Go Back   SEQanswers > Bioinformatics > Bioinformatics
Similar Threads
Thread Thread Starter Forum Replies Last Post
glimmer compile error anyone1985 Bioinformatics 26 11-29-2012 12:54 PM
Compile cufflinks in MacOSX10.7 (Lion)--error in make mrbirdy857 Bioinformatics 2 01-19-2012 04:49 AM
Help with samtools on solaris 10 sgaa201 Bioinformatics 1 03-08-2011 08:46 AM
BGZF ERROR: BEDtools on SPARC with Solaris 10 MILLHILL Bioinformatics 0 03-08-2011 07:05 AM
maq compile error on Ubuntu baozhi Bioinformatics 1 02-19-2009 01:28 PM

Thread Tools
Old 06-03-2010, 06:25 PM   #1
Location: Japan

Join Date: Feb 2009
Posts: 10
Unhappy Cufflinks on Solaris (compile error)

I want to install Cufflinks (the latest version 0.8.2) on Solaris 10 server.

I've already installed Boost C++ libraries Version 1.43.0 on the system. But I faced to the following errors when I compiled Cufflinks.

Does anyone known how to solve this problem? Cuffliks can work on Solaris system?

---- A part of error messages ----

bash$ make
make[1]: Entering directory `/home/user/Cufflinks/cufflinks-0.8.2'
Making all in src
make[2]: Entering directory `/home/user/Cufflinks/cufflinks-0.8.2/src'
if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -Wall -Wno-strict-aliasing -g -gdwarf-2 -m64 -O3 -DNDEBUG -I/home/user/Boost/boost_1_43_0/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 /home/user/Boost/boost_1_43_0/include/boost/thread/detail/platform.hpp:17,
from /home/user/Boost/boost_1_43_0/include/boost/thread/thread.hpp:12,
from /home/user/Boost/boost_1_43_0/include/boost/thread.hpp:13,
from scaffolds.h:22,
from abundances.h:21,
from clustering.h:32,
from clustering.cpp:10:
/home/user/Boost/boost_1_43_0/include/boost/config/requires_threads.hpp:47:5: #error "Compiler threading support is not turned on. Please set the correct command line options for threading: -pthread (Linux), -pthreads (Solaris) or -mthreads (Mingw32)

--- skip ---


Boost C++ libraries Version 1.43.0 was installed in /home/user/Boost/boost_1_43_0/ by using the following command.

bash$ bjam --prefix=/home/user/Boost/boost_1_43_0/ toolset=gcc link=static runtime-link=static stage install

After that I also configured Cufflinks like this

bash$ ./configure --prefix=/home/user/Cufflinks/ --with-boost=/home/user/Boost/boost_1_43_0/
luxmare is offline   Reply With Quote
Old 06-04-2010, 01:00 AM   #2
Senior Member
Location: 4530'25.22"N / 915'53.00"E

Join Date: Apr 2009
Posts: 258

Hi, I was trying to install on Nexenta, apparently I have a plenty of other errors not related to threads (system #include and #define instead).
BTW, I've built boost like this

$ ./ --prefix=/usr/local
$ ./bjam --toolset=gcc --build-dir=~/buildboost stage
$ sudo ./bjam install
It skips 6 modules (I think python ones).
dawe is offline   Reply With Quote

bioinformatics, cufflinks, error, installation

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 11:22 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO