Tophat installation errors

[metheuse]

Hi, this is my first time installing Tophat. I followed the instructions on the manual page, but after I ran "make", I got the error message as below. Does anyone know what "undefined reference to 'clock_gettime'" means?
The boost and samtools installation went smoothly and they were installed under /usr/local/

make  all-recursive
make[1]: Entering directory `/mnt/galaxy_tools_external/tophat-2.0.8'
Making all in src
make[2]: Entering directory `/mnt/galaxy_tools_external/tophat-2.0.8/src'
g++  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3  -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -I./SeqAn-1.3   -o segment_juncs  -L/usr/local/lib -L/usr/local/lib segment_juncs.o ../src/libtophat.a -lboost_thread -lboost_system -lbam -lz 
/usr/local/lib/libboost_thread.a(thread.o): In function `boost::this_thread::hiden::sleep_until(timespec const&)':
thread.cpp: (.text+0x1a73): undefined reference to `clock_gettime'
thread.cpp: (.text+0x1ae8): undefined reference to `clock_gettime'
thread.cpp: (.text+0x1b4f): undefined reference to `clock_gettime'
thread.cpp: (.text+0x1bb6): undefined reference to `clock_gettime'
thread.cpp: (.text+0x1c1d): undefined reference to `clock_gettime'
/usr/local/lib/libboost_thread.a(thread.o):thread.cpp: (.text+0x1c84): more undefined references to `clock_gettime' follow
collect2: ld returned 1 exit status
make[2]: *** [segment_juncs] Error 1
make[2]: Leaving directory `/mnt/galaxy_tools_external/tophat-2.0.8/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/mnt/galaxy_tools_external/tophat-2.0.8'
make: *** [all] Error 2

[GenoMax]

The boost and samtools installation went smoothly and they were installed under /usr/local/

Have you confirmed that the boost library files are indeed installed in /usr/local/lib?

Did you provide ".configure" command for TopHat with appropriate "--with-boost=/usr/local" directive?

[metheuse]

Have you confirmed that the boost library files are indeed installed in /usr/local/lib?

Did you provide ".configure" command for TopHat with appropriate "--with-boost=/usr/local" directive?

Yes to both.

$ ls /usr/local/lib
libbam.a              libboost_exception.a   libboost_math_c99f.a  libboost_prg_exec_monitor.a  libboost_signals.a            libboost_unit_test_framework.a
libboost_atomic.a     libboost_filesystem.a  libboost_math_c99l.a  libboost_program_options.a   libboost_system.a             libboost_wave.a
libboost_chrono.a     libboost_graph.a       libboost_math_tr1.a   libboost_random.a            libboost_test_exec_monitor.a  libboost_wserialization.a
libboost_context.a    libboost_locale.a      libboost_math_tr1f.a  libboost_regex.a             libboost_thread.a
libboost_date_time.a  libboost_math_c99.a    libboost_math_tr1l.a  libboost_serialization.a     libboost_timer.a

[Richard Finney]

Try this

Append a " -lrt" after
g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -I./SeqAn-1.3 -o segment_juncs -L/usr/local/lib -L/usr/local/lib segment_juncs.o ../src/libtophat.a -lboost_thread -lboost_system -lbam -lz

i.e ".... -lz -lrt"

Wherever the -lz is in the Makefile just append " -lrt", that's '[singlespace]-lrt" using your favorite editor (vim, emacs, whatev).

[GenoMax]

Is this an Ubuntu system?

Do you have "librt.a" in one of the "lib" directories?

See this thread for some info: http://stackoverflow.com/questions/8...or-g-in-ubuntu

[metheuse]

Try this

Append a " -lrt" after
g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -I./SeqAn-1.3 -o segment_juncs -L/usr/local/lib -L/usr/local/lib segment_juncs.o ../src/libtophat.a -lboost_thread -lboost_system -lbam -lz

i.e ".... -lz -lrt"

Wherever the -lz is in the Makefile just append " -lrt", that's '[singlespace]-lrt" using your favorite editor (vim, emacs, whatev).

Thanks so much Richard! This works!

[metheuse]

Is this an Ubuntu system?

Do you have "librt.a" in one of the "lib" directories?

See this thread for some info: http://stackoverflow.com/questions/8...or-g-in-ubuntu

Mine is redhat. But still thanks.

[ercfrtz]

I am getting this error trying to install tophat-2.0.8. I installed boost and samtools like it said and used the following configure command:

./configure --prefix=/shared/local/tophat-2.0.8/ --with-boost=/shared/local/boost_1_53_0/ --with-bam=/shared/local/samtools-0.1.18/

And I get the following output at the end of that command:

-- tophat 2.0.8 Configuration Results --
  C++ compiler:        g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3  -DNDEBUG -pthread -I/shared/local/boost_1_53_0//include -I/shared/local/samtools-0.1.18//include -I./SeqAn-1.3
  Linker flags:        
  GCC version:         gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
  Host System type:    x86_64-unknown-linux-gnu
  Install prefix:      /shared/local/tophat-2.0.8/
  Install eprefix:     ${prefix}

  See config.h for further configuration information.
  Email <[email protected], [email protected]> with questions and bug reports.

But when I look in the Makefile, I cannot find the line that was said to add " -lrt" to and when ran as default I get the following error info:

make  all-recursive
make[1]: Entering directory `/shared/local/tophat-2.0.8'
Making all in src
make[2]: Entering directory `/shared/local/tophat-2.0.8/src'
if g++ -DHAVE_CONFIG_H -I. -I. -I..     -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3  -DNDEBUG -pthread -I/shared/local/boost_1_53_0//include -I/shared/local/samtools-0.1.18//include -I./SeqAn-1.3 -MT reads.o -MD -MP -MF ".deps/reads.Tpo" -c -o reads.o reads.cpp; \
        then mv -f ".deps/reads.Tpo" ".deps/reads.Po"; else rm -f ".deps/reads.Tpo"; exit 1; fi
common.h: In member function ‘int32_t GBamWriter::get_tid(const char*)’:
common.h:508: error: ‘bam_get_tid’ was not declared in this scope
common.h: In member function ‘void GBamWriter::flush()’:
common.h:622: error: ‘bgzf_flush’ was not declared in this scope
make[2]: *** [reads.o] Error 1
make[2]: Leaving directory `/shared/local/tophat-2.0.8/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/shared/local/tophat-2.0.8'
make: *** [all] Error 2

Any help is appreciated as the pre-built tophat does not run on our server either.

[Word4Word]

I had this problem as well, and appending -lrt to -lz within the makefile did not work. However, when I ran

./configure LIBS=-lrt

and then tried make, it all worked fine. Maybe that will work for you.

[ercfrtz]

I tried adding that to my configure command and it looks like it changed the Error from 2 to 1. Now I'm getting the following:

Making install in src
make[1]: Entering directory `/shared/local/tophat-2.0.8/src'
if g++ -DHAVE_CONFIG_H -I. -I. -I..     -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3  -DNDEBUG -pthread -I/shared/local/boost_1_53_0//include -I/shared/local/samtools-0.1.18//include -I./SeqAn-1.3 -MT reads.o -MD -MP -MF ".deps/reads.Tpo" -c -o reads.o reads.cpp; \
        then mv -f ".deps/reads.Tpo" ".deps/reads.Po"; else rm -f ".deps/reads.Tpo"; exit 1; fi
common.h: In member function ‘int32_t GBamWriter::get_tid(const char*)’:
common.h:508: error: ‘bam_get_tid’ was not declared in this scope
common.h: In member function ‘void GBamWriter::flush()’:
common.h:622: error: ‘bgzf_flush’ was not declared in this scope
make[1]: *** [reads.o] Error 1
make[1]: Leaving directory `/shared/local/tophat-2.0.8/src'
make: *** [install-recursive] Error 1

[GenoMax]

I tried adding that to my configure command and it looks like it changed the Error from 2 to 1. Now I'm getting the following:

Making install in src
make[1]: Entering directory `/shared/local/tophat-2.0.8/src'
if g++ -DHAVE_CONFIG_H -I. -I. -I..     -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3  -DNDEBUG -pthread -I/shared/local/boost_1_53_0//include -I/shared/local/samtools-0.1.18//include -I./SeqAn-1.3 -MT reads.o -MD -MP -MF ".deps/reads.Tpo" -c -o reads.o reads.cpp; \
        then mv -f ".deps/reads.Tpo" ".deps/reads.Po"; else rm -f ".deps/reads.Tpo"; exit 1; fi
common.h: In member function ‘int32_t GBamWriter::get_tid(const char*)’:
common.h:508: error: ‘bam_get_tid’ was not declared in this scope
common.h: In member function ‘void GBamWriter::flush()’:
common.h:622: error: ‘bgzf_flush’ was not declared in this scope
make[1]: *** [reads.o] Error 1
make[1]: Leaving directory `/shared/local/tophat-2.0.8/src'
make: *** [install-recursive] Error 1

Are you using RHEL v.4.x? Did you build your own boost libraries?