[chenyao]

Glad you got it. I installed boost in the /usr/local and exported the path.

make and make install went fine. I was able to run the test_data.sam given in the cufflinks webpage. But, there was one warning. Pasted below is the output.


tiger123@ubuntu:~/data$ cufflinks ./test_data.sam
You are using Cufflinks v1.0.3, which is the most recent release.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File ./test_data.sam doesn't appear to be a valid BAM file, trying SAM...
[16:48:28] Inspecting reads and determining fragment length distribution.
> Processed 1 loci. [*************************] 100%
Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges. It is recommended that correct paramaters (--frag-len-mean and --frag-len-std-dev) be provided.
> Map Properties:
> Total Map Mass: 102.50
> Read Type: 75bp x 75bp
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
[16:48:28] Assembling transcripts and estimating abundances.
> Processed 1 loci.

I am not sure whether this will create problems when running the actual data.

Strange. I also run test_data.sam. That's what I got:

Processed 1 loci. [*************************] 100%
Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges. It is recommended that correct paramaters (--frag-len-mean and --frag-len-std-dev) be provided.
> Map Properties:
> Total Map Mass: 102.50
> Read Type: 75bp x 75bp
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
[11:34:41] Assembling transcripts and estimating abundances.
> Processing Locus test_chromosome:52-550 [************************ ] 99%段错误

[Tiger123]

Glad you got it. I installed boost in the /usr/local and exported the path.

make and make install went fine. I was able to run the test_data.sam given in the cufflinks webpage. But, there was one warning. Pasted below is the output.


tiger123@ubuntu:~/data$ cufflinks ./test_data.sam
You are using Cufflinks v1.0.3, which is the most recent release.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File ./test_data.sam doesn't appear to be a valid BAM file, trying SAM...
[16:48:28] Inspecting reads and determining fragment length distribution.
> Processed 1 loci. [*************************] 100%
Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges. It is recommended that correct paramaters (--frag-len-mean and --frag-len-std-dev) be provided.
> Map Properties:
> Total Map Mass: 102.50
> Read Type: 75bp x 75bp
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
[16:48:28] Assembling transcripts and estimating abundances.
> Processed 1 loci.

I am not sure whether this will create problems when running the actual data.

[chenyao]

OK , I fix it. It seems the boost is not installed in "/usr/local/boost"

[chenyao]

Hi, solved the problem with the error message (checking for boostlib >= 1.38.0... configure: error: ....) while cufflinks configuration.
Today I installed libboost using;
sudo apt-get install libboost-all-dev.

Then I configured successfully.

./configure --prefix=/usr/local/cufflinks/install --with-boost=/usr/local/boost

The output is below:

-------------------------------------
-----------------------------------

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
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking if zlib is wanted... yes
checking for inflateEnd in -lz... yes
------------------------------------------
---------------------------------------

-- cufflinks 1.0.3 Configuration Results --
C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/usr/local/boost/include -I/usr/local/include
GCC version: gcc (Ubuntu/Linaro 4.5.2-8ubuntu4) 4.5.2
Host System type: x86_64-unknown-linux-gnu
Install prefix: /usr/local/cufflinks/install
Install eprefix: ${prefix}

See config.h for further configuration information.
Email <[email protected]> with questions and bug reports.

Dear Tiger, using your command, I got the same message. It seems cufflinks has found "boost". But after that, I cannot get the "make" successful, which always showed the error. Did you "make" it?

[Tiger123]

Hi, solved the problem with the error message (checking for boostlib >= 1.38.0... configure: error: ....) while cufflinks configuration.
Today I installed libboost using;
sudo apt-get install libboost-all-dev.

Then I configured successfully.

./configure --prefix=/usr/local/cufflinks/install --with-boost=/usr/local/boost

The output is below:

-------------------------------------
-----------------------------------

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
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking if zlib is wanted... yes
checking for inflateEnd in -lz... yes
------------------------------------------
---------------------------------------

-- cufflinks 1.0.3 Configuration Results --
C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/usr/local/boost/include -I/usr/local/include
GCC version: gcc (Ubuntu/Linaro 4.5.2-8ubuntu4) 4.5.2
Host System type: x86_64-unknown-linux-gnu
Install prefix: /usr/local/cufflinks/install
Install eprefix: ${prefix}

See config.h for further configuration information.
Email <[email protected]> with questions and bug reports.

[chenyao]

Some additional information about the results got when I build the boost using:

bjam --prefix=\usr\local --toolset=gcc architecture=x86 address_model=32 link=static runtime-link=static stage install

/home/tiger123/boost/boost_1_47_0/tools/build/v2/build/property.jam:328: in validate1 from module property
error: Invalid property '<address_model>32': unknown feature 'address_model'.
/home/tiger123/boost/boost_1_47_0/tools/build/v2/build/property.jam:337: in property.validate from module property
/home/tiger123/boost/boost_1_47_0/tools/build/v2/build/build-request.jam:216: in convert-command-line-element from module build-request
/home/tiger123/boost/boost_1_47_0/tools/build/v2/build/build-request.jam:153: in build-request.from-command-line from module build-request
/home/tiger123/boost/boost_1_47_0/tools/build/v2/build-system.jam:612: in load from module build-system
/home/tiger123/boost/boost_1_47_0/tools/build/v2/kernel/modules.jam:283: in import from module modules
/home/tiger123/boost/boost_1_47_0/tools/build/v2/kernel/bootstrap.jam:142: in boost-build from module
/home/tiger123/boost/boost_1_47_0/boost-build.jam:17: in module scope from module


Any thoughts?

Same problem ,wait for the answer

[Tiger123]

Some additional information about the results got when I build the boost using:

bjam --prefix=\usr\local --toolset=gcc architecture=x86 address_model=32 link=static runtime-link=static stage install

/home/tiger123/boost/boost_1_47_0/tools/build/v2/build/property.jam:328: in validate1 from module property
error: Invalid property '<address_model>32': unknown feature 'address_model'.
/home/tiger123/boost/boost_1_47_0/tools/build/v2/build/property.jam:337: in property.validate from module property
/home/tiger123/boost/boost_1_47_0/tools/build/v2/build/build-request.jam:216: in convert-command-line-element from module build-request
/home/tiger123/boost/boost_1_47_0/tools/build/v2/build/build-request.jam:153: in build-request.from-command-line from module build-request
/home/tiger123/boost/boost_1_47_0/tools/build/v2/build-system.jam:612: in load from module build-system
/home/tiger123/boost/boost_1_47_0/tools/build/v2/kernel/modules.jam:283: in import from module modules
/home/tiger123/boost/boost_1_47_0/tools/build/v2/kernel/bootstrap.jam:142: in boost-build from module
/home/tiger123/boost/boost_1_47_0/boost-build.jam:17: in module scope from module


Any thoughts?

[Tiger123]

Hi Guys,

I am also having configuration problems for cufflinks.

I got the error as below for ./configure

checking for boostlib >= 1.38.0... configure: error: We could not detect the boost libraries (version 1.38 or higher). If you have a staged boost library (still not installed) please specify $BOOST_ROOT in your environment and do not give a PATH to --with-boost option. If you are sure you have boost installed, then check your version number looking in <boost/version.hpp>. See http://randspringer.de/boost for more documentation.

I installed the latest version of boost. But, my system is 32-bit. I tried to reinstall a 64-bit linux, which I failed in my system. Is there any solution to this problem? Thanks.

[hibachings2013]

here got the same error too !

Hi All,

I am trying to install cufflinks btw got the same error too.


checking for python platform... darwin
checking for python script directory... ${prefix}/lib/python2.7/site-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.7/site-packages
checking for boostlib >= 1.38.0... configure: error: We could not detect the boost libraries (version 1.38 or higher). If you have a staged boost library (still not installed) please specify $BOOST_ROOT in your environment and do not give a PATH to --with-boost option. If you are sure you have boost installed, then check your version number looking in <boost/version.hpp>. See http://randspringer.de/boost for more documentation.


so i'd specify the path to BOOST_ROOT as xi wang suggested rather than i give the path to boost_1_46_1.
sorry for a newbie question here, how do we know where the BOOST_ROOT is?

Thanks a lot in advance,

[emucaki]

Well that's just one of over a dozen warnings that occur during the make process, I just pasted the last one cause I thought that might be the one triggering the stop.

[jmarshall]

GList.hh(413): remark #981: operands are evaluated in unspecified order

You are using Intel's compiler and you have configured cufflinks so as to compile with -Werror.

This is a relatively useless warning, and it's hard to see why it's being triggered by this code. It seems that the usual advice is to switch the warning off: http://software.intel.com/en-us/foru...ad.php?t=62309.

[emucaki]

Gonna bump this thread again. I was able to get through all the boost and sam/bam issues for this installation (I've successfully installed bowtie and tophat as well), but now with Cufflinks I'm having a 'make' error (it is a 64 bit system).

GList.hh(413): remark #981: operands are evaluated in unspecified order
if (Found(item, result)) return true;
^

compilation aborted for clustering.cpp (code 2)
make[2]: *** [clustering.o] Error 1
make[2]: Leaving directory `/work/emucaki/goblin/Cufflinks/cufflinks-0.9.1/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/work/emucaki/goblin/Cufflinks/cufflinks-0.9.1'
make: *** [all] Error 2

Any ideas?

[repinementer]

FluxCapacitor and FluxStimulator

Have you installed these?
Seems pretty google code RNASEQ tools.

http://flux.sammeth.net/cap_installation.html

[Utrecht]

That's right, there are pre-compiled binaries for 64 bit systems and/or Macs. Much easier, eh? :-)

[repinementer]

yes 32 bit is not working

yes i used bjam.
yes i agree some thing wrong with 32 bit
seems 64 bit doesnt have any configure file so no need to run the commands??????????

./configure --prefix=/path/to/cufflinks/install --with-boost=/path/to/boost
make
make install

but ./command (ex: ./cufflinks) are working fine

[bogugk@Trivia cufflinks-0.8.2.Linux_x86_64]$ ./cufflinks ./test_data.sam
Counting hits in map
Total map density: 104.000000
Processing bundle [ test_chromosome:52-550 ] with 99 non-redundant alignments