CentOS 7 installation issues
Closed this issue · 7 comments
bio15anu commented
Hi there,
I've been trying to install RYUTO from source, following the instructions in README.md but am running into issues. The dependencies have been installed.
[adam@epi source]$ ./configure --prefix=/scr/epi/tools/ryuto/version/binary \
--with-htslib=/scr/epi/tools/htslib/1.9/binary/ \
--with-clp=/scr/epi/tools/clp/1.16.11/binary/ \
--with-lemon=/scr/epi/tools/lemon/version/binary/
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
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++... gcc3
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking if zlib is wanted... yes
checking for inflate in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for inflateEnd in -lz... yes
checking zlib in /usr... ok
checking if HTS is wanted... yes
checking sam.h usability... yes
checking sam.h presence... yes
checking for sam.h... yes
checking for hts_open in -lhts... yes
checking htslib... ok
checking for g++ option to support OpenMP... -fopenmp
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for boostlib >= 1.3... yes
./configure: line 4593: LDFLAGS: command not found
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... gcc3
checking whether the Boost::Program_Options library is available... yes
checking for exit in -lboost_program_options-mt... yes
checking if lemon is wanted... yes
checking lemon... ok
checking if clp is wanted... yes
checking clp... ok
checking whether C++ compiler accepts -std=c++0x... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: executing depfiles commands
Then running make gives this error:
[adam@epi source]$ make
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /scr/epi/tools/ryuto/version/source/missing aclocal-1.15
cd . && /bin/sh /scr/epi/tools/ryuto/version/source/missing automake-1.15 --foreign
configure.ac:25: error: required file './compile' not found
configure.ac:25: 'automake --add-missing' can install 'compile'
make: *** [Makefile.in] Error 1
I am running CentOS 7, so the latest version of automake is 1.13 but I installed automake-1.15 from an rpm file. It seems to be a dependency? I have also tried this both with and without running aclocal-1.15 again.
[adam@epi source]$ automake-1.15 --add-missing
configure.ac:25: installing './compile'
Makefile.am: error: required file './NEWS' not found
Makefile.am: error: required file './README' not found
Makefile.am: error: required file './AUTHORS' not found
Makefile.am: error: required file './ChangeLog' not found
The link to "compile" has been updated, despite above errors, so I run make again which leads to this:
[adam@epi source]$ make
cd . && /bin/sh /scr/epi/tools/ryuto/version/source/missing automake-1.15 --foreign
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /scr/epi/tools/ryuto/version/source/missing autoconf
/bin/sh ./config.status --recheck
running CONFIG_SHELL=/bin/sh /bin/sh ./configure --prefix=/scr/epi/tools/ryuto/version/binary --with-htslib=/scr/epi/tools/htslib/1.9/binary/ --with-clp=/scr/epi/tools/clp/1.16.11/binary/ --with-lemon=/scr/epi/tools/lemon/version/binary/ --no-create --no-recursion
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
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++... gcc3
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking if zlib is wanted... yes
checking for inflate in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for inflateEnd in -lz... yes
checking zlib in /usr... ok
checking if HTS is wanted... yes
checking sam.h usability... yes
checking sam.h presence... yes
checking for sam.h... yes
checking for hts_open in -lhts... yes
checking htslib... ok
checking for g++ option to support OpenMP... -fopenmp
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for boostlib >= 1.3... yes
./configure: line 4593: LDFLAGS: command not found
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... gcc3
checking whether the Boost::Program_Options library is available... yes
checking for exit in -lboost_program_options-mt... yes
checking if lemon is wanted... yes
checking lemon... ok
checking if clp is wanted... yes
checking clp... ok
checking whether C++ compiler accepts -std=c++0x... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
/bin/sh ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: executing depfiles commands
Making all in src
make[1]: Entering directory `/scr/epi/tools/ryuto/version/source/src'
depbase=`echo Logger/logger.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary//include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary//include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary//include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Logger/logger.o -MD -MP -MF $depbase.Tpo -c -o Logger/logger.o Logger/logger.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Controller/bam_controller.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary//include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary//include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary//include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Controller/bam_controller.o -MD -MP -MF $depbase.Tpo -c -o Controller/bam_controller.o Controller/bam_controller.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Controller/base_controller.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary//include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary//include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary//include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Controller/base_controller.o -MD -MP -MF $depbase.Tpo -c -o Controller/base_controller.o Controller/base_controller.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Reader/Chromosome/interval.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary//include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary//include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary//include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Reader/Chromosome/interval.o -MD -MP -MF $depbase.Tpo -c -o Reader/Chromosome/interval.o Reader/Chromosome/interval.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Reader/Chromosome/read_collection.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary//include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary//include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary//include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Reader/Chromosome/read_collection.o -MD -MP -MF $depbase.Tpo -c -o Reader/Chromosome/read_collection.o Reader/Chromosome/read_collection.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Reader/Chromosome/chromosome.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary//include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary//include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary//include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Reader/Chromosome/chromosome.o -MD -MP -MF $depbase.Tpo -c -o Reader/Chromosome/chromosome.o Reader/Chromosome/chromosome.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Reader/Chromosome/exon.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary//include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary//include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary//include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Reader/Chromosome/exon.o -MD -MP -MF $depbase.Tpo -c -o Reader/Chromosome/exon.o Reader/Chromosome/exon.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Reader/Chromosome/connection_iterator.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary//include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary//include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary//include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Reader/Chromosome/connection_iterator.o -MD -MP -MF $depbase.Tpo -c -o Reader/Chromosome/connection_iterator.o Reader/Chromosome/connection_iterator.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Reader/Chromosome/read.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary//include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary//include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary//include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Reader/Chromosome/read.o -MD -MP -MF $depbase.Tpo -c -o Reader/Chromosome/read.o Reader/Chromosome/read.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Reader/Chromosome/raw_series_counts.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary//include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary//include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary//include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Reader/Chromosome/raw_series_counts.o -MD -MP -MF $depbase.Tpo -c -o Reader/Chromosome/raw_series_counts.o Reader/Chromosome/raw_series_counts.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Reader/Chromosome/raw_atom.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary//include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary//include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary//include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Reader/Chromosome/raw_atom.o -MD -MP -MF $depbase.Tpo -c -o Reader/Chromosome/raw_atom.o Reader/Chromosome/raw_atom.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Reader/Chromosome/connected.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary//include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary//include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary//include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Reader/Chromosome/connected.o -MD -MP -MF $depbase.Tpo -c -o Reader/Chromosome/connected.o Reader/Chromosome/connected.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Reader/gffReader.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary//include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary//include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary//include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Reader/gffReader.o -MD -MP -MF $depbase.Tpo -c -o Reader/gffReader.o Reader/gffReader.cc &&\
mv -f $depbase.Tpo $depbase.Po
In file included from /usr/include/c++/4.8.2/algorithm:62:0,
from Reader/Chromosome/../../Datatype_Templates/reader_list.h:12,
from Reader/Chromosome/chromosome.h:13,
from Reader/gffReader.h:18,
from Reader/gffReader.cc:8:
/usr/include/c++/4.8.2/bits/stl_algo.h: In instantiation of ‘_RandomAccessIterator std::__unguarded_partition(_RandomAccessIterator, _RandomAccessIterator, const _Tp&) [with _RandomAccessIterator = std::_Deque_iterator<gffReader::transcript_info, gffReader::transcript_info&, gffReader::transcript_info*>; _Tp = gffReader::transcript_info]’:
/usr/include/c++/4.8.2/bits/stl_algo.h:2283:70: required from ‘_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator) [with _RandomAccessIterator = std::_Deque_iterator<gffReader::transcript_info, gffReader::transcript_info&, gffReader::transcript_info*>]’
/usr/include/c++/4.8.2/bits/stl_algo.h:2315:54: required from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size) [with _RandomAccessIterator = std::_Deque_iterator<gffReader::transcript_info, gffReader::transcript_info&, gffReader::transcript_info*>; _Size = long int]’
/usr/include/c++/4.8.2/bits/stl_algo.h:5461:36: required from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = std::_Deque_iterator<gffReader::transcript_info, gffReader::transcript_info&, gffReader::transcript_info*>]’
Reader/gffReader.cc:192:45: required from here
/usr/include/c++/4.8.2/bits/stl_algo.h:2245:19: error: passing ‘const gffReader::transcript_info’ as ‘this’ argument of ‘bool gffReader::transcript_info::operator<(const gffReader::transcript_info&)’ discards qualifiers [-fpermissive]
while (__pivot < *__last)
^
make[1]: *** [Reader/gffReader.o] Error 1
make[1]: Leaving directory `/scr/epi/tools/ryuto/version/source/src'
make: *** [all-recursive] Error 1
Do you know how I can get around this error?
TGatter commented
Hi,
this seems to be a weird automake error I don't fully understand. Could you try to run the '''./reset_autogen.sh''' script and then try again too see if automake still runs into errors?
As for the STL error I have to look into this. Your gcc seems to be rather old. Please try updating. I will try to compile you something in the meantime myself in a virtual machine.
bio15anu commented
Hi Thomas,
I tried both suggestions now. The latest version of GCC that is supported directly on CentOS 7 is only 4.8.5 but I installed 7.3.1 from an SCL. The I started from scratch, configured, then ran ./reset_autogen.sh then automake --add-missing. The "compile" link did not update automatically so I changed it manually. Now I get quite a lot of errors with make (sorry this is long):
[adam@epi source]$ make
/bin/sh ./config.status --recheck
running CONFIG_SHELL=/bin/sh /bin/sh ./configure --prefix=/scr/epi/tools/ryuto/version/binary --with-htslib=/scr/epi/tools/htslib/1.9/binary --with-clp=/scr/epi/tools/clp/1.16.11/binary --with-lemon=/scr/epi/tools/lemon/version/binary --no-create --no-recursion
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
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++... gcc3
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking if zlib is wanted... yes
checking for inflate in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for inflateEnd in -lz... yes
checking zlib in /usr... ok
checking if HTS is wanted... yes
checking sam.h usability... yes
checking sam.h presence... yes
checking for sam.h... yes
checking for hts_open in -lhts... yes
checking htslib... ok
checking for g++ option to support OpenMP... -fopenmp
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for boostlib >= 1.3... yes
./configure: line 4551: LDFLAGS: command not found
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 dependency style of gcc... gcc3
checking whether the Boost::Program_Options library is available... yes
checking for exit in -lboost_program_options-mt... yes
checking if lemon is wanted... yes
checking lemon... ok
checking if clp is wanted... yes
checking clp... ok
checking whether C++ compiler accepts -std=c++0x... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
/bin/sh ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: executing depfiles commands
Making all in src
make[1]: Entering directory '/scr/epi/tools/ryuto/version/source/src'
depbase=`echo Controller/bam_controller.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary/include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary/include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary/include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Controller/bam_controller.o -MD -MP -MF $depbase.Tpo -c -o Controller/bam_controller.o Controller/bam_controller.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Controller/base_controller.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary/include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary/include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary/include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Controller/base_controller.o -MD -MP -MF $depbase.Tpo -c -o Controller/base_controller.o Controller/base_controller.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Graph/flow_graph/arc_back_bridge.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary/include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary/include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary/include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Graph/flow_graph/arc_back_bridge.o -MD -MP -MF $depbase.Tpo -c -o Graph/flow_graph/arc_back_bridge.o Graph/flow_graph/arc_back_bridge.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Graph/flow_graph/arc_bridge.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary/include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary/include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary/include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Graph/flow_graph/arc_bridge.o -MD -MP -MF $depbase.Tpo -c -o Graph/flow_graph/arc_bridge.o Graph/flow_graph/arc_bridge.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Graph/flow_graph/arc_identifier.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary/include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary/include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary/include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Graph/flow_graph/arc_identifier.o -MD -MP -MF $depbase.Tpo -c -o Graph/flow_graph/arc_identifier.o Graph/flow_graph/arc_identifier.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Graph/flow_graph/build/count_raw_edge.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary/include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary/include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary/include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Graph/flow_graph/build/count_raw_edge.o -MD -MP -MF $depbase.Tpo -c -o Graph/flow_graph/build/count_raw_edge.o Graph/flow_graph/build/count_raw_edge.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Graph/flow_graph/build/count_raw_node.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary/include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary/include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary/include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Graph/flow_graph/build/count_raw_node.o -MD -MP -MF $depbase.Tpo -c -o Graph/flow_graph/build/count_raw_node.o Graph/flow_graph/build/count_raw_node.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Graph/flow_graph/build/region.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary/include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary/include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary/include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Graph/flow_graph/build/region.o -MD -MP -MF $depbase.Tpo -c -o Graph/flow_graph/build/region.o Graph/flow_graph/build/region.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Graph/flow_graph/coverage/capacity_mean.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary/include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary/include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary/include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Graph/flow_graph/coverage/capacity_mean.o -MD -MP -MF $depbase.Tpo -c -o Graph/flow_graph/coverage/capacity_mean.o Graph/flow_graph/coverage/capacity_mean.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Graph/flow_graph/coverage/flow_series.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary/include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary/include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary/include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Graph/flow_graph/coverage/flow_series.o -MD -MP -MF $depbase.Tpo -c -o Graph/flow_graph/coverage/flow_series.o Graph/flow_graph/coverage/flow_series.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Graph/flow_graph/edge_length.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary/include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary/include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary/include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Graph/flow_graph/edge_length.o -MD -MP -MF $depbase.Tpo -c -o Graph/flow_graph/edge_length.o Graph/flow_graph/edge_length.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Graph/flow_graph/exon_edge.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary/include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary/include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary/include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Graph/flow_graph/exon_edge.o -MD -MP -MF $depbase.Tpo -c -o Graph/flow_graph/exon_edge.o Graph/flow_graph/exon_edge.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Graph/flow_graph/path.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary/include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary/include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary/include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Graph/flow_graph/path.o -MD -MP -MF $depbase.Tpo -c -o Graph/flow_graph/path.o Graph/flow_graph/path.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Graph/flow_graph/path_evidence.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary/include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary/include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary/include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Graph/flow_graph/path_evidence.o -MD -MP -MF $depbase.Tpo -c -o Graph/flow_graph/path_evidence.o Graph/flow_graph/path_evidence.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Graph/flow_manager/base_manager_buildgraph.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary/include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary/include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary/include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Graph/flow_manager/base_manager_buildgraph.o -MD -MP -MF $depbase.Tpo -c -o Graph/flow_manager/base_manager_buildgraph.o Graph/flow_manager/base_manager_buildgraph.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo Graph/flow_manager/base_manager_flow_handler.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DPACKAGE_NAME=\"ttrans\" -DPACKAGE_TARNAME=\"ttrans\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"ttrans\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ttrans\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBZ=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PROGRAM_OPTIONS=/\*\*/ -I. -I/scr/epi/tools/htslib/1.9/binary/include/htslib/ -I/usr/include -I/scr/epi/tools/lemon/version/binary/include/ -fopenmp -I/scr/epi/tools/clp/1.16.11/binary/include/ -L/usr/lib -Wl,-rpath,/usr/lib/ -O2 -std=c++0x -MT Graph/flow_manager/base_manager_flow_handler.o -MD -MP -MF $depbase.Tpo -c -o Graph/flow_manager/base_manager_flow_handler.o Graph/flow_manager/base_manager_flow_handler.cc &&\
mv -f $depbase.Tpo $depbase.Po
Graph/flow_manager/base_manager_flow_handler.cc: In member function ‘void base_manager::compute_ratio(lemon::DigraphExtender<lemon::ListDigraphBase>::Node, lemon::DigraphExtender<lemon::ListDigraphBase>::ArcMap<arc_bridge>&, lemon::DigraphExtender<lemon::ListDigraphBase>::ArcMap<arc_back_bridge>&, std::set<int>&, lemon::ListDigraph&, lemon::DigraphExtender<lemon::ListDigraphBase>::ArcMap<flow_series>&, int, float&, capacity_type&)’:
Graph/flow_manager/base_manager_flow_handler.cc:4998:5: error: ‘Lp’ was not declared in this scope
Lp lp;
^~
Graph/flow_manager/base_manager_flow_handler.cc:4999:45: error: type/value mismatch at argument 2 in template parameter list for ‘template<class _Key, class _Tp, class _Compare, class _Alloc> class std::map’
std::map<std::pair< int, int > , Lp::Col> bi_edges;
^
Graph/flow_manager/base_manager_flow_handler.cc:4999:45: note: expected a type, got ‘Lp’
Graph/flow_manager/base_manager_flow_handler.cc:4999:45: error: template argument 4 is invalid
Graph/flow_manager/base_manager_flow_handler.cc:5000:23: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Alloc> class std::deque’
std::deque<Lp::Col> left_z;
^
Graph/flow_manager/base_manager_flow_handler.cc:5000:23: note: expected a type, got ‘Lp’
Graph/flow_manager/base_manager_flow_handler.cc:5000:23: error: template argument 2 is invalid
Graph/flow_manager/base_manager_flow_handler.cc:5001:23: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Alloc> class std::deque’
std::deque<Lp::Col> right_z;
^
Graph/flow_manager/base_manager_flow_handler.cc:5001:23: note: expected a type, got ‘Lp’
Graph/flow_manager/base_manager_flow_handler.cc:5001:23: error: template argument 2 is invalid
Graph/flow_manager/base_manager_flow_handler.cc:5002:5: error: ‘Lp’ is not a class, namespace, or enumeration
Lp::Expr optimize;
^~
Graph/flow_manager/base_manager_flow_handler.cc:5009:22: error: request for member ‘insert’ in ‘bi_edges’, which is of non-class type ‘int’
bi_edges.insert(std::make_pair(std::make_pair(wc.id(a), wc.id(right)), lp.addCol()));
^~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5009:84: error: ‘lp’ was not declared in this scope
bi_edges.insert(std::make_pair(std::make_pair(wc.id(a), wc.id(right)), lp.addCol()));
^~
Graph/flow_manager/base_manager_flow_handler.cc:5011:38: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
lp.colLowerBound(bi_edges[std::make_pair(wc.id(a), wc.id(right))], 0);
^
Graph/flow_manager/base_manager_flow_handler.cc:5012:38: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
lp.colUpperBound(bi_edges[std::make_pair(wc.id(a), wc.id(right))], Lp::INF);
^
Graph/flow_manager/base_manager_flow_handler.cc:5012:80: error: ‘Lp’ is not a class, namespace, or enumeration
lp.colUpperBound(bi_edges[std::make_pair(wc.id(a), wc.id(right))], Lp::INF);
^~
Graph/flow_manager/base_manager_flow_handler.cc:5020:9: error: ‘Lp’ is not a class, namespace, or enumeration
Lp::Expr abs1, abs2;
^~
Graph/flow_manager/base_manager_flow_handler.cc:5021:9: error: ‘abs1’ was not declared in this scope
abs1 += fsc[left].get_flow(guiding_id);
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5021:9: note: suggested alternative: ‘abs’
abs1 += fsc[left].get_flow(guiding_id);
^~~~
abs
Graph/flow_manager/base_manager_flow_handler.cc:5025:29: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
abs1 -= bi_edges[std::make_pair(wc.id(left), wc.id(right))];
^
Graph/flow_manager/base_manager_flow_handler.cc:5026:13: error: ‘abs2’ was not declared in this scope
abs2 += bi_edges[std::make_pair(wc.id(left), wc.id(right))];
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5026:13: note: suggested alternative: ‘abs’
abs2 += bi_edges[std::make_pair(wc.id(left), wc.id(right))];
^~~~
abs
Graph/flow_manager/base_manager_flow_handler.cc:5026:29: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
abs2 += bi_edges[std::make_pair(wc.id(left), wc.id(right))];
^
Graph/flow_manager/base_manager_flow_handler.cc:5029:16: error: request for member ‘push_back’ in ‘left_z’, which is of non-class type ‘int’
left_z.push_back(lp.addCol());
^~~~~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5029:26: error: ‘lp’ was not declared in this scope
left_z.push_back(lp.addCol());
^~
Graph/flow_manager/base_manager_flow_handler.cc:5030:26: error: request for member ‘back’ in ‘left_z’, which is of non-class type ‘int’
lp.addRow(left_z.back() >= abs1);
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5031:20: error: ‘abs2’ was not declared in this scope
lp.addRow( abs2 <= fsc[left].get_flow(guiding_id));
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5031:20: note: suggested alternative: ‘abs’
lp.addRow( abs2 <= fsc[left].get_flow(guiding_id));
^~~~
abs
Graph/flow_manager/base_manager_flow_handler.cc:5032:9: error: ‘optimize’ was not declared in this scope
optimize += left_z.back();// * fc[left];
^~~~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5032:9: note: suggested alternative: ‘options’
optimize += left_z.back();// * fc[left];
^~~~~~~~
options
Graph/flow_manager/base_manager_flow_handler.cc:5032:28: error: request for member ‘back’ in ‘left_z’, which is of non-class type ‘int’
optimize += left_z.back();// * fc[left];
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5038:9: error: ‘Lp’ is not a class, namespace, or enumeration
Lp::Expr abs1, abs2;
^~
Graph/flow_manager/base_manager_flow_handler.cc:5039:9: error: ‘abs1’ was not declared in this scope
abs1 += fsc[right].get_flow(guiding_id);
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5039:9: note: suggested alternative: ‘abs’
abs1 += fsc[right].get_flow(guiding_id);
^~~~
abs
Graph/flow_manager/base_manager_flow_handler.cc:5043:29: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
abs1 -= bi_edges[std::make_pair(wc.id(left), wc.id(right))];
^
Graph/flow_manager/base_manager_flow_handler.cc:5044:13: error: ‘abs2’ was not declared in this scope
abs2 += bi_edges[std::make_pair(wc.id(left), wc.id(right))];
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5044:13: note: suggested alternative: ‘abs’
abs2 += bi_edges[std::make_pair(wc.id(left), wc.id(right))];
^~~~
abs
Graph/flow_manager/base_manager_flow_handler.cc:5044:29: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
abs2 += bi_edges[std::make_pair(wc.id(left), wc.id(right))];
^
Graph/flow_manager/base_manager_flow_handler.cc:5047:17: error: request for member ‘push_back’ in ‘right_z’, which is of non-class type ‘int’
right_z.push_back(lp.addCol());
^~~~~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5047:27: error: ‘lp’ was not declared in this scope
right_z.push_back(lp.addCol());
^~
Graph/flow_manager/base_manager_flow_handler.cc:5048:27: error: request for member ‘back’ in ‘right_z’, which is of non-class type ‘int’
lp.addRow(right_z.back() >= abs1);
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5049:19: error: ‘abs2’ was not declared in this scope
lp.addRow(abs2 <= fsc[right].get_flow(guiding_id));
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5049:19: note: suggested alternative: ‘abs’
lp.addRow(abs2 <= fsc[right].get_flow(guiding_id));
^~~~
abs
Graph/flow_manager/base_manager_flow_handler.cc:5050:9: error: ‘optimize’ was not declared in this scope
optimize += right_z.back();// * fc[right];
^~~~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5050:9: note: suggested alternative: ‘options’
optimize += right_z.back();// * fc[right];
^~~~~~~~
options
Graph/flow_manager/base_manager_flow_handler.cc:5050:29: error: request for member ‘back’ in ‘right_z’, which is of non-class type ‘int’
optimize += right_z.back();// * fc[right];
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5054:5: error: ‘lp’ was not declared in this scope
lp.min();
^~
Graph/flow_manager/base_manager_flow_handler.cc:5055:12: error: ‘optimize’ was not declared in this scope
lp.obj(optimize);
^~~~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5055:12: note: suggested alternative: ‘options’
lp.obj(optimize);
^~~~~~~~
options
Graph/flow_manager/base_manager_flow_handler.cc:5060:28: error: ‘Lp’ is not a class, namespace, or enumeration
if (lp.primalType() != Lp::OPTIMAL) {
^~
Graph/flow_manager/base_manager_flow_handler.cc:5075:53: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
xee_sum += std::round(lp.primal(bi_edges[std::make_pair(wc.id(left), wc.id(right))]));
^
Graph/flow_manager/base_manager_flow_handler.cc:5088:53: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
xee_sum += std::round(lp.primal(bi_edges[std::make_pair(wc.id(left), wc.id(right))]));
^
Graph/flow_manager/base_manager_flow_handler.cc: In static member function ‘static void base_manager::compute_flow_two_step(lemon::DigraphExtender<lemon::ListDigraphBase>::Node, int, std::map<std::pair<int, int>, long unsigned int>&, std::map<int, base_manager::evidence_group>&, std::map<int, base_manager::evidence_group>&, std::map<int, std::set<int> >&, std::map<int, std::set<int> >&, std::deque<base_manager::resolve_count_set>&, lemon::ListDigraph&, lemon::DigraphExtender<lemon::ListDigraphBase>::ArcMap<flow_series>&, lemon::DigraphExtender<lemon::ListDigraphBase>::ArcMap<arc_identifier>&, lemon::DigraphExtender<lemon::ListDigraphBase>::NodeMap<unsigned int>&, lemon::DigraphExtender<lemon::ListDigraphBase>::ArcMap<arc_bridge>&, lemon::DigraphExtender<lemon::ListDigraphBase>::ArcMap<arc_back_bridge>&)’:
Graph/flow_manager/base_manager_flow_handler.cc:5180:5: error: ‘Lp’ was not declared in this scope
Lp lp;
^~
Graph/flow_manager/base_manager_flow_handler.cc:5181:45: error: type/value mismatch at argument 2 in template parameter list for ‘template<class _Key, class _Tp, class _Compare, class _Alloc> class std::map’
std::map<std::pair< int, int > , Lp::Col> bi_edges;
^
Graph/flow_manager/base_manager_flow_handler.cc:5181:45: note: expected a type, got ‘Lp’
Graph/flow_manager/base_manager_flow_handler.cc:5181:45: error: template argument 4 is invalid
Graph/flow_manager/base_manager_flow_handler.cc:5182:23: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Alloc> class std::deque’
std::deque<Lp::Col> left_z;
^
Graph/flow_manager/base_manager_flow_handler.cc:5182:23: note: expected a type, got ‘Lp’
Graph/flow_manager/base_manager_flow_handler.cc:5182:23: error: template argument 2 is invalid
Graph/flow_manager/base_manager_flow_handler.cc:5183:23: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Alloc> class std::deque’
std::deque<Lp::Col> right_z;
^
Graph/flow_manager/base_manager_flow_handler.cc:5183:23: note: expected a type, got ‘Lp’
Graph/flow_manager/base_manager_flow_handler.cc:5183:23: error: template argument 2 is invalid
Graph/flow_manager/base_manager_flow_handler.cc:5184:5: error: ‘Lp’ is not a class, namespace, or enumeration
Lp::Expr optimize;
^~
Graph/flow_manager/base_manager_flow_handler.cc:5194:18: error: request for member ‘insert’ in ‘bi_edges’, which is of non-class type ‘int’
bi_edges.insert(std::make_pair(std::make_pair(lg, rg), lp.addCol()));
^~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5194:64: error: ‘lp’ was not declared in this scope
bi_edges.insert(std::make_pair(std::make_pair(lg, rg), lp.addCol()));
^~
Graph/flow_manager/base_manager_flow_handler.cc:5194:64: note: suggested alternative: ‘lg’
bi_edges.insert(std::make_pair(std::make_pair(lg, rg), lp.addCol()));
^~
lg
Graph/flow_manager/base_manager_flow_handler.cc:5196:34: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
lp.colLowerBound(bi_edges[std::make_pair(lg, rg)], 0);
^
Graph/flow_manager/base_manager_flow_handler.cc:5197:34: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
lp.colUpperBound(bi_edges[std::make_pair(lg, rg)], Lp::INF);
^
Graph/flow_manager/base_manager_flow_handler.cc:5197:60: error: ‘Lp’ is not a class, namespace, or enumeration
lp.colUpperBound(bi_edges[std::make_pair(lg, rg)], Lp::INF);
^~
Graph/flow_manager/base_manager_flow_handler.cc:5211:9: error: ‘Lp’ is not a class, namespace, or enumeration
Lp::Expr sum, sub;
^~
Graph/flow_manager/base_manager_flow_handler.cc:5212:9: error: ‘sub’ was not declared in this scope
sub += group_cap;
^~~
Graph/flow_manager/base_manager_flow_handler.cc:5212:9: note: suggested alternative: ‘swab’
sub += group_cap;
^~~
swab
Graph/flow_manager/base_manager_flow_handler.cc:5215:13: error: ‘sum’ was not declared in this scope
sum += bi_edges[std::make_pair(lg, rg)];
^~~
Graph/flow_manager/base_manager_flow_handler.cc:5215:28: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
sum += bi_edges[std::make_pair(lg, rg)];
^
Graph/flow_manager/base_manager_flow_handler.cc:5216:28: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
sub -= bi_edges[std::make_pair(lg, rg)];
^
Graph/flow_manager/base_manager_flow_handler.cc:5219:16: error: request for member ‘push_back’ in ‘left_z’, which is of non-class type ‘int’
left_z.push_back(lp.addCol());
^~~~~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5219:26: error: ‘lp’ was not declared in this scope
left_z.push_back(lp.addCol());
^~
Graph/flow_manager/base_manager_flow_handler.cc:5219:26: note: suggested alternative: ‘lg’
left_z.push_back(lp.addCol());
^~
lg
Graph/flow_manager/base_manager_flow_handler.cc:5220:26: error: request for member ‘back’ in ‘left_z’, which is of non-class type ‘int’
lp.addRow(left_z.back() >= sub);
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5221:20: error: ‘sum’ was not declared in this scope
lp.addRow( sum <= group_cap);
^~~
Graph/flow_manager/base_manager_flow_handler.cc:5222:9: error: ‘optimize’ was not declared in this scope
optimize += left_z.back();
^~~~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5222:9: note: suggested alternative: ‘options’
optimize += left_z.back();
^~~~~~~~
options
Graph/flow_manager/base_manager_flow_handler.cc:5222:28: error: request for member ‘back’ in ‘left_z’, which is of non-class type ‘int’
optimize += left_z.back();
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5235:9: error: ‘Lp’ is not a class, namespace, or enumeration
Lp::Expr sum, sub;
^~
Graph/flow_manager/base_manager_flow_handler.cc:5236:9: error: ‘sub’ was not declared in this scope
sub += group_cap;
^~~
Graph/flow_manager/base_manager_flow_handler.cc:5236:9: note: suggested alternative: ‘swab’
sub += group_cap;
^~~
swab
Graph/flow_manager/base_manager_flow_handler.cc:5239:13: error: ‘sum’ was not declared in this scope
sum += bi_edges[std::make_pair(lg, rg)];
^~~
Graph/flow_manager/base_manager_flow_handler.cc:5239:28: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
sum += bi_edges[std::make_pair(lg, rg)];
^
Graph/flow_manager/base_manager_flow_handler.cc:5240:28: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
sub -= bi_edges[std::make_pair(lg, rg)];
^
Graph/flow_manager/base_manager_flow_handler.cc:5243:16: error: request for member ‘push_back’ in ‘left_z’, which is of non-class type ‘int’
left_z.push_back(lp.addCol());
^~~~~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5243:26: error: ‘lp’ was not declared in this scope
left_z.push_back(lp.addCol());
^~
Graph/flow_manager/base_manager_flow_handler.cc:5244:26: error: request for member ‘back’ in ‘left_z’, which is of non-class type ‘int’
lp.addRow(left_z.back() >= sub);
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5245:20: error: ‘sum’ was not declared in this scope
lp.addRow( sum <= group_cap);
^~~
Graph/flow_manager/base_manager_flow_handler.cc:5246:9: error: ‘optimize’ was not declared in this scope
optimize += left_z.back();
^~~~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5246:9: note: suggested alternative: ‘options’
optimize += left_z.back();
^~~~~~~~
options
Graph/flow_manager/base_manager_flow_handler.cc:5246:28: error: request for member ‘back’ in ‘left_z’, which is of non-class type ‘int’
optimize += left_z.back();
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5249:5: error: ‘Lp’ is not a class, namespace, or enumeration
Lp::Expr optimize2;
^~
Graph/flow_manager/base_manager_flow_handler.cc:5250:23: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Alloc> class std::deque’
std::deque<Lp::Col> opts;
^
Graph/flow_manager/base_manager_flow_handler.cc:5250:23: note: expected a type, got ‘Lp’
Graph/flow_manager/base_manager_flow_handler.cc:5250:23: error: template argument 2 is invalid
Graph/flow_manager/base_manager_flow_handler.cc:5251:23: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Alloc> class std::deque’
std::deque<Lp::Col> constraints;
^
Graph/flow_manager/base_manager_flow_handler.cc:5251:23: note: expected a type, got ‘Lp’
Graph/flow_manager/base_manager_flow_handler.cc:5251:23: error: template argument 2 is invalid
Graph/flow_manager/base_manager_flow_handler.cc:5253:46: error: type/value mismatch at argument 2 in template parameter list for ‘template<class _Key, class _Tp, class _Compare, class _Alloc> class std::map’
std::map<std::pair< int, int > , Lp::Expr> constraint_map_plus;
^
Graph/flow_manager/base_manager_flow_handler.cc:5253:46: note: expected a type, got ‘Lp’
Graph/flow_manager/base_manager_flow_handler.cc:5253:46: error: template argument 4 is invalid
Graph/flow_manager/base_manager_flow_handler.cc:5254:46: error: type/value mismatch at argument 2 in template parameter list for ‘template<class _Key, class _Tp, class _Compare, class _Alloc> class std::map’
std::map<std::pair< int, int > , Lp::Expr> constraint_map_minus;
^
Graph/flow_manager/base_manager_flow_handler.cc:5254:46: note: expected a type, got ‘Lp’
Graph/flow_manager/base_manager_flow_handler.cc:5254:46: error: template argument 4 is invalid
Graph/flow_manager/base_manager_flow_handler.cc:5266:9: error: ‘Lp’ is not a class, namespace, or enumeration
Lp::Expr all_combos = 0;
^~
Graph/flow_manager/base_manager_flow_handler.cc:5271:30: error: request for member ‘find’ in ‘bi_edges’, which is of non-class type ‘int’
if (bi_edges.find(std::make_pair(*li,*ri)) == bi_edges.end()) { // we only add in ACTUAL valid edges!
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5271:72: error: request for member ‘end’ in ‘bi_edges’, which is of non-class type ‘int’
if (bi_edges.find(std::make_pair(*li,*ri)) == bi_edges.end()) { // we only add in ACTUAL valid edges!
^~~
Graph/flow_manager/base_manager_flow_handler.cc:5277:29: error: request for member ‘push_back’ in ‘constraints’, which is of non-class type ‘int’
constraints.push_back(lp.addCol());
^~~~~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5277:39: error: ‘lp’ was not declared in this scope
constraints.push_back(lp.addCol());
^~
Graph/flow_manager/base_manager_flow_handler.cc:5277:39: note: suggested alternative: ‘li’
constraints.push_back(lp.addCol());
^~
li
Graph/flow_manager/base_manager_flow_handler.cc:5278:46: error: request for member ‘back’ in ‘constraints’, which is of non-class type ‘int’
lp.colLowerBound(constraints.back(), 0);
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5279:46: error: request for member ‘back’ in ‘constraints’, which is of non-class type ‘int’
lp.colUpperBound(constraints.back(), ha->corrected_count);
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5280:17: error: ‘all_combos’ was not declared in this scope
all_combos += constraints.back();
^~~~~~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5280:43: error: request for member ‘back’ in ‘constraints’, which is of non-class type ‘int’
all_combos += constraints.back();
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5282:41: error: request for member ‘find’ in ‘constraint_map_plus’, which is of non-class type ‘int’
if (constraint_map_plus.find(std::make_pair(*li,*ri)) == constraint_map_plus.end()) {
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5282:95: error: request for member ‘end’ in ‘constraint_map_plus’, which is of non-class type ‘int’
if (constraint_map_plus.find(std::make_pair(*li,*ri)) == constraint_map_plus.end()) {
^~~
Graph/flow_manager/base_manager_flow_handler.cc:5283:40: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
constraint_map_plus[std::make_pair(*li,*ri)] = 0;
^
Graph/flow_manager/base_manager_flow_handler.cc:5285:42: error: request for member ‘find’ in ‘constraint_map_minus’, which is of non-class type ‘int’
if (constraint_map_minus.find(std::make_pair(*li,*ri)) == constraint_map_minus.end()) {
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5285:97: error: request for member ‘end’ in ‘constraint_map_minus’, which is of non-class type ‘int’
if (constraint_map_minus.find(std::make_pair(*li,*ri)) == constraint_map_minus.end()) {
^~~
Graph/flow_manager/base_manager_flow_handler.cc:5286:41: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
constraint_map_minus[std::make_pair(*li,*ri)] = bi_edges[std::make_pair(*li,*ri)];
^
Graph/flow_manager/base_manager_flow_handler.cc:5286:77: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
constraint_map_minus[std::make_pair(*li,*ri)] = bi_edges[std::make_pair(*li,*ri)];
^
Graph/flow_manager/base_manager_flow_handler.cc:5289:36: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
constraint_map_plus[std::make_pair(*li,*ri)] += constraints.back();
^
Graph/flow_manager/base_manager_flow_handler.cc:5289:77: error: request for member ‘back’ in ‘constraints’, which is of non-class type ‘int’
constraint_map_plus[std::make_pair(*li,*ri)] += constraints.back();
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5290:37: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
constraint_map_minus[std::make_pair(*li,*ri)] -= constraints.back();
^
Graph/flow_manager/base_manager_flow_handler.cc:5290:78: error: request for member ‘back’ in ‘constraints’, which is of non-class type ‘int’
constraint_map_minus[std::make_pair(*li,*ri)] -= constraints.back();
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5298:13: error: ‘lp’ was not declared in this scope
lp.addRow(all_combos == ha->corrected_count);
^~
Graph/flow_manager/base_manager_flow_handler.cc:5298:23: error: ‘all_combos’ was not declared in this scope
lp.addRow(all_combos == ha->corrected_count);
^~~~~~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5308:18: error: request for member ‘push_back’ in ‘opts’, which is of non-class type ‘int’
opts.push_back(lp.addCol());
^~~~~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5308:28: error: ‘lp’ was not declared in this scope
opts.push_back(lp.addCol());
^~
Graph/flow_manager/base_manager_flow_handler.cc:5308:28: note: suggested alternative: ‘lg’
opts.push_back(lp.addCol());
^~
lg
Graph/flow_manager/base_manager_flow_handler.cc:5309:28: error: request for member ‘back’ in ‘opts’, which is of non-class type ‘int’
lp.addRow(opts.back() >= constraint_map_plus[std::make_pair(lg, rg)] - bi_edges[std::make_pair(lg, rg)]);
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5309:57: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
lp.addRow(opts.back() >= constraint_map_plus[std::make_pair(lg, rg)] - bi_edges[std::make_pair(lg, rg)]);
^
Graph/flow_manager/base_manager_flow_handler.cc:5309:92: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
lp.addRow(opts.back() >= constraint_map_plus[std::make_pair(lg, rg)] - bi_edges[std::make_pair(lg, rg)]);
^
Graph/flow_manager/base_manager_flow_handler.cc:5310:28: error: request for member ‘back’ in ‘opts’, which is of non-class type ‘int’
lp.addRow(opts.back() >= constraint_map_minus[std::make_pair(lg, rg)]);
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5310:58: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
lp.addRow(opts.back() >= constraint_map_minus[std::make_pair(lg, rg)]);
^
Graph/flow_manager/base_manager_flow_handler.cc:5311:13: error: ‘optimize2’ was not declared in this scope
optimize2 += opts.back();
^~~~~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5311:31: error: request for member ‘back’ in ‘opts’, which is of non-class type ‘int’
optimize2 += opts.back();
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5316:5: error: ‘lp’ was not declared in this scope
lp.min();
^~
Graph/flow_manager/base_manager_flow_handler.cc:5317:12: error: ‘optimize2’ was not declared in this scope
lp.obj(optimize2);
^~~~~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5322:28: error: ‘Lp’ is not a class, namespace, or enumeration
if (lp.primalType() != Lp::OPTIMAL) {
^~
Graph/flow_manager/base_manager_flow_handler.cc:5344:8: error: expected ‘;’ before ‘lp2’
Lp lp2;
^~~
Graph/flow_manager/base_manager_flow_handler.cc:5345:45: error: type/value mismatch at argument 2 in template parameter list for ‘template<class _Key, class _Tp, class _Compare, class _Alloc> class std::map’
std::map<std::pair< int, int > , Lp::Col> bi_edges2;
^
Graph/flow_manager/base_manager_flow_handler.cc:5345:45: note: expected a type, got ‘Lp’
Graph/flow_manager/base_manager_flow_handler.cc:5345:45: error: template argument 4 is invalid
Graph/flow_manager/base_manager_flow_handler.cc:5346:23: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Alloc> class std::deque’
std::deque<Lp::Col> left_z2;
^
Graph/flow_manager/base_manager_flow_handler.cc:5346:23: note: expected a type, got ‘Lp’
Graph/flow_manager/base_manager_flow_handler.cc:5346:23: error: template argument 2 is invalid
Graph/flow_manager/base_manager_flow_handler.cc:5347:23: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Tp, class _Alloc> class std::deque’
std::deque<Lp::Col> right_z2;
^
Graph/flow_manager/base_manager_flow_handler.cc:5347:23: note: expected a type, got ‘Lp’
Graph/flow_manager/base_manager_flow_handler.cc:5347:23: error: template argument 2 is invalid
Graph/flow_manager/base_manager_flow_handler.cc:5348:5: error: ‘Lp’ is not a class, namespace, or enumeration
Lp::Expr optimize3;
^~
Graph/flow_manager/base_manager_flow_handler.cc:5354:19: error: request for member ‘insert’ in ‘bi_edges2’, which is of non-class type ‘int’
bi_edges2.insert(std::make_pair(std::make_pair(lg, rg), lp2.addCol()));
^~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5354:65: error: ‘lp2’ was not declared in this scope
bi_edges2.insert(std::make_pair(std::make_pair(lg, rg), lp2.addCol()));
^~~
Graph/flow_manager/base_manager_flow_handler.cc:5354:65: note: suggested alternative: ‘dup2’
bi_edges2.insert(std::make_pair(std::make_pair(lg, rg), lp2.addCol()));
^~~
dup2
Graph/flow_manager/base_manager_flow_handler.cc:5356:36: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
lp2.colLowerBound(bi_edges2[std::make_pair(lg, rg)], lp.primal(bi_edges[std::make_pair(lg, rg)]));
^
Graph/flow_manager/base_manager_flow_handler.cc:5356:80: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
lp2.colLowerBound(bi_edges2[std::make_pair(lg, rg)], lp.primal(bi_edges[std::make_pair(lg, rg)]));
^
Graph/flow_manager/base_manager_flow_handler.cc:5357:36: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
lp2.colUpperBound(bi_edges2[std::make_pair(lg, rg)], Lp::INF);
^
Graph/flow_manager/base_manager_flow_handler.cc:5357:62: error: ‘Lp’ is not a class, namespace, or enumeration
lp2.colUpperBound(bi_edges2[std::make_pair(lg, rg)], Lp::INF);
^~
Graph/flow_manager/base_manager_flow_handler.cc:5370:9: error: ‘Lp’ is not a class, namespace, or enumeration
Lp::Expr abs1, abs2;
^~
Graph/flow_manager/base_manager_flow_handler.cc:5371:9: error: ‘abs1’ was not declared in this scope
abs1 += group_cap;
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5371:9: note: suggested alternative: ‘abs’
abs1 += group_cap;
^~~~
abs
Graph/flow_manager/base_manager_flow_handler.cc:5375:30: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
abs1 -= bi_edges2[std::make_pair(lg, rg)];
^
Graph/flow_manager/base_manager_flow_handler.cc:5376:13: error: ‘abs2’ was not declared in this scope
abs2 += bi_edges2[std::make_pair(lg, rg)];
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5376:13: note: suggested alternative: ‘abs’
abs2 += bi_edges2[std::make_pair(lg, rg)];
^~~~
abs
Graph/flow_manager/base_manager_flow_handler.cc:5376:30: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
abs2 += bi_edges2[std::make_pair(lg, rg)];
^
Graph/flow_manager/base_manager_flow_handler.cc:5379:17: error: request for member ‘push_back’ in ‘left_z2’, which is of non-class type ‘int’
left_z2.push_back(lp2.addCol());
^~~~~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5379:27: error: ‘lp2’ was not declared in this scope
left_z2.push_back(lp2.addCol());
^~~
Graph/flow_manager/base_manager_flow_handler.cc:5379:27: note: suggested alternative: ‘dup2’
left_z2.push_back(lp2.addCol());
^~~
dup2
Graph/flow_manager/base_manager_flow_handler.cc:5380:28: error: request for member ‘back’ in ‘left_z2’, which is of non-class type ‘int’
lp2.addRow(left_z2.back() >= abs1);
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5381:21: error: ‘abs2’ was not declared in this scope
lp2.addRow( abs2 <= group_cap);
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5381:21: note: suggested alternative: ‘abs’
lp2.addRow( abs2 <= group_cap);
^~~~
abs
Graph/flow_manager/base_manager_flow_handler.cc:5382:9: error: ‘optimize3’ was not declared in this scope
optimize3 += left_z2.back();
^~~~~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5382:30: error: request for member ‘back’ in ‘left_z2’, which is of non-class type ‘int’
optimize3 += left_z2.back();
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5394:9: error: ‘Lp’ is not a class, namespace, or enumeration
Lp::Expr abs1, abs2;
^~
Graph/flow_manager/base_manager_flow_handler.cc:5395:9: error: ‘abs1’ was not declared in this scope
abs1 += group_cap;
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5395:9: note: suggested alternative: ‘abs’
abs1 += group_cap;
^~~~
abs
Graph/flow_manager/base_manager_flow_handler.cc:5399:30: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
abs1 -= bi_edges2[std::make_pair(lg, rg)];
^
Graph/flow_manager/base_manager_flow_handler.cc:5400:13: error: ‘abs2’ was not declared in this scope
abs2 += bi_edges2[std::make_pair(lg, rg)];
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5400:13: note: suggested alternative: ‘abs’
abs2 += bi_edges2[std::make_pair(lg, rg)];
^~~~
abs
Graph/flow_manager/base_manager_flow_handler.cc:5400:30: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
abs2 += bi_edges2[std::make_pair(lg, rg)];
^
Graph/flow_manager/base_manager_flow_handler.cc:5403:17: error: request for member ‘push_back’ in ‘left_z2’, which is of non-class type ‘int’
left_z2.push_back(lp2.addCol());
^~~~~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5403:27: error: ‘lp2’ was not declared in this scope
left_z2.push_back(lp2.addCol());
^~~
Graph/flow_manager/base_manager_flow_handler.cc:5403:27: note: suggested alternative: ‘dup2’
left_z2.push_back(lp2.addCol());
^~~
dup2
Graph/flow_manager/base_manager_flow_handler.cc:5404:28: error: request for member ‘back’ in ‘left_z2’, which is of non-class type ‘int’
lp2.addRow(left_z2.back() >= abs1);
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5405:21: error: ‘abs2’ was not declared in this scope
lp2.addRow( abs2 <= group_cap);
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5405:21: note: suggested alternative: ‘abs’
lp2.addRow( abs2 <= group_cap);
^~~~
abs
Graph/flow_manager/base_manager_flow_handler.cc:5406:9: error: ‘optimize3’ was not declared in this scope
optimize3 += left_z2.back();
^~~~~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5406:30: error: request for member ‘back’ in ‘left_z2’, which is of non-class type ‘int’
optimize3 += left_z2.back();
^~~~
Graph/flow_manager/base_manager_flow_handler.cc:5410:5: error: ‘lp2’ was not declared in this scope
lp2.min();
^~~
Graph/flow_manager/base_manager_flow_handler.cc:5410:5: note: suggested alternative: ‘dup2’
lp2.min();
^~~
dup2
Graph/flow_manager/base_manager_flow_handler.cc:5411:13: error: ‘optimize3’ was not declared in this scope
lp2.obj(optimize3);
^~~~~~~~~
Graph/flow_manager/base_manager_flow_handler.cc:5416:29: error: ‘Lp’ is not a class, namespace, or enumeration
if (lp2.primalType() != Lp::OPTIMAL) {
^~
Graph/flow_manager/base_manager_flow_handler.cc:5435:43: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::pair<int, int>’)
ggi->second = lp2.primal(bi_edges2[std::make_pair(lg, rg)]) + 0.001;
^
make[1]: *** [Makefile:737: Graph/flow_manager/base_manager_flow_handler.o] Error 1
make[1]: Leaving directory '/scr/epi/tools/ryuto/version/source/src'
make: *** [Makefile:356: all-recursive] Error 1
TGatter commented
I was able to recreate the compile problem on a fresh virtual machine of CentOS 7.
Autoconf worked out of the box for me, however, so you might have a problem with file rights or your local autoconf configuration.
The main problem are gcc and glibc. As RYUTO needs C11, compiling requires gcc 4.7 and glibc 3.4.20 as mininum requirements. Both are not available for CentOS 7.
It does seem that your SCL installation did fix this, as we see another error. Namely an external library is not resolved. Please make sure that you point the configure file of RYUTO to the correct positions. you called ./configure --prefix=/scr/epi/tools/ryuto/version/binary --with-htslib=/scr/epi/tools/htslib/1.9/binary --with-clp=/scr/epi/tools/clp/1.16.11/binary --with-lemon=/scr/epi/tools/lemon/version/binary
- The '--prefix' prefix should not be necessary.
- --with-htslib should point to the directory defined with --prefix=DIR in the configure call of HTSlib
- --with-clp points to the directory defined with --prefix=DIR in the configure call of CLP
- --with-lemon points to the -DCMAKE_INSTALL_PREFIX=DIR defined in the cmake call of Lemon
Please also see if you executed all 'make install' calls correctly.
ALTERNATIVELY:
If you have actually fixed the glibc at it's standard url, the Fedora 27 binary should run fine for you.
I installed gcc 7.3 manually like here: http://xgenecode.com/wp/2017/11/27/install-latest-gcc-7-3-ubuntucentosrehl-linux/
Afterwards I copied the glibc library over to its standard location, i.e. : sudo cp /usr/local/lib64/libstdc++.* /usr/lib64/
I will see and try, if I can compile a completely static binary for CentOS users in future.
bio15anu commented
Hmmm, so the default gcc version on our system is 4.8.5 but it does seem that the glibc version is only 2.17? As far as I can tell, the SCL updated these to meet the requirements but they are not in standard locations. They follow this kind of architecture: /opt/rh/devtoolset-7/root/usr/bin/gcc
As far as I can tell the following libraries were all installed correctly (zlib and boost are already on the system):
[adam@epi source]$ ls /scr/epi/tools/{htslib,clp,lemon}/*/binary
/scr/epi/tools/clp/1.16.11/binary:
bin include lib share
/scr/epi/tools/htslib/1.9/binary:
bin include lib share
/scr/epi/tools/lemon/version/binary:
bin include lib share
Should I recompile the dependencies with devtoolset-7 active before installing RYUTO?
If I run ./reset_autogen it doesn't link the compile file correctly, but if I run the individual steps replacing eg. aclocal (v1.13) with aclocal-1.15 then it seems to be fine. Then I pass the LDFLAGS="-L/opt/rh/devtoolset-7/root/usr/lib" option to the ./configure script. It seems I get all the same errors as before though.
bio15anu commented
I am hesitant to replace system gcc and glibc libraries with versions that are not directly supported by the CentOS package manager, mainly as I'm concerned about issues with the other software installations on the server
TGatter commented
I can relate to your hesitation. It is somewhat of a dilemma.
I will leave another warning for other reading this: I remembered that if you had the libraries unpacked in the ryuto subfolder, ./reset_autogen.sh could also have broken stuff. i.e. causing make to try to build these files as well.
However, the solution is easier. I pre-compiled a binary that is static linked for all but the system libraries: binary
I tested it thoroughly on a virgin vanilla CenOS 7 without making any changes or installing anything. It worked perfectly on my testing datasets.
I hope this will solve your problem.
bio15anu commented
Awesome! Seems to work for me. Thanks a lot for taking the time to do that and for responding so quickly.