c++/5/ios:40,
from /usr/include/c++/5/ostream:38,
from /usr/include/c++/5/iostream:39,
from hits.cpp:17:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: mismatched types 'Y*' and 'boost::shared_ptr<const ReadGroupProperties>'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from /usr/include/boost/format/alt_sstream.hpp:21,
from /usr/include/boost/format/internals.hpp:23,
from /usr/include/boost/format.hpp:38,
from /usr/include/boost/math/policies/error_handling.hpp:31,
from /usr/include/boost/math/special_functions/gamma.hpp:23,
from /usr/include/boost/math/special_functions/erf.hpp:15,
from /usr/include/boost/math/distributions/normal.hpp:19,
from common.h:21,
from hits.cpp:21:
/usr/include/boost/smart_ptr/shared_ptr.hpp:334:5: note: candidate: boost::shared_ptr<T>::shared_ptr() [with T = void]
shared_ptr() BOOST_NOEXCEPT : px( 0 ), pn() // never throws in 1.30+
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:334:5: note: candidate expects 0 arguments, 1 provided
/usr/include/boost/smart_ptr/shared_ptr.hpp:323:25: note: candidate: boost::shared_ptr<void>::shared_ptr(const boost::shared_ptr<void>&)
template<class T> class shared_ptr
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:323:25: note: no known conversion for argument 1 from 'const boost::shared_ptr<const ReadGroupProperties>' to 'const boost::shared_ptr<void>&'
In file included from hits.cpp:21:0:
/usr/include/boost/serialization/vector.hpp: In instantiation of 'void boost::serialization::load(Archive&, std::vector<U, Allocator>&, unsigned int, mpl_::false_) [with Archive = boost::archive::binary_iarchive; U = LocusCount; Allocator = std::allocator<LocusCount>; mpl_::false_ = mpl_::bool_<false>]':
/usr/include/boost/serialization/vector.hpp:173:9: required from 'void boost::serialization::load(Archive&, std::vector<U, Allocator>&, unsigned int) [with Archive = boost::archive::binary_iarchive; U = LocusCount; Allocator = std::allocator<LocusCount>]'
/usr/include/boost/serialization/split_free.hpp:58:13: required from 'static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = std::vector<LocusCount>]'
/usr/include/boost/serialization/split_free.hpp:74:18: required from 'void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = std::vector<LocusCount>]'
/usr/include/boost/serialization/vector.hpp:184:37: required from 'void boost::serialization::serialize(Archive&, std::vector<U, Allocator>&, unsigned int) [with Archive = boost::archive::binary_iarchive; U = LocusCount; Allocator = std::allocator<LocusCount>]'
/usr/include/boost/serialization/serialization.hpp:128:18: required from 'void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = std::vector<LocusCount>]'
/usr/include/boost/archive/detail/iserializer.hpp:184:40: [ skipping 127 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/boost/archive/detail/iserializer.hpp:618:18: required from 'void boost::archive::load(Archive&, T&) [with Archive = boost::archive::binary_iarchive; T = std::pair<int, AbundanceGroup>]'
/usr/include/boost/archive/detail/common_iarchive.hpp:66:22: required from 'void boost::archive::detail::common_iarchive<Archive>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
/usr/include/boost/archive/basic_binary_iarchive.hpp:76:7: required from 'void boost::archive::basic_binary_iarchive<Archive>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
/usr/include/boost/archive/binary_iarchive_impl.hpp:62:9: required from 'void boost::archive::binary_iarchive_impl<Archive, Elem, Tr>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive; Elem = char; Tr = std::char_traits<char>]'
/usr/include/boost/archive/detail/interface_iarchive.hpp:60:9: required from 'Archive& boost::archive::detail::interface_iarchive<Archive>::operator>>(T&) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
hits.cpp:1125:15: required from here
common.h:387:5: error: 'LocusCount::LocusCount()' is private
LocusCount() {} //needs an empty constructor for serialization
^
In file included from common.h:34:0,
from hits.cpp:21:
/usr/include/boost/serialization/vector.hpp:90:9: error: within this context
t.resize(count);
^
/usr/include/boost/serialization/vector.hpp:90:9: note: when instantiating default argument for call to void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type, std::vector<_Tp, _Alloc>::value_type) [with _Tp = LocusCount; _Alloc = std::allocator<LocusCount>; std::vector<_Tp, _Alloc>::size_type = long unsigned int; std::vector<_Tp, _Alloc>::value_type = LocusCount]
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/bits/char_traits.h:39,
from /usr/include/c++/5/ios:40,
from /usr/include/c++/5/ostream:38,
from /usr/include/c++/5/iostream:39,
from hits.cpp:17:
/usr/include/c++/5/bits/stl_pair.h: In instantiation of 'std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const void*; _U2 = boost::shared_ptr<const EmpDist>; _T1 = const void* const; _T2 = boost::shared_ptr<void>]':
/usr/include/boost/serialization/shared_ptr_helper.hpp:182:20: required from 'void boost::serialization::shared_ptr_helper<SPT>::reset(SPT<T>&, T*) [with T = const EmpDist; SPT = boost::shared_ptr]'
/usr/include/boost/serialization/shared_ptr.hpp:171:5: required from 'void boost::serialization::load(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]'
/usr/include/boost/serialization/split_free.hpp:58:13: required from 'static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const EmpDist>]'
/usr/include/boost/serialization/split_free.hpp:74:18: required from 'void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const EmpDist>]'
/usr/include/boost/serialization/shared_ptr.hpp:187:37: required from 'void boost::serialization::serialize(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]'
/usr/include/boost/serialization/serialization.hpp:128:18: [ skipping 128 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/boost/archive/detail/iserializer.hpp:618:18: required from 'void boost::archive::load(Archive&, T&) [with Archive = boost::archive::binary_iarchive; T = std::pair<int, AbundanceGroup>]'
/usr/include/boost/archive/detail/common_iarchive.hpp:66:22: required from 'void boost::archive::detail::common_iarchive<Archive>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
/usr/include/boost/archive/basic_binary_iarchive.hpp:76:7: required from 'void boost::archive::basic_binary_iarchive<Archive>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
/usr/include/boost/archive/binary_iarchive_impl.hpp:62:9: required from 'void boost::archive::binary_iarchive_impl<Archive, Elem, Tr>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive; Elem = char; Tr = std::char_traits<char>]'
/usr/include/boost/archive/detail/interface_iarchive.hpp:60:9: required from 'Archive& boost::archive::detail::interface_iarchive<Archive>::operator>>(T&) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
hits.cpp:1125:15: required from here
/usr/include/c++/5/bits/stl_pair.h:119:39: error: no matching function for call to 'boost::shared_ptr<void>::shared_ptr(const boost::shared_ptr<const EmpDist>&)'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from /usr/include/boost/format/alt_sstream.hpp:21,
from /usr/include/boost/format/internals.hpp:23,
from /usr/include/boost/format.hpp:38,
from /usr/include/boost/math/policies/error_handling.hpp:31,
from /usr/include/boost/math/special_functions/gamma.hpp:23,
from /usr/include/boost/math/special_functions/erf.hpp:15,
from /usr/include/boost/math/distributions/normal.hpp:19,
from common.h:21,
from hits.cpp:21:
/usr/include/boost/smart_ptr/shared_ptr.hpp:467:14: note: candidate: template<class Ap> boost::shared_ptr<T>::shared_ptr(Ap, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type)
explicit shared_ptr( Ap r, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type = 0 ): px( r.get() ), pn()
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:467:14: note: template argument deduction/substitution failed:
/usr/include/boost/smart_ptr/shared_ptr.hpp: In substitution of 'template<class Ap> boost::shared_ptr<T>::shared_ptr(Ap, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type) [with Ap = boost::shared_ptr<const EmpDist>]':
/usr/include/c++/5/bits/stl_pair.h:119:39: required from 'std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const void*; _U2 = boost::shared_ptr<const EmpDist>; _T1 = const void* const; _T2 = boost::shared_ptr<void>]'
/usr/include/boost/serialization/shared_ptr_helper.hpp:182:20: required from 'void boost::serialization::shared_ptr_helper<SPT>::reset(SPT<T>&, T*) [with T = const EmpDist; SPT = boost::shared_ptr]'
/usr/include/boost/serialization/shared_ptr.hpp:171:5: required from 'void boost::serialization::load(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]'
/usr/include/boost/serialization/split_free.hpp:58:13: required from 'static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const EmpDist>]'
/usr/include/boost/serialization/split_free.hpp:74:18: required from 'void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const EmpDist>]'
/usr/include/boost/serialization/shared_ptr.hpp:187:37: [ skipping 129 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/boost/archive/detail/iserializer.hpp:618:18: required from 'void boost::archive::load(Archive&, T&) [with Archive = boost::archive::binary_iarchive; T = std::pair<int, AbundanceGroup>]'
/usr/include/boost/archive/detail/common_iarchive.hpp:66:22: required from 'void boost::archive::detail::common_iarchive<Archive>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
/usr/include/boost/archive/basic_binary_iarchive.hpp:76:7: required from 'void boost::archive::basic_binary_iarchive<Archive>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
/usr/include/boost/archive/binary_iarchive_impl.hpp:62:9: required from 'void boost::archive::binary_iarchive_impl<Archive, Elem, Tr>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive; Elem = char; Tr = std::char_traits<char>]'
/usr/include/boost/archive/detail/interface_iarchive.hpp:60:9: required from 'Archive& boost::archive::detail::interface_iarchive<Archive>::operator>>(T&) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
hits.cpp:1125:15: required from here
/usr/include/boost/smart_ptr/shared_ptr.hpp:467:14: error: no type named 'type' in 'struct boost::detail::sp_enable_if_auto_ptr<boost::shared_ptr<const EmpDist>, int>'
/usr/include/c++/5/bits/stl_pair.h: In instantiation of 'std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const void*; _U2 = boost::shared_ptr<const EmpDist>; _T1 = const void* const; _T2 = boost::shared_ptr<void>]':
/usr/include/boost/serialization/shared_ptr_helper.hpp:182:20: required from 'void boost::serialization::shared_ptr_helper<SPT>::reset(SPT<T>&, T*) [with T = const EmpDist; SPT = boost::shared_ptr]'
/usr/include/boost/serialization/shared_ptr.hpp:171:5: required from 'void boost::serialization::load(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]'
/usr/include/boost/serialization/split_free.hpp:58:13: required from 'static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const EmpDist>]'
/usr/include/boost/serialization/split_free.hpp:74:18: required from 'void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const EmpDist>]'
/usr/include/boost/serialization/shared_ptr.hpp:187:37: required from 'void boost::serialization::serialize(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]'
/usr/include/boost/serialization/serialization.hpp:128:18: [ skipping 128 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/boost/archive/detail/iserializer.hpp:618:18: required from 'void boost::archive::load(Archive&, T&) [with Archive = boost::archive::binary_iarchive; T = std::pair<int, AbundanceGroup>]'
/usr/include/boost/archive/detail/common_iarchive.hpp:66:22: required from 'void boost::archive::detail::common_iarchive<Archive>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
/usr/include/boost/archive/basic_binary_iarchive.hpp:76:7: required from 'void boost::archive::basic_binary_iarchive<Archive>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
/usr/include/boost/archive/binary_iarchive_impl.hpp:62:9: required from 'void boost::archive::binary_iarchive_impl<Archive, Elem, Tr>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive; Elem = char; Tr = std::char_traits<char>]'
/usr/include/boost/archive/detail/interface_iarchive.hpp:60:9: required from 'Archive& boost::archive::detail::interface_iarchive<Archive>::operator>>(T&) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
hits.cpp:1125:15: required from here
/usr/include/boost/smart_ptr/shared_ptr.hpp:441:14: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(std::auto_ptr<_Tp1>&)
explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:441:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/bits/char_traits.h:39,
from /usr/include/c++/5/ios:40,
from /usr/include/c++/5/ostream:38,
from /usr/include/c++/5/iostream:39,
from hits.cpp:17:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: types 'std::auto_ptr<Y>' and 'const boost::shared_ptr<const EmpDist>' have incompatible cv-qualifiers
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from /usr/include/boost/format/alt_sstream.hpp:21,
from /usr/include/boost/format/internals.hpp:23,
from /usr/include/boost/format.hpp:38,
from /usr/include/boost/math/policies/error_handling.hpp:31,
from /usr/include/boost/math/special_functions/gamma.hpp:23,
from /usr/include/boost/math/special_functions/erf.hpp:15,
from /usr/include/boost/math/distributions/normal.hpp:19,
from common.h:21,
from hits.cpp:21:
/usr/include/boost/smart_ptr/shared_ptr.hpp:434:5: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(const boost::shared_ptr<Y>&, boost::shared_ptr<T>::element_type*)
shared_ptr( shared_ptr<Y> const & r, element_type * p ) BOOST_NOEXCEPT : px( p ), pn( r.pn )
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:434:5: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/bits/char_traits.h:39,
from /usr/include/c++/5/ios:40,
from /usr/include/c++/5/ostream:38,
from /usr/include/c++/5/iostream:39,
from hits.cpp:17:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: candidate expects 2 arguments, 1 provided
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from /usr/include/boost/format/alt_sstream.hpp:21,
from /usr/include/boost/format/internals.hpp:23,
from /usr/include/boost/format.hpp:38,
from /usr/include/boost/math/policies/error_handling.hpp:31,
from /usr/include/boost/math/special_functions/gamma.hpp:23,
from /usr/include/boost/math/special_functions/erf.hpp:15,
from /usr/include/boost/math/distributions/normal.hpp:19,
from common.h:21,
from hits.cpp:21:
/usr/include/boost/smart_ptr/shared_ptr.hpp:420:5: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(const boost::shared_ptr<Y>&, typename boost::detail::sp_enable_if_convertible<Y, T>::type)
shared_ptr( shared_ptr<Y> const & r, typename boost::detail::sp_enable_if_convertible<Y,T>::type = boost::detail::sp_empty() )
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:420:5: note: template argument deduction/substitution failed:
/usr/include/boost/smart_ptr/shared_ptr.hpp: In substitution of 'template<class Y> boost::shared_ptr<T>::shared_ptr(const boost::shared_ptr<Y>&, typename boost::detail::sp_enable_if_convertible<Y, T>::type) [with Y = const EmpDist]':
/usr/include/c++/5/bits/stl_pair.h:119:39: required from 'std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const void*; _U2 = boost::shared_ptr<const EmpDist>; _T1 = const void* const; _T2 = boost::shared_ptr<void>]'
/usr/include/boost/serialization/shared_ptr_helper.hpp:182:20: required from 'void boost::serialization::shared_ptr_helper<SPT>::reset(SPT<T>&, T*) [with T = const EmpDist; SPT = boost::shared_ptr]'
/usr/include/boost/serialization/shared_ptr.hpp:171:5: required from 'void boost::serialization::load(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]'
/usr/include/boost/serialization/split_free.hpp:58:13: required from 'static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const EmpDist>]'
/usr/include/boost/serialization/split_free.hpp:74:18: required from 'void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const EmpDist>]'
/usr/include/boost/serialization/shared_ptr.hpp:187:37: [ skipping 129 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/boost/archive/detail/iserializer.hpp:618:18: required from 'void boost::archive::load(Archive&, T&) [with Archive = boost::archive::binary_iarchive; T = std::pair<int, AbundanceGroup>]'
/usr/include/boost/archive/detail/common_iarchive.hpp:66:22: required from 'void boost::archive::detail::common_iarchive<Archive>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
/usr/include/boost/archive/basic_binary_iarchive.hpp:76:7: required from 'void boost::archive::basic_binary_iarchive<Archive>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
/usr/include/boost/archive/binary_iarchive_impl.hpp:62:9: required from 'void boost::archive::binary_iarchive_impl<Archive, Elem, Tr>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive; Elem = char; Tr = std::char_traits<char>]'
/usr/include/boost/archive/detail/interface_iarchive.hpp:60:9: required from 'Archive& boost::archive::detail::interface_iarchive<Archive>::operator>>(T&) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
hits.cpp:1125:15: required from here
/usr/include/boost/smart_ptr/shared_ptr.hpp:420:5: error: no type named 'type' in 'struct boost::detail::sp_enable_if_convertible<const EmpDist, void>'
/usr/include/c++/5/bits/stl_pair.h: In instantiation of 'std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const void*; _U2 = boost::shared_ptr<const EmpDist>; _T1 = const void* const; _T2 = boost::shared_ptr<void>]':
/usr/include/boost/serialization/shared_ptr_helper.hpp:182:20: required from 'void boost::serialization::shared_ptr_helper<SPT>::reset(SPT<T>&, T*) [with T = const EmpDist; SPT = boost::shared_ptr]'
/usr/include/boost/serialization/shared_ptr.hpp:171:5: required from 'void boost::serialization::load(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]'
/usr/include/boost/serialization/split_free.hpp:58:13: required from 'static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const EmpDist>]'
/usr/include/boost/serialization/split_free.hpp:74:18: required from 'void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const EmpDist>]'
/usr/include/boost/serialization/shared_ptr.hpp:187:37: required from 'void boost::serialization::serialize(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]'
/usr/include/boost/serialization/serialization.hpp:128:18: [ skipping 128 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/boost/archive/detail/iserializer.hpp:618:18: required from 'void boost::archive::load(Archive&, T&) [with Archive = boost::archive::binary_iarchive; T = std::pair<int, AbundanceGroup>]'
/usr/include/boost/archive/detail/common_iarchive.hpp:66:22: required from 'void boost::archive::detail::common_iarchive<Archive>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
/usr/include/boost/archive/basic_binary_iarchive.hpp:76:7: required from 'void boost::archive::basic_binary_iarchive<Archive>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
/usr/include/boost/archive/binary_iarchive_impl.hpp:62:9: required from 'void boost::archive::binary_iarchive_impl<Archive, Elem, Tr>::load_override(T&, int) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive; Elem = char; Tr = std::char_traits<char>]'
/usr/include/boost/archive/detail/interface_iarchive.hpp:60:9: required from 'Archive& boost::archive::detail::interface_iarchive<Archive>::operator>>(T&) [with T = std::pair<int, AbundanceGroup>; Archive = boost::archive::binary_iarchive]'
hits.cpp:1125:15: required from here
/usr/include/boost/smart_ptr/shared_ptr.hpp:408:5: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(const boost::weak_ptr<Y>&, boost::detail::sp_nothrow_tag)
shared_ptr( weak_ptr<Y> const & r, boost::detail::sp_nothrow_tag )
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:408:5: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/bits/char_traits.h:39,
from /usr/include/c++/5/ios:40,
from /usr/include/c++/5/ostream:38,
from /usr/include/c++/5/iostream:39,
from hits.cpp:17:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: 'const boost::shared_ptr<const EmpDist>' is not derived from 'const boost::weak_ptr<Y>'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from /usr/include/boost/format/alt_sstream.hpp:21,
from /usr/include/boost/format/internals.hpp:23,
from /usr/include/boost/format.hpp:38,
from /usr/include/boost/math/policies/error_handling.hpp:31,
from /usr/include/boost/math/special_functions/gamma.hpp:23,
from /usr/include/boost/math/special_functions/erf.hpp:15,
from /usr/include/boost/math/distributions/normal.hpp:19,
from common.h:21,
from hits.cpp:21:
/usr/include/boost/smart_ptr/shared_ptr.hpp:399:14: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(const boost::weak_ptr<Y>&)
explicit shared_ptr( weak_ptr<Y> const & r ): pn( r.pn ) // may throw
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:399:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/bits/char_traits.h:39,
from /usr/include/c++/5/ios:40,
from /usr/include/c++/5/ostream:38,
from /usr/include/c++/5/iostream:39,
from hits.cpp:17:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: 'const boost::shared_ptr<const EmpDist>' is not derived from 'const boost::weak_ptr<Y>'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from /usr/include/boost/format/alt_sstream.hpp:21,
from /usr/include/boost/format/internals.hpp:23,
from /usr/include/boost/format.hpp:38,
from /usr/include/boost/math/policies/error_handling.hpp:31,
from /usr/include/boost/math/special_functions/gamma.hpp:23,
from /usr/include/boost/math/special_functions/erf.hpp:15,
from /usr/include/boost/math/distributions/normal.hpp:19,
from common.h:21,
from hits.cpp:21:
/usr/include/boost/smart_ptr/shared_ptr.hpp:373:41: note: candidate: template<class Y, class D, class A> boost::shared_ptr<T>::shared_ptr(Y*, D, A)
template<class Y, class D, class A> shared_ptr( Y * p, D d, A a ): px( p ), pn( p, d, a )
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:373:41: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/bits/char_traits.h:39,
from /usr/include/c++/5/ios:40,
from /usr/include/c++/5/ostream:38,
from /usr/include/c++/5/iostream:39,
from hits.cpp:17:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: mismatched types 'Y*' and 'boost::shared_ptr<const EmpDist>'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from /usr/include/boost/format/alt_sstream.hpp:21,
from /usr/include/boost/format/internals.hpp:23,
from /usr/include/boost/format.hpp:38,
from /usr/include/boost/math/policies/error_handling.hpp:31,
from /usr/include/boost/math/special_functions/gamma.hpp:23,
from /usr/include/boost/math/special_functions/erf.hpp:15,
from /usr/include/boost/math/distributions/normal.hpp:19,
from common.h:21,
from hits.cpp:21:
/usr/include/boost/smart_ptr/shared_ptr.hpp:358:32: note: candidate: template<class Y, class D> boost::shared_ptr<T>::shared_ptr(Y*, D)
template<class Y, class D> shared_ptr( Y * p, D d ): px( p ), pn( p, d )
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:358:32: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/bits/char_traits.h:39,
from /usr/include/c++/5/ios:40,
from /usr/include/c++/5/ostream:38,
from /usr/include/c++/5/iostream:39,
from hits.cpp:17:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: mismatched types 'Y*' and 'boost::shared_ptr<const EmpDist>'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from /usr/include/boost/format/alt_sstream.hpp:21,
from /usr/include/boost/format/internals.hpp:23,
from /usr/include/boost/format.hpp:38,
from /usr/include/boost/math/policies/error_handling.hpp:31,
from /usr/include/boost/math/special_functions/gamma.hpp:23,
from /usr/include/boost/math/special_functions/erf.hpp:15,
from /usr/include/boost/math/distributions/normal.hpp:19,
from common.h:21,
from hits.cpp:21:
/usr/include/boost/smart_ptr/shared_ptr.hpp:347:14: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(Y*)
explicit shared_ptr( Y * p ): px( p ), pn() // Y must be complete
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:347:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/bits/char_traits.h:39,
from /usr/include/c++/5/ios:40,
from /usr/include/c++/5/ostream:38,
from /usr/include/c++/5/iostream:39,
from hits.cpp:17:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: mismatched types 'Y*' and 'boost::shared_ptr<const EmpDist>'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from /usr/include/boost/format/alt_sstream.hpp:21,
from /usr/include/boost/format/internals.hpp:23,
from /usr/include/boost/format.hpp:38,
from /usr/include/boost/math/policies/error_handling.hpp:31,
from /usr/include/boost/math/special_functions/gamma.hpp:23,
from /usr/include/boost/math/special_functions/erf.hpp:15,
from /usr/include/boost/math/distributions/normal.hpp:19,
from common.h:21,
from hits.cpp:21:
/usr/include/boost/smart_ptr/shared_ptr.hpp:334:5: note: candidate: boost::shared_ptr<T>::shared_ptr() [with T = void]
shared_ptr() BOOST_NOEXCEPT : px( 0 ), pn() // never throws in 1.30+
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:334:5: note: candidate expects 0 arguments, 1 provided
/usr/include/boost/smart_ptr/shared_ptr.hpp:323:25: note: candidate: boost::shared_ptr<void>::shared_ptr(const boost::shared_ptr<void>&)
template<class T> class shared_ptr
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:323:25: note: no known conversion for argument 1 from 'const boost::shared_ptr<const EmpDist>' to 'const boost::shared_ptr<void>&'
filters.cpp: In function 'void clip_by_3_prime_dropoff(std::vector<Scaffold>&)':
filters.cpp:876:63: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (avg_cov >= trim_3_avgcov_thresh && min_cost_x < exon_3->genomic_length)
^
filters.cpp:802:20: warning: variable 'mean_to_keep' set but not used [-Wunused-but-set-variable]
double mean_to_keep = 0.0;
^
filters.cpp:803:20: warning: variable 'mean_to_trim' set but not used [-Wunused-but-set-variable]
double mean_to_trim = 0.0;
^
filters.cpp:930:36: warning: variable 'exon_3' set but not used [-Wunused-but-set-variable]
const AugmentedCuffOp* exon_3 = NULL;
^
filters.cpp:931:17: warning: variable 'mult' set but not used [-Wunused-but-set-variable]
int mult;
^
filters.cpp:932:17: warning: variable 'offset' set but not used [-Wunused-but-set-variable]
int offset;
^
abundances.cpp: In constructor 'AbundanceGroup::AbundanceGroup(const std::vector<boost::shared_ptr<Abundance> >&, const boost::numeric::ublas::matrix<double>&, const boost::numeric::ublas::matrix<double>&, const boost::numeric::ublas::matrix<double>&, const boost::numeric::ublas::matrix<double>&, const std::set<boost::shared_ptr<const ReadGroupProperties> >&)':
abundances.cpp:518:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (no_js_tests == false && _read_group_props.size() >= min_reps_for_js_test)
^
abundances.cpp: In member function 'virtual AbundanceStatus AbundanceGroup::status() const':
abundances.cpp:526:10: warning: variable 'has_lowdata_member' set but not used [-Wunused-but-set-variable]
bool has_lowdata_member = false;
^
In file included from differential.cpp:24:0:
sampling.h: In function 'double boost::numeric::ublas::cholesky_factorize(M&)':
sampling.h:50:13: warning: typedef 'matrix_type' locally defined but not used [-Wunused-local-typedefs]
typedef M matrix_type;
^
In file included from differential.cpp:24:0:
sampling.h: In function 'void boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::vector_expression<E2>&)':
sampling.h:113:19: warning: typedef 'const_matrix_type' locally defined but not used [-Wunused-local-typedefs]
typedef const M const_matrix_type;
^
sampling.h:114:42: warning: typedef 'vector_type' locally defined but not used [-Wunused-local-typedefs]
typedef vector<typename E::value_type> vector_type;
^
sampling.h: In function 'void boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::matrix_expression<E2>&)':
sampling.h:120:19: warning: typedef 'const_matrix_type' locally defined but not used [-Wunused-local-typedefs]
typedef const M const_matrix_type;
^
sampling.h:121:42: warning: typedef 'matrix_type' locally defined but not used [-Wunused-local-typedefs]
typedef matrix<typename E::value_type> matrix_type;
^
sampling.h: In function 'void boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::vector_expression<E>&, const M&)':
sampling.h:127:19: warning: typedef 'const_matrix_type' locally defined but not used [-Wunused-local-typedefs]
typedef const M const_matrix_type;
^
sampling.h:128:42: warning: typedef 'vector_type' locally defined but not used [-Wunused-local-typedefs]
typedef vector<typename E::value_type> vector_type;
^
sampling.h: In function 'void boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::matrix_expression<E>&, const M&)':
sampling.h:134:19: warning: typedef 'const_matrix_type' locally defined but not used [-Wunused-local-typedefs]
typedef const M const_matrix_type;
^
sampling.h:135:42: warning: typedef 'matrix_type' locally defined but not used [-Wunused-local-typedefs]
typedef matrix<typename E::value_type> matrix_type;
^
differential.cpp: In member function 'void TestLauncher::perform_testing(std::vector<boost::shared_ptr<SampleAbundances> >)':
differential.cpp:131:31: warning: unused variable 's2' [-Wunused-variable]
const AbundanceGroup& s2 = prev.transcripts;
^
differential.cpp: In member function 'void TestLauncher::record_tracking_data(std::vector<boost::shared_ptr<SampleAbundances> >&)':
differential.cpp:159:31: warning: unused variable 's2' [-Wunused-variable]
const AbundanceGroup& s2 = prev.transcripts;
^
abundances.cpp: In member function 'void AbundanceGroup::collect_per_replicate_mass(const std::vector<MateHit>&, std::vector<boost::shared_ptr<Abundance> >&)':
abundances.cpp:1043:20: warning: unused variable 'curr_mass' [-Wunused-variable]
double curr_mass = inserted.first->second;
^
differential.cpp: In function 'SampleDifference test_diffexp(const FPKMContext&, const FPKMContext&)':
differential.cpp:460:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (next_sample_idx >= 0 && next_sample_idx < prev.fpkm_samples.size())
^
differential.cpp:468:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (next_sample_idx >= 0 && next_sample_idx < prev.fpkm_samples.size())
^
differential.cpp:490:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (next_sample_idx >= 0 && next_sample_idx < curr.fpkm_samples.size())
^
differential.cpp:498:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (next_sample_idx >= 0 && next_sample_idx < curr.fpkm_samples.size())
^
abundances.cpp: In function 'void collapse_equivalent_hits(const std::vector<MateHit>&, std::vector<boost::shared_ptr<Abundance> >&, std::vector<MateHit>&, std::vector<double>&, bool)':
abundances.cpp:1160:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < N; ++j)
^
abundances.cpp:1347:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0 ; i < nr_alignments.size(); ++i)
^
abundances.cpp: In function 'AbundanceStatus bootstrap_gamma_mle(const std::vector<boost::shared_ptr<Abundance> >&, const std::vector<MateHit>&, const std::vector<double>&, boost::numeric::ublas::vector<double, boost::numeric::ublas::unbounded_array<double, std::allocator<double> > >&, boost::numeric::ublas::matrix<double>&, double&)':
abundances.cpp:1488:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < num_bootstrap_samples; ++i)
^
abundances.cpp:1491:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < num_sample_frags; ++j)
^
abundances.cpp:1505:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
sample_idxs[curr_sample] >= processed_hits &&
^
abundances.cpp: In function 'bool generate_count_assignment_samples(int, const std::vector<double>&, const boost::numeric::ublas::matrix<double>&, std::vector<boost::numeric::ublas::vector<double, boost::numeric::ublas::unbounded_array<double, std::allocator<double> > > >&)':
abundances.cpp:1693:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t assign_idx = 0; assign_idx < num_draws; ++assign_idx)
^
differential.cpp: In function 'bool test_js(const AbundanceGroup&, const AbundanceGroup&, double&, double&)':
differential.cpp:742:57: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (next_sample_idx >= 0 && next_sample_idx < prev_abundance.member_fpkm_samples().size())
^
abundances.cpp: In function 'void calculate_gamma_mle_covariance(const std::map<boost::shared_ptr<const ReadGroupProperties>, boost::shared_ptr<AbundanceGroup> >&, boost::numeric::ublas::vector<double, boost::numeric::ublas::unbounded_array<double, std::allocator<double> > >&, boost::numeric::ublas::matrix<double>&)':
abundances.cpp:1760:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < all_assigned_count_samples[i].size(); ++j)
^
abundances.cpp:1775:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < num_transcripts; ++i)
^
abundances.cpp:1777:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < num_transcripts; ++j)
^
abundances.cpp: In function 'void calculate_fragment_assignment_distribution(const std::map<boost::shared_ptr<const ReadGroupProperties>, boost::shared_ptr<const AbundanceGroup> >&, boost::numeric::ublas::vector<double, boost::numeric::ublas::unbounded_array<double, std::allocator<double> > >&, boost::numeric::ublas::matrix<double>&, std::vector<boost::numeric::ublas::vector<double, boost::numeric::ublas::unbounded_array<double, std::allocator<double> > > >&)':
abundances.cpp:1870:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < all_assigned_count_samples[i].size(); ++j)
^
abundances.cpp:1885:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < num_transcripts; ++i)
^
abundances.cpp:1887:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < num_transcripts; ++j)
^
differential.cpp:754:57: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (next_sample_idx >= 0 && next_sample_idx < prev_abundance.member_fpkm_samples().size())
^
differential.cpp:780:57: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (next_sample_idx >= 0 && next_sample_idx < curr_abundance.member_fpkm_samples().size())
^
differential.cpp:792:57: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (next_sample_idx >= 0 && next_sample_idx < curr_abundance.member_fpkm_samples().size())
^
abundances.cpp: In member function 'void AbundanceGroup::calculate_abundance_group_variance(const std::vector<boost::shared_ptr<Abundance> >&, const std::map<boost::shared_ptr<const ReadGroupProperties>, boost::shared_ptr<const AbundanceGroup> >&)':
abundances.cpp:1968:62: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (no_js_tests == false && _read_group_props.size() >= min_reps_for_js_test)
^
abundances.cpp: In member function 'void AbundanceGroup::aggregate_replicate_abundances(const std::map<boost::shared_ptr<const ReadGroupProperties>, boost::shared_ptr<const AbundanceGroup> >&)':
abundances.cpp:2070:58: warning: unused variable 'sc_ab' [-Wunused-variable]
const vector<boost::shared_ptr<Abundance> >& sc_ab = itr->second->abundances();
^
abundances.cpp: In function 'bool estimate_count_variance(long double&, double, double, double, double, double)':
abundances.cpp:2277:17: warning: variable 'bnb_mean' set but not used [-Wunused-but-set-variable]
long double bnb_mean = 0.0;
^
abundances.cpp: In member function 'void AbundanceGroup::generate_fpkm_samples()':
abundances.cpp:2668:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < sample.size(); ++j)
^
abundances.cpp: In member function 'void AbundanceGroup::calculate_FPKM_covariance()':
abundances.cpp:2783:42: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if (length_i > 0 && length_j > 0 & M > 0)
^
abundances.cpp:2796:24: warning: unused variable 'fpkm' [-Wunused-variable]
double fpkm = _abundances[i]->FPKM();
^
abundances.cpp: In member function 'void AbundanceGroup::calculate_conf_intervals()':
abundances.cpp:2920:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < N; ++j)
^
abundances.cpp:2939:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < N; ++j)
^
differential.cpp: In function 'void test_differential(const string&, const std::vector<boost::shared_ptr<SampleAbundances> >&, const std::vector<std::pair<long unsigned int, long unsigned int> >&, Tests&, Tracking&)':
differential.cpp:1506:76: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool enough_reads = (curr_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test &&
^
differential.cpp:1507:76: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
prev_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test);
^
differential.cpp:1545:77: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool enough_reads = (curr_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test &&
^
differential.cpp:1546:77: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
prev_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test);
^
differential.cpp:1583:76: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool enough_reads = (curr_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test &&
^
differential.cpp:1584:76: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
prev_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test);
^
abundances.cpp: In function 'void calculate_assignment_probs(const VectorXd&, const MatrixXd&, const VectorXd&, Eigen::MatrixXd&)':
abundances.cpp:3352:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < alignment_multiplicities.size(); ++i)
^
abundances.cpp: In function 'void calculate_average_assignment_probs(const VectorXd&, const MatrixXd&, const VectorXd&, Eigen::MatrixXd&)':
abundances.cpp:3378:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < alignment_multiplicities.size(); ++i)
^
abundances.cpp:3393:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < alignment_multiplicities.size(); ++i)
^
abundances.cpp:3395:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < proposed_gammas.size(); ++j)
^
abundances.cpp:3408:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < proposed_gammas.size(); ++j)
^
assemble.cpp: In function 'void create_reachability_bp_graph(DAG&, ReachGraph&, std::vector<lemon::BidirBpUGraphExtender<lemon::SmartBpUGraphBase>::BNode, std::allocator<lemon::BidirBpUGraphExtender<lemon::SmartBpUGraphBase>::BNode> >, DagToBp&, const boost::adjacency_list<>&, const std::vector<bool>&)':
assemble.cpp:123:17: warning: variable 'hits_for_node' set but not used [-Wunused-but-set-variable]
HitsForNodeMap hits_for_node = get(vertex_name, dag);
^
Makefile:1627: recipe for target 'hits.o' failed
make[3]: *** [hits.o] Error 1
make[3]: *** Waiting for unfinished jobs....
abundances.cpp: In function 'bool is_identifiable(M&, PM&)':
abundances.cpp:4254:15: warning: typedef 'matrix_type' locally defined but not used [-Wunused-local-typedefs]
typedef M matrix_type;
^
abundances.cpp: In function 'AbundanceStatus gamma_mle(const std::vector<boost::shared_ptr<Abundance> >&, const std::vector<MateHit>&, const std::vector<double>&, std::vector<double>&, bool)':
abundances.cpp:4322:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < cond_probs.rows(); ++j)
^
abundances.cpp:4324:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < cond_probs.cols(); ++i)
^
abundances.cpp:4318:10: warning: variable 'logL' set but not used [-Wunused-but-set-variable]
double logL;
^
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/5/bits/stl_pair.h: In instantiation of 'std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const void*; _U2 = boost::shared_ptr<const ReadGroupProperties>; _T1 = const void* const; _T2 = boost::shared_ptr<void>]':
/usr/include/boost/serialization/shared_ptr_helper.hpp:182:20: required from 'void boost::serialization::shared_ptr_helper<SPT>::reset(SPT<T>&, T*) [with T = const ReadGroupProperties; SPT = boost::shared_ptr]'
/usr/include/boost/serialization/shared_ptr.hpp:171:5: required from 'void boost::serialization::load(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]'
/usr/include/boost/serialization/split_free.hpp:58:13: required from 'static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const ReadGroupProperties>]'
/usr/include/boost/serialization/split_free.hpp:74:18: required from 'void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const ReadGroupProperties>]'
/usr/include/boost/serialization/shared_ptr.hpp:187:37: required from 'void boost::serialization::serialize(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]'
/usr/include/boost/serialization/serialization.hpp:128:18: [ skipping 56 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/boost/serialization/export.hpp:86:1: required from 'struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>'
/usr/include/boost/archive/detail/register_archive.hpp:25:8: required from 'struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>'
/usr/include/boost/archive/binary_iarchive.hpp:57:1: required by substitution of 'template<class Serializable> typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable*, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]'
/usr/include/boost/serialization/export.hpp:132:38: required from 'void boost::archive::detail::extra_detail::guid_initializer<T>::export_guid(mpl_::false_) const [with T = AbundanceGroup; mpl_::false_ = mpl_::bool_<false>]'
/usr/include/boost/serialization/export.hpp:142:20: required from 'const boost::archive::detail::extra_detail::guid_initializer<T>& boost::archive::detail::extra_detail::guid_initializer<T>::export_guid() const [with T = AbundanceGroup]'
abundances.cpp:5162:1: required from here
/usr/include/c++/5/bits/stl_pair.h:119:39: error: no matching function for call to 'boost::shared_ptr<void>::shared_ptr(const boost::shared_ptr<const ReadGroupProperties>&)'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
/usr/include/boost/smart_ptr/shared_ptr.hpp:467:14: note: candidate: template<class Ap> boost::shared_ptr<T>::shared_ptr(Ap, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type)
explicit shared_ptr( Ap r, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type = 0 ): px( r.get() ), pn()
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:467:14: note: template argument deduction/substitution failed:
/usr/include/boost/smart_ptr/shared_ptr.hpp: In substitution of 'template<class Ap> boost::shared_ptr<T>::shared_ptr(Ap, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type) [with Ap = boost::shared_ptr<const ReadGroupProperties>]':
/usr/include/c++/5/bits/stl_pair.h:119:39: required from 'std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const void*; _U2 = boost::shared_ptr<const ReadGroupProperties>; _T1 = const void* const; _T2 = boost::shared_ptr<void>]'
/usr/include/boost/serialization/shared_ptr_helper.hpp:182:20: required from 'void boost::serialization::shared_ptr_helper<SPT>::reset(SPT<T>&, T*) [with T = const ReadGroupProperties; SPT = boost::shared_ptr]'
/usr/include/boost/serialization/shared_ptr.hpp:171:5: required from 'void boost::serialization::load(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]'
/usr/include/boost/serialization/split_free.hpp:58:13: required from 'static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const ReadGroupProperties>]'
/usr/include/boost/serialization/split_free.hpp:74:18: required from 'void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const ReadGroupProperties>]'
/usr/include/boost/serialization/shared_ptr.hpp:187:37: [ skipping 57 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/boost/serialization/export.hpp:86:1: required from 'struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>'
/usr/include/boost/archive/detail/register_archive.hpp:25:8: required from 'struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>'
/usr/include/boost/archive/binary_iarchive.hpp:57:1: required by substitution of 'template<class Serializable> typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable*, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]'
/usr/include/boost/serialization/export.hpp:132:38: required from 'void boost::archive::detail::extra_detail::guid_initializer<T>::export_guid(mpl_::false_) const [with T = AbundanceGroup; mpl_::false_ = mpl_::bool_<false>]'
/usr/include/boost/serialization/export.hpp:142:20: required from 'const boost::archive::detail::extra_detail::guid_initializer<T>& boost::archive::detail::extra_detail::guid_initializer<T>::export_guid() const [with T = AbundanceGroup]'
abundances.cpp:5162:1: required from here
/usr/include/boost/smart_ptr/shared_ptr.hpp:467:14: error: no type named 'type' in 'struct boost::detail::sp_enable_if_auto_ptr<boost::shared_ptr<const ReadGroupProperties>, int>'
/usr/include/c++/5/bits/stl_pair.h: In instantiation of 'std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const void*; _U2 = boost::shared_ptr<const ReadGroupProperties>; _T1 = const void* const; _T2 = boost::shared_ptr<void>]':
/usr/include/boost/serialization/shared_ptr_helper.hpp:182:20: required from 'void boost::serialization::shared_ptr_helper<SPT>::reset(SPT<T>&, T*) [with T = const ReadGroupProperties; SPT = boost::shared_ptr]'
/usr/include/boost/serialization/shared_ptr.hpp:171:5: required from 'void boost::serialization::load(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]'
/usr/include/boost/serialization/split_free.hpp:58:13: required from 'static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const ReadGroupProperties>]'
/usr/include/boost/serialization/split_free.hpp:74:18: required from 'void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const ReadGroupProperties>]'
/usr/include/boost/serialization/shared_ptr.hpp:187:37: required from 'void boost::serialization::serialize(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]'
/usr/include/boost/serialization/serialization.hpp:128:18: [ skipping 56 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/boost/serialization/export.hpp:86:1: required from 'struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>'
/usr/include/boost/archive/detail/register_archive.hpp:25:8: required from 'struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>'
/usr/include/boost/archive/binary_iarchive.hpp:57:1: required by substitution of 'template<class Serializable> typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable*, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]'
/usr/include/boost/serialization/export.hpp:132:38: required from 'void boost::archive::detail::extra_detail::guid_initializer<T>::export_guid(mpl_::false_) const [with T = AbundanceGroup; mpl_::false_ = mpl_::bool_<false>]'
/usr/include/boost/serialization/export.hpp:142:20: required from 'const boost::archive::detail::extra_detail::guid_initializer<T>& boost::archive::detail::extra_detail::guid_initializer<T>::export_guid() const [with T = AbundanceGroup]'
abundances.cpp:5162:1: required from here
/usr/include/boost/smart_ptr/shared_ptr.hpp:441:14: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(std::auto_ptr<_Tp1>&)
explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:441:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: types 'std::auto_ptr<Y>' and 'const boost::shared_ptr<const ReadGroupProperties>' have incompatible cv-qualifiers
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
/usr/include/boost/smart_ptr/shared_ptr.hpp:434:5: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(const boost::shared_ptr<Y>&, boost::shared_ptr<T>::element_type*)
shared_ptr( shared_ptr<Y> const & r, element_type * p ) BOOST_NOEXCEPT : px( p ), pn( r.pn )
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:434:5: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: candidate expects 2 arguments, 1 provided
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
/usr/include/boost/smart_ptr/shared_ptr.hpp:420:5: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(const boost::shared_ptr<Y>&, typename boost::detail::sp_enable_if_convertible<Y, T>::type)
shared_ptr( shared_ptr<Y> const & r, typename boost::detail::sp_enable_if_convertible<Y,T>::type = boost::detail::sp_empty() )
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:420:5: note: template argument deduction/substitution failed:
/usr/include/boost/smart_ptr/shared_ptr.hpp: In substitution of 'template<class Y> boost::shared_ptr<T>::shared_ptr(const boost::shared_ptr<Y>&, typename boost::detail::sp_enable_if_convertible<Y, T>::type) [with Y = const ReadGroupProperties]':
/usr/include/c++/5/bits/stl_pair.h:119:39: required from 'std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const void*; _U2 = boost::shared_ptr<const ReadGroupProperties>; _T1 = const void* const; _T2 = boost::shared_ptr<void>]'
/usr/include/boost/serialization/shared_ptr_helper.hpp:182:20: required from 'void boost::serialization::shared_ptr_helper<SPT>::reset(SPT<T>&, T*) [with T = const ReadGroupProperties; SPT = boost::shared_ptr]'
/usr/include/boost/serialization/shared_ptr.hpp:171:5: required from 'void boost::serialization::load(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]'
/usr/include/boost/serialization/split_free.hpp:58:13: required from 'static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const ReadGroupProperties>]'
/usr/include/boost/serialization/split_free.hpp:74:18: required from 'void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const ReadGroupProperties>]'
/usr/include/boost/serialization/shared_ptr.hpp:187:37: [ skipping 57 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/boost/serialization/export.hpp:86:1: required from 'struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>'
/usr/include/boost/archive/detail/register_archive.hpp:25:8: required from 'struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>'
/usr/include/boost/archive/binary_iarchive.hpp:57:1: required by substitution of 'template<class Serializable> typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable*, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]'
/usr/include/boost/serialization/export.hpp:132:38: required from 'void boost::archive::detail::extra_detail::guid_initializer<T>::export_guid(mpl_::false_) const [with T = AbundanceGroup; mpl_::false_ = mpl_::bool_<false>]'
/usr/include/boost/serialization/export.hpp:142:20: required from 'const boost::archive::detail::extra_detail::guid_initializer<T>& boost::archive::detail::extra_detail::guid_initializer<T>::export_guid() const [with T = AbundanceGroup]'
abundances.cpp:5162:1: required from here
/usr/include/boost/smart_ptr/shared_ptr.hpp:420:5: error: no type named 'type' in 'struct boost::detail::sp_enable_if_convertible<const ReadGroupProperties, void>'
/usr/include/c++/5/bits/stl_pair.h: In instantiation of 'std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const void*; _U2 = boost::shared_ptr<const ReadGroupProperties>; _T1 = const void* const; _T2 = boost::shared_ptr<void>]':
/usr/include/boost/serialization/shared_ptr_helper.hpp:182:20: required from 'void boost::serialization::shared_ptr_helper<SPT>::reset(SPT<T>&, T*) [with T = const ReadGroupProperties; SPT = boost::shared_ptr]'
/usr/include/boost/serialization/shared_ptr.hpp:171:5: required from 'void boost::serialization::load(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]'
/usr/include/boost/serialization/split_free.hpp:58:13: required from 'static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const ReadGroupProperties>]'
/usr/include/boost/serialization/split_free.hpp:74:18: required from 'void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const ReadGroupProperties>]'
/usr/include/boost/serialization/shared_ptr.hpp:187:37: required from 'void boost::serialization::serialize(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const ReadGroupProperties]'
/usr/include/boost/serialization/serialization.hpp:128:18: [ skipping 56 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/boost/serialization/export.hpp:86:1: required from 'struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>'
/usr/include/boost/archive/detail/register_archive.hpp:25:8: required from 'struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>'
/usr/include/boost/archive/binary_iarchive.hpp:57:1: required by substitution of 'template<class Serializable> typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable*, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]'
/usr/include/boost/serialization/export.hpp:132:38: required from 'void boost::archive::detail::extra_detail::guid_initializer<T>::export_guid(mpl_::false_) const [with T = AbundanceGroup; mpl_::false_ = mpl_::bool_<false>]'
/usr/include/boost/serialization/export.hpp:142:20: required from 'const boost::archive::detail::extra_detail::guid_initializer<T>& boost::archive::detail::extra_detail::guid_initializer<T>::export_guid() const [with T = AbundanceGroup]'
abundances.cpp:5162:1: required from here
/usr/include/boost/smart_ptr/shared_ptr.hpp:408:5: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(const boost::weak_ptr<Y>&, boost::detail::sp_nothrow_tag)
shared_ptr( weak_ptr<Y> const & r, boost::detail::sp_nothrow_tag )
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:408:5: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: 'const boost::shared_ptr<const ReadGroupProperties>' is not derived from 'const boost::weak_ptr<Y>'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
/usr/include/boost/smart_ptr/shared_ptr.hpp:399:14: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(const boost::weak_ptr<Y>&)
explicit shared_ptr( weak_ptr<Y> const & r ): pn( r.pn ) // may throw
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:399:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: 'const boost::shared_ptr<const ReadGroupProperties>' is not derived from 'const boost::weak_ptr<Y>'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
/usr/include/boost/smart_ptr/shared_ptr.hpp:373:41: note: candidate: template<class Y, class D, class A> boost::shared_ptr<T>::shared_ptr(Y*, D, A)
template<class Y, class D, class A> shared_ptr( Y * p, D d, A a ): px( p ), pn( p, d, a )
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:373:41: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: mismatched types 'Y*' and 'boost::shared_ptr<const ReadGroupProperties>'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
/usr/include/boost/smart_ptr/shared_ptr.hpp:358:32: note: candidate: template<class Y, class D> boost::shared_ptr<T>::shared_ptr(Y*, D)
template<class Y, class D> shared_ptr( Y * p, D d ): px( p ), pn( p, d )
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:358:32: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: mismatched types 'Y*' and 'boost::shared_ptr<const ReadGroupProperties>'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
/usr/include/boost/smart_ptr/shared_ptr.hpp:347:14: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(Y*)
explicit shared_ptr( Y * p ): px( p ), pn() // Y must be complete
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:347:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: mismatched types 'Y*' and 'boost::shared_ptr<const ReadGroupProperties>'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
/usr/include/boost/smart_ptr/shared_ptr.hpp:334:5: note: candidate: boost::shared_ptr<T>::shared_ptr() [with T = void]
shared_ptr() BOOST_NOEXCEPT : px( 0 ), pn() // never throws in 1.30+
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:334:5: note: candidate expects 0 arguments, 1 provided
/usr/include/boost/smart_ptr/shared_ptr.hpp:323:25: note: candidate: boost::shared_ptr<void>::shared_ptr(const boost::shared_ptr<void>&)
template<class T> class shared_ptr
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:323:25: note: no known conversion for argument 1 from 'const boost::shared_ptr<const ReadGroupProperties>' to 'const boost::shared_ptr<void>&'
In file included from hits.h:23:0,
from abundances.h:23,
from abundances.cpp:16:
/usr/include/boost/serialization/vector.hpp: In instantiation of 'void boost::serialization::load(Archive&, std::vector<U, Allocator>&, unsigned int, mpl_::false_) [with Archive = boost::archive::binary_iarchive; U = LocusCount; Allocator = std::allocator<LocusCount>; mpl_::false_ = mpl_::bool_<false>]':
/usr/include/boost/serialization/vector.hpp:173:9: required from 'void boost::serialization::load(Archive&, std::vector<U, Allocator>&, unsigned int) [with Archive = boost::archive::binary_iarchive; U = LocusCount; Allocator = std::allocator<LocusCount>]'
/usr/include/boost/serialization/split_free.hpp:58:13: required from 'static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = std::vector<LocusCount>]'
/usr/include/boost/serialization/split_free.hpp:74:18: required from 'void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = std::vector<LocusCount>]'
/usr/include/boost/serialization/vector.hpp:184:37: required from 'void boost::serialization::serialize(Archive&, std::vector<U, Allocator>&, unsigned int) [with Archive = boost::archive::binary_iarchive; U = LocusCount; Allocator = std::allocator<LocusCount>]'
/usr/include/boost/serialization/serialization.hpp:128:18: required from 'void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = std::vector<LocusCount>]'
/usr/include/boost/archive/detail/iserializer.hpp:184:40: [ skipping 103 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/boost/serialization/export.hpp:86:1: required from 'struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>'
/usr/include/boost/archive/detail/register_archive.hpp:25:8: required from 'struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>'
/usr/include/boost/archive/binary_iarchive.hpp:57:1: required by substitution of 'template<class Serializable> typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable*, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]'
/usr/include/boost/serialization/export.hpp:132:38: required from 'void boost::archive::detail::extra_detail::guid_initializer<T>::export_guid(mpl_::false_) const [with T = AbundanceGroup; mpl_::false_ = mpl_::bool_<false>]'
/usr/include/boost/serialization/export.hpp:142:20: required from 'const boost::archive::detail::extra_detail::guid_initializer<T>& boost::archive::detail::extra_detail::guid_initializer<T>::export_guid() const [with T = AbundanceGroup]'
abundances.cpp:5162:1: required from here
common.h:387:5: error: 'LocusCount::LocusCount()' is private
LocusCount() {} //needs an empty constructor for serialization
^
In file included from common.h:34:0,
from hits.h:23,
from abundances.h:23,
from abundances.cpp:16:
/usr/include/boost/serialization/vector.hpp:90:9: error: within this context
t.resize(count);
^
/usr/include/boost/serialization/vector.hpp:90:9: note: when instantiating default argument for call to void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type, std::vector<_Tp, _Alloc>::value_type) [with _Tp = LocusCount; _Alloc = std::allocator<LocusCount>; std::vector<_Tp, _Alloc>::size_type = long unsigned int; std::vector<_Tp, _Alloc>::value_type = LocusCount]
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/5/bits/stl_pair.h: In instantiation of 'std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const void*; _U2 = boost::shared_ptr<const EmpDist>; _T1 = const void* const; _T2 = boost::shared_ptr<void>]':
/usr/include/boost/serialization/shared_ptr_helper.hpp:182:20: required from 'void boost::serialization::shared_ptr_helper<SPT>::reset(SPT<T>&, T*) [with T = const EmpDist; SPT = boost::shared_ptr]'
/usr/include/boost/serialization/shared_ptr.hpp:171:5: required from 'void boost::serialization::load(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]'
/usr/include/boost/serialization/split_free.hpp:58:13: required from 'static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const EmpDist>]'
/usr/include/boost/serialization/split_free.hpp:74:18: required from 'void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const EmpDist>]'
/usr/include/boost/serialization/shared_ptr.hpp:187:37: required from 'void boost::serialization::serialize(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]'
/usr/include/boost/serialization/serialization.hpp:128:18: [ skipping 104 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/boost/serialization/export.hpp:86:1: required from 'struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>'
/usr/include/boost/archive/detail/register_archive.hpp:25:8: required from 'struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>'
/usr/include/boost/archive/binary_iarchive.hpp:57:1: required by substitution of 'template<class Serializable> typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable*, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]'
/usr/include/boost/serialization/export.hpp:132:38: required from 'void boost::archive::detail::extra_detail::guid_initializer<T>::export_guid(mpl_::false_) const [with T = AbundanceGroup; mpl_::false_ = mpl_::bool_<false>]'
/usr/include/boost/serialization/export.hpp:142:20: required from 'const boost::archive::detail::extra_detail::guid_initializer<T>& boost::archive::detail::extra_detail::guid_initializer<T>::export_guid() const [with T = AbundanceGroup]'
abundances.cpp:5162:1: required from here
/usr/include/c++/5/bits/stl_pair.h:119:39: error: no matching function for call to 'boost::shared_ptr<void>::shared_ptr(const boost::shared_ptr<const EmpDist>&)'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
/usr/include/boost/smart_ptr/shared_ptr.hpp:467:14: note: candidate: template<class Ap> boost::shared_ptr<T>::shared_ptr(Ap, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type)
explicit shared_ptr( Ap r, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type = 0 ): px( r.get() ), pn()
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:467:14: note: template argument deduction/substitution failed:
/usr/include/boost/smart_ptr/shared_ptr.hpp: In substitution of 'template<class Ap> boost::shared_ptr<T>::shared_ptr(Ap, typename boost::detail::sp_enable_if_auto_ptr<Ap, int>::type) [with Ap = boost::shared_ptr<const EmpDist>]':
/usr/include/c++/5/bits/stl_pair.h:119:39: required from 'std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const void*; _U2 = boost::shared_ptr<const EmpDist>; _T1 = const void* const; _T2 = boost::shared_ptr<void>]'
/usr/include/boost/serialization/shared_ptr_helper.hpp:182:20: required from 'void boost::serialization::shared_ptr_helper<SPT>::reset(SPT<T>&, T*) [with T = const EmpDist; SPT = boost::shared_ptr]'
/usr/include/boost/serialization/shared_ptr.hpp:171:5: required from 'void boost::serialization::load(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]'
/usr/include/boost/serialization/split_free.hpp:58:13: required from 'static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const EmpDist>]'
/usr/include/boost/serialization/split_free.hpp:74:18: required from 'void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const EmpDist>]'
/usr/include/boost/serialization/shared_ptr.hpp:187:37: [ skipping 105 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/boost/serialization/export.hpp:86:1: required from 'struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>'
/usr/include/boost/archive/detail/register_archive.hpp:25:8: required from 'struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>'
/usr/include/boost/archive/binary_iarchive.hpp:57:1: required by substitution of 'template<class Serializable> typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable*, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]'
/usr/include/boost/serialization/export.hpp:132:38: required from 'void boost::archive::detail::extra_detail::guid_initializer<T>::export_guid(mpl_::false_) const [with T = AbundanceGroup; mpl_::false_ = mpl_::bool_<false>]'
/usr/include/boost/serialization/export.hpp:142:20: required from 'const boost::archive::detail::extra_detail::guid_initializer<T>& boost::archive::detail::extra_detail::guid_initializer<T>::export_guid() const [with T = AbundanceGroup]'
abundances.cpp:5162:1: required from here
/usr/include/boost/smart_ptr/shared_ptr.hpp:467:14: error: no type named 'type' in 'struct boost::detail::sp_enable_if_auto_ptr<boost::shared_ptr<const EmpDist>, int>'
/usr/include/c++/5/bits/stl_pair.h: In instantiation of 'std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const void*; _U2 = boost::shared_ptr<const EmpDist>; _T1 = const void* const; _T2 = boost::shared_ptr<void>]':
/usr/include/boost/serialization/shared_ptr_helper.hpp:182:20: required from 'void boost::serialization::shared_ptr_helper<SPT>::reset(SPT<T>&, T*) [with T = const EmpDist; SPT = boost::shared_ptr]'
/usr/include/boost/serialization/shared_ptr.hpp:171:5: required from 'void boost::serialization::load(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]'
/usr/include/boost/serialization/split_free.hpp:58:13: required from 'static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const EmpDist>]'
/usr/include/boost/serialization/split_free.hpp:74:18: required from 'void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const EmpDist>]'
/usr/include/boost/serialization/shared_ptr.hpp:187:37: required from 'void boost::serialization::serialize(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]'
/usr/include/boost/serialization/serialization.hpp:128:18: [ skipping 104 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/boost/serialization/export.hpp:86:1: required from 'struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>'
/usr/include/boost/archive/detail/register_archive.hpp:25:8: required from 'struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>'
/usr/include/boost/archive/binary_iarchive.hpp:57:1: required by substitution of 'template<class Serializable> typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable*, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]'
/usr/include/boost/serialization/export.hpp:132:38: required from 'void boost::archive::detail::extra_detail::guid_initializer<T>::export_guid(mpl_::false_) const [with T = AbundanceGroup; mpl_::false_ = mpl_::bool_<false>]'
/usr/include/boost/serialization/export.hpp:142:20: required from 'const boost::archive::detail::extra_detail::guid_initializer<T>& boost::archive::detail::extra_detail::guid_initializer<T>::export_guid() const [with T = AbundanceGroup]'
abundances.cpp:5162:1: required from here
/usr/include/boost/smart_ptr/shared_ptr.hpp:441:14: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(std::auto_ptr<_Tp1>&)
explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:441:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: types 'std::auto_ptr<Y>' and 'const boost::shared_ptr<const EmpDist>' have incompatible cv-qualifiers
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
/usr/include/boost/smart_ptr/shared_ptr.hpp:434:5: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(const boost::shared_ptr<Y>&, boost::shared_ptr<T>::element_type*)
shared_ptr( shared_ptr<Y> const & r, element_type * p ) BOOST_NOEXCEPT : px( p ), pn( r.pn )
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:434:5: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: candidate expects 2 arguments, 1 provided
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
/usr/include/boost/smart_ptr/shared_ptr.hpp:420:5: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(const boost::shared_ptr<Y>&, typename boost::detail::sp_enable_if_convertible<Y, T>::type)
shared_ptr( shared_ptr<Y> const & r, typename boost::detail::sp_enable_if_convertible<Y,T>::type = boost::detail::sp_empty() )
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:420:5: note: template argument deduction/substitution failed:
/usr/include/boost/smart_ptr/shared_ptr.hpp: In substitution of 'template<class Y> boost::shared_ptr<T>::shared_ptr(const boost::shared_ptr<Y>&, typename boost::detail::sp_enable_if_convertible<Y, T>::type) [with Y = const EmpDist]':
/usr/include/c++/5/bits/stl_pair.h:119:39: required from 'std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const void*; _U2 = boost::shared_ptr<const EmpDist>; _T1 = const void* const; _T2 = boost::shared_ptr<void>]'
/usr/include/boost/serialization/shared_ptr_helper.hpp:182:20: required from 'void boost::serialization::shared_ptr_helper<SPT>::reset(SPT<T>&, T*) [with T = const EmpDist; SPT = boost::shared_ptr]'
/usr/include/boost/serialization/shared_ptr.hpp:171:5: required from 'void boost::serialization::load(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]'
/usr/include/boost/serialization/split_free.hpp:58:13: required from 'static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const EmpDist>]'
/usr/include/boost/serialization/split_free.hpp:74:18: required from 'void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const EmpDist>]'
/usr/include/boost/serialization/shared_ptr.hpp:187:37: [ skipping 105 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/boost/serialization/export.hpp:86:1: required from 'struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>'
/usr/include/boost/archive/detail/register_archive.hpp:25:8: required from 'struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>'
/usr/include/boost/archive/binary_iarchive.hpp:57:1: required by substitution of 'template<class Serializable> typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable*, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]'
/usr/include/boost/serialization/export.hpp:132:38: required from 'void boost::archive::detail::extra_detail::guid_initializer<T>::export_guid(mpl_::false_) const [with T = AbundanceGroup; mpl_::false_ = mpl_::bool_<false>]'
/usr/include/boost/serialization/export.hpp:142:20: required from 'const boost::archive::detail::extra_detail::guid_initializer<T>& boost::archive::detail::extra_detail::guid_initializer<T>::export_guid() const [with T = AbundanceGroup]'
abundances.cpp:5162:1: required from here
/usr/include/boost/smart_ptr/shared_ptr.hpp:420:5: error: no type named 'type' in 'struct boost::detail::sp_enable_if_convertible<const EmpDist, void>'
/usr/include/c++/5/bits/stl_pair.h: In instantiation of 'std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const void*; _U2 = boost::shared_ptr<const EmpDist>; _T1 = const void* const; _T2 = boost::shared_ptr<void>]':
/usr/include/boost/serialization/shared_ptr_helper.hpp:182:20: required from 'void boost::serialization::shared_ptr_helper<SPT>::reset(SPT<T>&, T*) [with T = const EmpDist; SPT = boost::shared_ptr]'
/usr/include/boost/serialization/shared_ptr.hpp:171:5: required from 'void boost::serialization::load(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]'
/usr/include/boost/serialization/split_free.hpp:58:13: required from 'static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const EmpDist>]'
/usr/include/boost/serialization/split_free.hpp:74:18: required from 'void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = boost::shared_ptr<const EmpDist>]'
/usr/include/boost/serialization/shared_ptr.hpp:187:37: required from 'void boost::serialization::serialize(Archive&, boost::shared_ptr<U>&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = const EmpDist]'
/usr/include/boost/serialization/serialization.hpp:128:18: [ skipping 104 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/boost/serialization/export.hpp:86:1: required from 'struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>'
/usr/include/boost/archive/detail/register_archive.hpp:25:8: required from 'struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, AbundanceGroup>'
/usr/include/boost/archive/binary_iarchive.hpp:57:1: required by substitution of 'template<class Serializable> typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable*, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = AbundanceGroup]'
/usr/include/boost/serialization/export.hpp:132:38: required from 'void boost::archive::detail::extra_detail::guid_initializer<T>::export_guid(mpl_::false_) const [with T = AbundanceGroup; mpl_::false_ = mpl_::bool_<false>]'
/usr/include/boost/serialization/export.hpp:142:20: required from 'const boost::archive::detail::extra_detail::guid_initializer<T>& boost::archive::detail::extra_detail::guid_initializer<T>::export_guid() const [with T = AbundanceGroup]'
abundances.cpp:5162:1: required from here
/usr/include/boost/smart_ptr/shared_ptr.hpp:408:5: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(const boost::weak_ptr<Y>&, boost::detail::sp_nothrow_tag)
shared_ptr( weak_ptr<Y> const & r, boost::detail::sp_nothrow_tag )
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:408:5: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: 'const boost::shared_ptr<const EmpDist>' is not derived from 'const boost::weak_ptr<Y>'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
/usr/include/boost/smart_ptr/shared_ptr.hpp:399:14: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(const boost::weak_ptr<Y>&)
explicit shared_ptr( weak_ptr<Y> const & r ): pn( r.pn ) // may throw
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:399:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: 'const boost::shared_ptr<const EmpDist>' is not derived from 'const boost::weak_ptr<Y>'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
/usr/include/boost/smart_ptr/shared_ptr.hpp:373:41: note: candidate: template<class Y, class D, class A> boost::shared_ptr<T>::shared_ptr(Y*, D, A)
template<class Y, class D, class A> shared_ptr( Y * p, D d, A a ): px( p ), pn( p, d, a )
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:373:41: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: mismatched types 'Y*' and 'boost::shared_ptr<const EmpDist>'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
/usr/include/boost/smart_ptr/shared_ptr.hpp:358:32: note: candidate: template<class Y, class D> boost::shared_ptr<T>::shared_ptr(Y*, D)
template<class Y, class D> shared_ptr( Y * p, D d ): px( p ), pn( p, d )
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:358:32: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: mismatched types 'Y*' and 'boost::shared_ptr<const EmpDist>'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
/usr/include/boost/smart_ptr/shared_ptr.hpp:347:14: note: candidate: template<class Y> boost::shared_ptr<T>::shared_ptr(Y*)
explicit shared_ptr( Y * p ): px( p ), pn() // Y must be complete
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:347:14: note: template argument deduction/substitution failed:
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
from /usr/include/c++/5/vector:60,
from abundances.h:17,
from abundances.cpp:16:
/usr/include/c++/5/bits/stl_pair.h:119:39: note: mismatched types 'Y*' and 'boost::shared_ptr<const EmpDist>'
: first(__p.first), second(__p.second) { }
^
In file included from /usr/include/boost/shared_ptr.hpp:17:0,
from hits.h:19,
from abundances.h:23,
from abundances.cpp:16:
/usr/include/boost/smart_ptr/shared_ptr.hpp:334:5: note: candidate: boost::shared_ptr<T>::shared_ptr() [with T = void]
shared_ptr() BOOST_NOEXCEPT : px( 0 ), pn() // never throws in 1.30+
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:334:5: note: candidate expects 0 arguments, 1 provided
/usr/include/boost/smart_ptr/shared_ptr.hpp:323:25: note: candidate: boost::shared_ptr<void>::shared_ptr(const boost::shared_ptr<void>&)
template<class T> class shared_ptr
^
/usr/include/boost/smart_ptr/shared_ptr.hpp:323:25: note: no known conversion for argument 1 from 'const boost::shared_ptr<const EmpDist>' to 'const boost::shared_ptr<void>&'
Makefile:1627: recipe for target 'abundances.o' failed
make[3]: *** [abundances.o] Error 1
make[3]: Leaving directory '/scratch/packages/tmp/cufflinks-2.2.1/src'
Makefile:401: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/scratch/packages/tmp/cufflinks-2.2.1'
Makefile:342: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/scratch/packages/tmp/cufflinks-2.2.1'
dh_auto_build: make -j12 returned exit code 2
debian/rules:13: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
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