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  • cufflinks 2.0.0 source missing a header?

    Has anyone had success installing the latest cufflinks (2.0.0 beta) from source? It seems like a required local header file "rounding.h" is not included in the source distribution. I have emailed their support email about this, but I just wanted to double check that I am not the only one having this issue. Thanks!

    Code:
    g++44 -DHAVE_CONFIG_H -I. -I..  -I../src  -I/usr/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -m64 -march=nocona -O3  -DNDEBUG  -pthread -I/hive/groups/genomeAssem/include -I/hive/groups/genomeAssem/src/samtools_svn/include -I/hive/groups/genomeAssem/include -MT abundances.o -MD -MP -MF .deps/abundances.Tpo -c -o abundances.o abundances.cpp
    abundances.cpp:38:22: error: rounding.h: No such file or directory
    The reason I think that it is a local file rather than something my system is missing is that it is included right in the middle of a block of other locally included header files, and the include statement uses the double quote syntax rather than the <> syntax. Thanks!

  • #2
    Er..I didn't know there was a 2.0. I thought they were working on 1.4 still.
    /* Shawn Driscoll, Gene Expression Laboratory, Pfaff
    Salk Institute for Biological Studies, La Jolla, CA, USA */

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    • #3
      There is a 2.0 version as of yesterday.

      Comment


      • #4
        Hi Kopi-o,
        Did you figure out the installation problem yet? I am having another problem with the Eigen libray. I downloaded and copied the eigen-eigen-b23437e61a07/Eigen to a directory in my PATH and gave --with-eigen arguments while configuring. But the configure log still says could not find eigen libraries. Any idea?

        Thanks

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        • #5
          Hi segmagician,
          Thanks for the tip. If possible, can you please provide the round.h? I am also having problem with that.
          Thanks.

          Comment


          • #6
            I corresponded with Cole earlier today about problems with the original tar file.

            He has kindly provided a new source tar ball that fixed problems we were noticing. Get the latest source from the download link.

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            • #7
              Yes... I just noticed that... the source file has been updated.

              Comment


              • #8
                Hi,
                I stills can not install Cufflinks. My make is successful but when I try to execute the cufflinks executable it gives me the following error:

                error while loading shared libraries: libboost_thread.so.1.48.0: cannot open shared object file: No such file or directory

                I tried installing with boost 1.49 but got the same error. Any idea?

                Thanks.

                Comment


                • #9
                  Try appending the LD_LIBRARY_PATH as described here.

                  Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc



                  Originally posted by vinay052003 View Post
                  Hi,
                  I stills can not install Cufflinks. My make is successful but when I try to execute the cufflinks executable it gives me the following error:

                  error while loading shared libraries: libboost_thread.so.1.48.0: cannot open shared object file: No such file or directory

                  I tried installing with boost 1.49 but got the same error. Any idea?

                  Thanks.

                  Comment


                  • #10
                    Thank GenoMax..
                    for some reason I can't find libboost_thread.so.1.48.0 on my system. My boost installation was successful though. I noticed that /my_boost_install_dir/lib is empty. Is this the place where libboost_thread.so.1.48.0 supposed to be?

                    Comment


                    • #11
                      The file (libboost_thread.so.1.*) should be in the "lib" directory. Perhaps your boost installation did not work right.

                      Originally posted by vinay052003 View Post
                      Thank GenoMax..
                      for some reason I can't find libboost_thread.so.1.48.0 on my system. My boost installation was successful though. I noticed that /my_boost_install_dir/lib is empty. Is this the place where libboost_thread.so.1.48.0 supposed to be?

                      Comment

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