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Old 11-13-2010, 04:32 AM   #1
masylichu
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Default an error when using cufflinks

hi.
i have installed samtools and boost librarires.
after that, i download the cufflinks source code because my linux is 32-bit.

Everything went fine. However, when I tested using cufflinks test_data.sam, the following error message appears.

cufflinks: error while loading shared libraries: libboost_thread.so.1.44.0: cann
ot open shared object file: No such file or directory

It seems that cufflinks is not seeing the shared object file. However, when I ran the configure, it said as the following:
checking whether the Boost::Thread library is available... yes

Can anyone help me solve this problem?
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Old 12-13-2010, 03:27 AM   #2
Sparx
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I have the same problem.
Did anyone manage to get this fixed?

Or explain what the problem is?

Last edited by Sparx; 12-15-2010 at 02:54 AM.
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Old 12-17-2010, 01:20 PM   #3
polyatail
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Hi,

What Linux are you running? I would start by checking the libraries cufflinks is compiled to require by running:

Code:
ldd /path/to/cufflinks
And the location of the installed boost libraries with:

Code:
ldconfig -p | grep boost
Post the output of those if you can.


Andrew

Last edited by polyatail; 12-17-2010 at 01:29 PM. Reason: better params to run as non-root
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Old 12-18-2010, 11:11 AM   #4
Sparx
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Thanks for the response.

Quote:
What Linux are you running?
Code:
$ cat /proc/version 
Linux version 2.6.18-128.7.1.el5.pdc5noib (gcc version 4.1.2 20080704 (Red Hat 4.1.2-44))
My setup is a homefolder on afs and I'm trying to run cufflinks on a cluster.


Quote:
I would start by checking the libraries cufflinks is compiled to require by running:
I actually tried to make a local install of boost in $HOME/boost/ and compile cufflinks with the --with-boost and --with-bam flags.
However it does'nt seem to reflect that in the output of the commands.

Code:
$ ldd Data/cufflinks-0.9.3.save/bin/cufflinks 
	libboost_thread.so.1.45.0 => not found
	libz.so.1 => /usr/lib64/libz.so.1 (0x00000039f4600000)
	libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00000039f7200000)
	libm.so.6 => /lib64/libm.so.6 (0x00000039f3600000)
	libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000039f4e00000)
	libpthread.so.0 => /lib64/libpthread.so.0 (0x00000039f3a00000)
	libc.so.6 => /lib64/libc.so.6 (0x00000039f2e00000)
	/lib64/ld-linux-x86-64.so.2 (0x00000039f2a00000)
Code:
$ /sbin/ldconfig -p | grep boost
	libboost_wserialization.so.2 (libc6,x86-64) => /usr/lib64/libboost_wserialization.so.2
	libboost_wserialization.so (libc6,x86-64) => /usr/lib64/libboost_wserialization.so
	libboost_unit_test_framework.so.2 (libc6,x86-64) => /usr/lib64/libboost_unit_test_framework.so.2
	libboost_unit_test_framework.so (libc6,x86-64) => /usr/lib64/libboost_unit_test_framework.so
	libboost_thread.so.2 (libc6,x86-64) => /usr/lib64/libboost_thread.so.2
	libboost_thread.so (libc6,x86-64) => /usr/lib64/libboost_thread.so
	libboost_test_exec_monitor.so.2 (libc6,x86-64) => /usr/lib64/libboost_test_exec_monitor.so.2
	libboost_test_exec_monitor.so (libc6,x86-64) => /usr/lib64/libboost_test_exec_monitor.so
	libboost_signals.so.2 (libc6,x86-64) => /usr/lib64/libboost_signals.so.2
	libboost_signals.so (libc6,x86-64) => /usr/lib64/libboost_signals.so
	libboost_serialization.so.2 (libc6,x86-64) => /usr/lib64/libboost_serialization.so.2
	libboost_serialization.so (libc6,x86-64) => /usr/lib64/libboost_serialization.so
	libboost_regex.so.2 (libc6,x86-64) => /usr/lib64/libboost_regex.so.2
	libboost_regex.so (libc6,x86-64) => /usr/lib64/libboost_regex.so
	libboost_python.so.2 (libc6,x86-64) => /usr/lib64/libboost_python.so.2
	libboost_python.so (libc6,x86-64) => /usr/lib64/libboost_python.so
	libboost_program_options.so.2 (libc6,x86-64) => /usr/lib64/libboost_program_options.so.2
	libboost_program_options.so (libc6,x86-64) => /usr/lib64/libboost_program_options.so
	libboost_prg_exec_monitor.so.2 (libc6,x86-64) => /usr/lib64/libboost_prg_exec_monitor.so.2
	libboost_prg_exec_monitor.so (libc6,x86-64) => /usr/lib64/libboost_prg_exec_monitor.so
	libboost_iostreams.so.2 (libc6,x86-64) => /usr/lib64/libboost_iostreams.so.2
	libboost_iostreams.so (libc6,x86-64) => /usr/lib64/libboost_iostreams.so
	libboost_filesystem.so.2 (libc6,x86-64) => /usr/lib64/libboost_filesystem.so.2
	libboost_filesystem.so (libc6,x86-64) => /usr/lib64/libboost_filesystem.so
	libboost_date_time.so.2 (libc6,x86-64) => /usr/lib64/libboost_date_time.so.2
	libboost_date_time.so (libc6,x86-64) => /usr/lib64/libboost_date_time.so
Thanks for the help.
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Old 12-18-2010, 04:15 PM   #5
polyatail
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If you want to use your local installation of boost, I would try:

Code:
env LD_LIBRARY_PATH=/path/to/boost /path/to/cufflinks
This should tell the loader to look for the library in your home directory before the rest of the system.

You might also try installing the libboost-devel RPM and recompiling cufflinks with that.


Andrew
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