cufflinks source install error

[peromhc]

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

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

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?

[lib]

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.

[peromhc]

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.

[lisann_5]

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!

[peromhc]

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

[lisann_5]

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!

[peromhc]

try another version of boost-- for instance Boost 1.45.0

[lisann_5]

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

[bharat_iyengar]

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:

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

[Stefan Janssen]

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"

[hong]

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!

[bharat_iyengar]

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