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  • cufflinks source install error

    I am having problems with a source install of cufflinks: Seems to be Boost related, but, configure does not show error

    Using Boost 1.48.0 and Cufflinks 1.3.0.

    Here are the relevant lines from configure
    Code:
    checking for boostlib >= 1.38.0... yes
    checking for bamlib... yes
    checking build system type... x86_64-unknown-linux-gnu
    checking whether the Boost::Thread library is available... yes
    ...
    -- cufflinks 1.3.0 Configuration Results --
      C++ compiler:        g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3  -DNDEBUG  -pthread -I/home/matthew/local/include/boost-1_48 -I/usr/local/include 
      GCC version:         gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1
      Host System type:    x86_64-unknown-linux-gnu
      Install prefix:      /home/matthew/software
      Install eprefix:     ${prefix}
    when making, however, I get errors

    Code:
    matthew@macmanes:~/cufflinks-1.3.0$ make
    make  all-recursive
    make[1]: Entering directory `/home/matthew/cufflinks-1.3.0'
    Making all in src
    make[2]: Entering directory `/home/matthew/cufflinks-1.3.0/src'
    if g++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src  -I/usr/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3  -DNDEBUG  -pthread -I/home/matthew/local/include/boost-1_48 -I/usr/local/include -MT clustering.o -MD -MP -MF ".deps/clustering.Tpo" -c -o clustering.o clustering.cpp; \
    	then mv -f ".deps/clustering.Tpo" ".deps/clustering.Po"; else rm -f ".deps/clustering.Tpo"; exit 1; fi
    In file included from abundances.h:22:0,
                     from clustering.h:38,
                     from clustering.cpp:10:
    bundles.h: In constructor ‘BundleFactory::BundleFactory(boost::shared_ptr<HitFactory>, BundleMode)’:
    bundles.h:363:9: warning: ‘BundleFactory::_curr_bundle’ will be initialized after [-Wreorder]
    bundles.h:209:39: warning:   ‘boost::random::uniform_01<boost::random::mersenne_twister_engine<unsigned int, 32ul, 624ul, 397ul, 31ul, 2567483615u, 11ul, 4294967295u, 7ul, 2636928640u, 15ul, 4022730752u, 18ul, 1812433253u> > BundleFactory::_zeroone’ [-Wreorder]
    bundles.h:213:2: warning:   when initialized here [-Wreorder]
    In file included from clustering.h:38:0,
                     from clustering.cpp:10:
    abundances.h: In constructor ‘AbundanceGroup::AbundanceGroup(const std::vector<boost::shared_ptr<Abundance> >&)’:
    abundances.h:448:27: warning: ‘AbundanceGroup::_iterated_exp_count_covariance’ will be initialized after [-Wreorder]
    abundances.h:443:27: warning:   ‘boost::numeric::ublas::matrix<double> AbundanceGroup::_count_covariance’ [-Wreorder]
    abundances.h:302:2: warning:   when initialized here [-Wreorder]
    if g++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src  -I/usr/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3  -DNDEBUG  -pthread -I/home/matthew/local/include/boost-1_48 -I/usr/local/include -MT differential.o -MD -MP -MF ".deps/differential.Tpo" -c -o differential.o differential.cpp; \
    	then mv -f ".deps/differential.Tpo" ".deps/differential.Po"; else rm -f ".deps/differential.Tpo"; exit 1; fi
    In file included from abundances.h:22:0,
                     from differential.cpp:17:
    bundles.h: In constructor ‘BundleFactory::BundleFactory(boost::shared_ptr<HitFactory>, BundleMode)’:
    bundles.h:363:9: warning: ‘BundleFactory::_curr_bundle’ will be initialized after [-Wreorder]
    bundles.h:209:39: warning:   ‘boost::random::uniform_01<boost::random::mersenne_twister_engine<unsigned int, 32ul, 624ul, 397ul, 31ul, 2567483615u, 11ul, 4294967295u, 7ul, 2636928640u, 15ul, 4022730752u, 18ul, 1812433253u> > BundleFactory::_zeroone’ [-Wreorder]
    bundles.h:213:2: warning:   when initialized here [-Wreorder]
    In file included from differential.cpp:17:0:
    abundances.h: In constructor ‘AbundanceGroup::AbundanceGroup(const std::vector<boost::shared_ptr<Abundance> >&)’:
    abundances.h:448:27: warning: ‘AbundanceGroup::_iterated_exp_count_covariance’ will be initialized after [-Wreorder]
    abundances.h:443:27: warning:   ‘boost::numeric::ublas::matrix<double> AbundanceGroup::_count_covariance’ [-Wreorder]
    abundances.h:302:2: warning:   when initialized here [-Wreorder]
    In file included from hits.h:21:0,
                     from abundances.h:20,
                     from differential.cpp:17:
    common.h: At global scope:
    common.h:25:25: error: ‘boost::BOOST_FOREACH’ has not been declared
    In file included from differential.h:29:0,
                     from differential.cpp:18:
    replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&)’:
    replicates.h:141:50: warning: unused variable ‘s2’ [-Wunused-variable]
    differential.cpp: In member function ‘void TestLauncher::perform_testing(std::vector<boost::shared_ptr<SampleAbundances> >&)’:
    differential.cpp:112:31: warning: unused variable ‘s2’ [-Wunused-variable]
    differential.cpp: In function ‘void sample_abundance_worker(const string&, SampleAbundances&, HitBundle*, bool, bool)’:
    differential.cpp:1073:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    make[2]: *** [differential.o] Error 1
    make[2]: Leaving directory `/home/matthew/cufflinks-1.3.0/src'
    make[1]: *** [all-recursive] Error 1
    make[1]: Leaving directory `/home/matthew/cufflinks-1.3.0'
    Any ideas about this?

  • #2
    foreach fix

    The error is caused by the re-define of foreach in common.h:

    #define foreach BOOST_FOREACH

    You can run a bash script to change all the foreach to for_each as:

    for x in *.cpp *.h; do sed 's/foreach/for_each/' $x > x; mv x $x; done

    and manually change back the #include <boost/foreach.hpp> in common.h.

    Comment


    • #3
      Ah, thanks. Should have updated the thread-- also can get around this issue by using a different version of Boost, as the error seems to be specific to Boost 1.48.0.

      Comment


      • #4
        error: invalid conversion from ‘const char*’ to ‘char*’

        Dear All,

        I want to use cufflinks to analyze RNA-seq Data. Therefore I first installed Boost_1_48_0.tar.gz and built it with this code:

        tar -zxf boost_1_48_0.tar.gz
        cd boost_1_48_0
        ./bootstrap.sh
        ./b2
        ./bjam --prefix-/home/lisanne/Downloads/boost toolset=gcc link=static runtime-link=static stage install

        It seems like the correct way for building. After the installation of boots, i installed cufflinks and buit it with this code:

        tar -zxf cufflinks-0.7.0.tar.gz
        cd cufflinks-0.7.0
        ./configure --with-boost=/home/lisanne/Downloads/boost
        make

        The last "make" command gives the following error:

        make all-recursive
        make[1]: Entering directory `/home/lisanne/Downloads/cufflinks-0.7.0'
        Making all in src
        make[2]: Entering directory `/home/lisanne/Downloads/cufflinks-0.7.0/src'
        g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wall -Wno-strict-aliasing -g -gdwarf-2 -m64 -O3 -DNDEBUG -pthread -I/home/lisanne/Downloads/boost/include -MT common.o -MD -MP -MF .deps/common.Tpo -c -o common.o common.cpp
        mv -f .deps/common.Tpo .deps/common.Po
        g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wall -Wno-strict-aliasing -g -gdwarf-2 -m64 -O3 -DNDEBUG -pthread -I/home/lisanne/Downloads/boost/include -MT assemble.o -MD -MP -MF .deps/assemble.Tpo -c -o assemble.o assemble.cpp
        assemble.cpp:37:41: fatal error: boost/vector_property_map.hpp: No such file or directory
        compilation terminated.
        make[2]: *** [assemble.o] Error 1
        make[2]: Leaving directory `/home/lisanne/Downloads/cufflinks-0.7.0/src'
        make[1]: *** [all-recursive] Error 1
        make[1]: Leaving directory `/home/lisanne/Downloads/cufflinks-0.7.0'
        make: *** [all] Error 2

        The file vector_property_map.hpp is not is the map boost, but in the map property_map. I changed the file assemble.cpp on line 37 from the boost/vector_property_map.hpp to boost/property_map.hpp. That solve this error, but by running the command again, there is another error in the file hits.cpp that i don't understand.

        make all-recursive
        make[1]: Entering directory `/home/lisanne/Downloads/cufflinks-0.7.0'
        Making all in src
        make[2]: Entering directory `/home/lisanne/Downloads/cufflinks-0.7.0/src'
        g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wall -Wno-strict-aliasing -g -gdwarf-2 -m64 -O3 -DNDEBUG -pthread -I/home/lisanne/Downloads/boost/include -MT hits.o -MD -MP -MF .deps/hits.Tpo -c -o hits.o hits.cpp
        hits.cpp: In member function ‘virtual bool SAMHitFactory::get_hit_from_buf(const char*, ReadHit&, bool, char*, char*)’:
        hits.cpp:262:32: error: invalid conversion from ‘const char*’ to ‘char*’
        hits.cpp:270:33: error: invalid conversion from ‘const char*’ to ‘char*’
        make[2]: *** [hits.o] Error 1
        make[2]: Leaving directory `/home/lisanne/Downloads/cufflinks-0.7.0/src'
        make[1]: *** [all-recursive] Error 1
        make[1]: Leaving directory `/home/lisanne/Downloads/cufflinks-0.7.0'
        make: *** [all] Error 2

        and this is the code in the hits.cpp file where it is all about:

        // Copy the tag out of the name field before we might wipe it out
        char* pipe = strrchr(name, '|');
        if (pipe)
        {
        if (name_tags)
        strcpy(name_tags, pipe);
        *pipe = 0;
        }
        // Stripping the slash and number following it gives the insert name
        char* slash = strrchr(name, '/');
        if (strip_slash && slash)
        *slash = 0;

        Can anyone help me with this kind of error? Many thanks!

        Comment


        • #5
          Can I ask why you are using such an old version of Cufflinks? Using a more recent version might solve your issue alone-- I will tell you however, then Boost 1.48.0 may be problematic

          See https://svn.boost.org/trac/boost/ticket/6131

          Comment


          • #6
            You are right peromhc, it is an very old version. I don't see that when i downloaded cufflinks. By downloading cufflinks 1.3 I create the same error as you before. How did you solve that?

            Thanks!

            Comment


            • #7
              try another version of boost-- for instance Boost 1.45.0

              Comment


              • #8
                Thanks peromhc, I downloaded boost-1.44.0 and that works for me!

                Comment


                • #9
                  Originally posted by lib View Post
                  The error is caused by the re-define of foreach in common.h:

                  #define foreach BOOST_FOREACH

                  You can run a bash script to change all the foreach to for_each as:

                  for x in *.cpp *.h; do sed 's/foreach/for_each/' $x > x; mv x $x; done

                  and manually change back the #include <boost/foreach.hpp> in common.h.

                  I did this but there happens to be one more error:

                  Code:
                  make  all-recursive
                  make[1]: Entering directory `/media/sda8/bharat/genomes/cufflinks-2.0.2'
                  Making all in src
                  make[2]: Entering directory `/media/sda8/bharat/genomes/cufflinks-2.0.2/src'
                  g++  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -m64 -O3  -DNDEBUG  -pthread -I/usr/local/include -I/usr/local/include    -o cufflinks  -L/usr/local/lib -L/usr/local/lib  cufflinks.o libcufflinks.a libgc.a -lboost_thread -lbam  -lz
                  cufflinks.o: In function `thread_exception':
                  /usr/local/include/boost/thread/exceptions.hpp:49: undefined reference to `boost::system::system_category()'
                  cufflinks.o: In function `__static_initialization_and_destruction_0':
                  /usr/local/include/boost/system/error_code.hpp:214: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:215: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:216: undefined reference to `boost::system::system_category()'
                  libcufflinks.a(bundles.o): In function `thread_exception':
                  /usr/local/include/boost/thread/exceptions.hpp:49: undefined reference to `boost::system::system_category()'
                  /usr/local/include/boost/thread/exceptions.hpp:49: undefined reference to `boost::system::system_category()'
                  libcufflinks.a(bundles.o): In function `__static_initialization_and_destruction_0':
                  /usr/local/include/boost/system/error_code.hpp:214: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:215: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:216: undefined reference to `boost::system::system_category()'
                  /usr/local/lib/libboost_thread.a(thread.o): In function `boost::condition_error::condition_error(int, char const*)':
                  thread.cpp:(.text._ZN5boost15condition_errorC2EiPKc[_ZN5boost15condition_errorC5EiPKc]+0x21): undefined reference to `boost::system::system_category()'
                  /usr/local/lib/libboost_thread.a(thread.o): In function `boost::thread_resource_error::thread_resource_error(int, char const*)':
                  thread.cpp:(.text._ZN5boost21thread_resource_errorC2EiPKc[_ZN5boost21thread_resource_errorC5EiPKc]+0x21): undefined reference to `boost::system::system_category()'
                  libcufflinks.a(clustering.o): In function `__static_initialization_and_destruction_0':
                  /usr/local/include/boost/system/error_code.hpp:214: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:215: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:216: undefined reference to `boost::system::system_category()'
                  libcufflinks.a(common.o): In function `__static_initialization_and_destruction_0':
                  /usr/local/include/boost/system/error_code.hpp:214: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:215: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:216: undefined reference to `boost::system::system_category()'
                  libcufflinks.a(assemble.o): In function `__static_initialization_and_destruction_0':
                  /usr/local/include/boost/system/error_code.hpp:214: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:215: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:216: undefined reference to `boost::system::system_category()'
                  libcufflinks.a(abundances.o): In function `__static_initialization_and_destruction_0':
                  /usr/local/include/boost/system/error_code.hpp:214: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:215: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:216: undefined reference to `boost::system::system_category()'
                  libcufflinks.a(scaffolds.o): In function `__static_initialization_and_destruction_0':
                  /usr/local/include/boost/system/error_code.hpp:214: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:215: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:216: undefined reference to `boost::system::system_category()'
                  libcufflinks.a(hits.o): In function `__static_initialization_and_destruction_0':
                  /usr/local/include/boost/system/error_code.hpp:214: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:215: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:216: undefined reference to `boost::system::system_category()'
                  libcufflinks.a(genes.o): In function `__static_initialization_and_destruction_0':
                  /usr/local/include/boost/system/error_code.hpp:214: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:215: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:216: undefined reference to `boost::system::system_category()'
                  libcufflinks.a(filters.o): In function `__static_initialization_and_destruction_0':
                  /usr/local/include/boost/system/error_code.hpp:214: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:215: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:216: undefined reference to `boost::system::system_category()'
                  libcufflinks.a(scaffold_graph.o): In function `__static_initialization_and_destruction_0':
                  /usr/local/include/boost/system/error_code.hpp:214: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:215: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:216: undefined reference to `boost::system::system_category()'
                  libcufflinks.a(matching_merge.o): In function `__static_initialization_and_destruction_0':
                  /usr/local/include/boost/system/error_code.hpp:214: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:215: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:216: undefined reference to `boost::system::system_category()'
                  libcufflinks.a(graph_optimize.o): In function `__static_initialization_and_destruction_0':
                  /usr/local/include/boost/system/error_code.hpp:214: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:215: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:216: undefined reference to `boost::system::system_category()'
                  libcufflinks.a(biascorrection.o): In function `__static_initialization_and_destruction_0':
                  /usr/local/include/boost/system/error_code.hpp:214: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:215: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:216: undefined reference to `boost::system::system_category()'
                  libcufflinks.a(sampling.o): In function `__static_initialization_and_destruction_0':
                  /usr/local/include/boost/system/error_code.hpp:214: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:215: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:216: undefined reference to `boost::system::system_category()'
                  libcufflinks.a(replicates.o): In function `__static_initialization_and_destruction_0':
                  /usr/local/include/boost/system/error_code.hpp:214: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:215: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:216: undefined reference to `boost::system::system_category()'
                  libcufflinks.a(multireads.o): In function `thread_exception':
                  /usr/local/include/boost/thread/exceptions.hpp:49: undefined reference to `boost::system::system_category()'
                  libcufflinks.a(multireads.o): In function `__static_initialization_and_destruction_0':
                  /usr/local/include/boost/system/error_code.hpp:214: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:215: undefined reference to `boost::system::generic_category()'
                  /usr/local/include/boost/system/error_code.hpp:216: undefined reference to `boost::system::system_category()'
                  collect2: ld returned 1 exit status
                  make[2]: *** [cufflinks] Error 1
                  make[2]: Leaving directory `/media/sda8/bharat/genomes/cufflinks-2.0.2/src'
                  make[1]: *** [all-recursive] Error 1
                  make[1]: Leaving directory `/media/sda8/bharat/genomes/cufflinks-2.0.2'
                  make: *** [all] Error 2

                  i read elsewhere that boost system library needs to be added to ldflags.

                  i tried editing Makefile.am in cufflinks/src directory and also Makefile in Cufflinks directory:

                  I added "libboost_system.a" to cufflinks_LDADD > didnt work (in src/makefile.am)
                  I changed it to "$(BOOST_SYS_LIB) > didnt work either (in src/makefile.am after setting BOOST_SYS_LIB = -lboost_system in Makefile )
                  Changed it to "-lboost_system" > still doesnt work (in src/makefile.am)

                  I assume that this is a problem with linking the libraries but i am not sure how to edit the compiler command. Please help
                  Last edited by bharat_iyengar; 12-17-2012, 02:35 AM.

                  Comment


                  • #10
                    I got the very same error as user "peromhc". My solution was to "abuse" the --with-boost-thread config option to additionally add another boost library containing the missing references:

                    --with-boost-thread="-lboost_thread-gcc44-mt-1_53 -lboost_system-gcc44-mt-1_53"

                    Please note that I installed boost with gcc 4.4.6, --layout=versioned --threading=multi that's the reason for the "-gcc44-mt-1_53" suffix, which might be different on your machine.
                    I also had to apply the "foreach" renaming trick, described by user "lib"

                    Comment


                    • #11
                      cufflinks-2.0.2 install error

                      Hi,
                      My cufflinks version is 2.0.2 abd boost is 1.52.0 version.

                      installed error:
                      make[2]: *** [differential.o] Error 1
                      make[2]: Leaving directory `cufflinks-2.0.2/src'
                      make[1]: *** [all-recursive] Error 1
                      make[1]: Leaving directory `cufflinks-2.0.2'
                      make: *** [all] Error 2

                      boost-1.52.0 -> 1.47.0, there was the same problem.

                      Can you help me ?

                      Thanks!

                      Comment


                      • #12
                        Easiest thing to do would be to get the executables directly. Boost 1.52 has some problem linking with cufflinks.

                        Comment

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