SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Help installing Cufflinks 2.0.1 on Cygwin BenS RNA Sequencing 9 07-26-2012 12:25 AM
problem while installing coreutils-8.12 vinila86 Bioinformatics 0 02-22-2012 03:02 AM
error while installing cufflinks 9.x plantae Bioinformatics 0 12-02-2010 06:34 AM
tophat installing problem deepsea Bioinformatics 13 08-17-2010 08:14 AM
Problem installing MAQ sam253 Bioinformatics 0 03-25-2010 01:38 AM

Reply
 
Thread Tools
Old 12-16-2012, 08:31 PM   #1
bharat_iyengar
Member
 
Location: Delhi, India

Join Date: Dec 2012
Posts: 20
Default problem installing cufflinks

there was no problem configuring Cufflinks v2.02 but when i make it i get an error like this

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'
if g++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src  -I/usr/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -m64 -O3  -DNDEBUG  -pthread -I usr/local/include -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
if g++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src  -I/usr/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -m64 -O3  -DNDEBUG  -pthread -I usr/local/include -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 hits.h:21:0,
                 from abundances.h:23,
                 from differential.cpp:17:
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:152:50: warning: unused variable 's2' [-Wunused-variable]
In file included from differential.cpp:18:0:
differential.h: In constructor 'FPKMContext::FPKMContext(double, double, double,                                                                                uble, AbundanceStatus, const StatusPerReplicateTable&)':
differential.h:142:21: warning: 'FPKMContext::status' will be initialized after
differential.h:139:29: warning:   'StatusPerReplicateTable FPKMContext::status_p
differential.h:131:2: warning:   when initialized here [-Wreorder]
differential.cpp: In member function 'void TestLauncher::perform_testing(std::ve
differential.cpp:212:31: warning: unused variable 's2' [-Wunused-variable]
differential.cpp: In member function 'void TestLauncher::record_tracking_data(st
differential.cpp:240:31: warning: unused variable 's2' [-Wunused-variable]
differential.cpp: In function 'SampleDifference get_ds_tests(const AbundanceGrou
differential.cpp:790:16: warning: unused variable 'name' [-Wunused-variable]
differential.cpp: In function 'void test_differential(const string&, const std::
differential.cpp:1771:83: warning: comparison between signed and unsigned intege
differential.cpp:1772:83: warning: comparison between signed and unsigned intege
differential.cpp:1814:83: warning: comparison between signed and unsigned intege
differential.cpp:1815:83: warning: comparison between signed and unsigned intege
differential.cpp:1856:83: warning: comparison between signed and unsigned intege
differential.cpp:1857:83: warning: comparison between signed and unsigned intege
make[2]: *** [differential.o] 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 dont understand where to troubleshoot. All boost1.52 and Eigen libraries are copied in /usr/local/lib

Last edited by bharat_iyengar; 12-16-2012 at 08:36 PM.
bharat_iyengar is offline   Reply With Quote
Old 12-17-2012, 06:39 AM   #2
aafc
Member
 
Location: canada

Join Date: Dec 2012
Posts: 10
Default

Try using boost version 1.47. I think I had a similar issue when trying using the latest version of boost, which was 1.51. The version specified by cufflinks in the manual is 1.47, I think.
aafc is offline   Reply With Quote
Old 12-17-2012, 07:02 AM   #3
bharat_iyengar
Member
 
Location: Delhi, India

Join Date: Dec 2012
Posts: 20
Default

I had corrected that particular problem,which was because of improper definition of a variable. But then another one appeared which is perhaps because boost_system library is not linked during compilation.

this is what is written in Cufflinks Manual.

Quote:
If you see any errors during configuration, verify that you are using Boost version 1.47 or higher
I shall nonetheless try 1.47/48

I have observed that this is a general problem with others using boost libraries.

Last edited by bharat_iyengar; 12-17-2012 at 07:06 AM.
bharat_iyengar is offline   Reply With Quote
Old 12-17-2012, 07:06 AM   #4
aafc
Member
 
Location: canada

Join Date: Dec 2012
Posts: 10
Default

Unless the developers of cufflinks tested every single release of boost beyond 1.47, that statement doesn't really mean much. It is possible for newer libraries to not work on software that was designed on older versions of those libraries.

I just confirmed that my system has 1.47 installed - try that version.
aafc is offline   Reply With Quote
Old 12-17-2012, 07:07 AM   #5
bharat_iyengar
Member
 
Location: Delhi, India

Join Date: Dec 2012
Posts: 20
Default

i shall try. thanks
bharat_iyengar is offline   Reply With Quote
Old 12-17-2012, 07:07 AM   #6
aafc
Member
 
Location: canada

Join Date: Dec 2012
Posts: 10
Default

Also, make sure $LD_LIBRARY_PATH is defined as the path to the dynamic boost library files (the .so files)
aafc is offline   Reply With Quote
Reply

Tags
cufflinks 2.0.2

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:16 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO