[twotwo]

Are you using the directions for "Getting started" located here: http://tophat.cbcb.umd.edu/tutorial.shtml?

Update: TopHat developers have updated that page to take out the reference to "address-model". Based on the current info there you can omit the last three options (--toolset=gcc architecture=x86 address_model=64).

See my post #70 this thread. The address-model requires a "-" (hyphen) and not an underscore.

never mind my other reply. When I changed address-model from underscore to hyphen, the three options worked!!! Thank you so much!!! I felt much better.

[twotwo]

Are you using the directions for "Getting started" located here: http://tophat.cbcb.umd.edu/tutorial.shtml?

Update: TopHat developers have updated that page to take out the reference to "address-model". Based on the current info there you can omit the last three options (--toolset=gcc architecture=x86 address_model=64).

See my post #70 this thread. The address-model requires a "-" (hyphen) and not an underscore.

Thanks for being so helpful! Yes, I did not update my tophat since I already have my SAM files. Should I update the tophat if I only want to run cuffdiff?
And if I used
1. ./bootstrap.sh
2. ./b2 install --prefix=/home/twotwo/software/boost153
Did boost install well? Should I still need to run bjam?

Thanks so much!

[GenoMax]

The OS is the linux. And I removed some of the option:
bjam --prefix=/home/twotwo/software/boost153/ link=static runtime-link=static stage install
Then it works. Can I install without the option of:
--toolset=gcc architecture=x86 address_model=64
Is there any difference?

Are you using the directions for "Getting started" located here: http://tophat.cbcb.umd.edu/tutorial.shtml?

Update: TopHat developers have updated that page to take out the reference to "address-model". Based on the current info there you can omit the last three options (--toolset=gcc architecture=x86 address_model=64).

See my post #70 this thread. The address-model requires a "-" (hyphen) and not an underscore.

[twotwo]

Can you provide additional details?

What OS? What version of boost are you trying to compile? What is the exact command line you are using? Even if the error appears to be the same it may help us diagnose the problem if you can post it here.

The OS is the linux. And I removed some of the option:
bjam --prefix=/home/twotwo/software/boost153/ link=static runtime-link=static stage install
Then it works. Can I install without the option of:
--toolset=gcc architecture=x86 address_model=64
Is there any difference?

[GenoMax]

It appears that boost has not been compiled correctly. Do you see bjam in /home/twotwo/software/boost153/?

The link you posted is the way to build boost. You will need to replace PREFIX with the path you want for your boost libraries which would be (--prefix=/home/twotwo/software/boost153).

[twotwo]

Can you provide additional details?

What OS? What version of boost are you trying to compile? What is the exact command line you are using? Even if the error appears to be the same it may help us diagnose the problem if you can post it here.

Thanks for replying so quick!
bjam --prefix=/home/twotwo/software/boost153 --toolset=gcc architecture=x86 address_model=64 link=static runtime-link=static stage install


And I got the following error:
/home/twotwo/software/boost_1_53_0/tools/build/v2/build/property.jam:328: in validate1 from module property
error: Invalid property '<address_model>64': unknown feature 'address_model'.
/home/twotwo/software/boost_1_53_0/tools/build/v2/build/property.jam:337: in property.validate from module property
/home/twotwo/software/boost_1_53_0/tools/build/v2/build/build-request.jam:216: in convert-command-line-element from module build-request
/home/twotwo/software/boost_1_53_0/tools/build/v2/build/build-request.jam:154: in build-request.from-command-line from module build-request
/home/twotwo/software/boost_1_53_0/tools/build/v2/build-system.jam:613: in load from module build-system
/home/twotwo/software/boost_1_53_0/tools/build/v2/kernel/modules.jam:283: in import from module modules
/home/twotwo/software/boost_1_53_0/tools/build/v2/kernel/bootstrap.jam:142: in boost-build from module
/home/twotwo/software/boost_1_53_0/boost-build.jam:17: in module scope from module

In the bjam command, I put the prefix with another folder boost153. However, even I used /home/twotwo/software/boost_1_53_0, I have the same error.

By the way, I just found the following command:
./bootstrap.sh
./b2 install --prefix=PREFIX
from the following web:

http://www.boost.org/doc/libs/1_53_0/doc/html/bbv2/installation.html

Is this also the way to install boost? Thanks so much!
However, after I run those two command, I still cannot run bjam command that I showed above...

[GenoMax]

I have the same problem. Any comments???

Can you provide additional details?

What OS? What version of boost are you trying to compile? What is the exact command line you are using? Even if the error appears to be the same it may help us diagnose the problem if you can post it here.

[twotwo]

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?

I have the same problem. Any comments???

[GenoMax]

Dave,

Now my head is starting to hurt

I feel that all these problems are because of additional directive in red:

--with-boost=/usr/local/boost_1_53_0 --with-boost-libdir=/usr/local/lib

Can you try the compile removing the second option?

Everything related to your boost libraries should be under the original location where you had compiled boost.

Can you tell me where exactly did you initially compile the boost libraries? In /usr/local/boost_1_53_0 or in /usr/local.

The reason I had asked you to create the "boost" top level directory was that way both "include" and "lib" from boost would be nicely segregated under that directory. Then when you compile cufflinks all you will need to include would be "--with-boost=path_to_top_level_boost" directory. No other boost related directives should be needed as long as your library had compiled correctly.

[Dave-bo_Baggins]

I was troubleshooting and looking into the error messages and I thoughts Id share some progress, well I hope progress

Looking at the error statement again

g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -march=i686 -O3 -DNDEBUG -pthread -I/usr/local/boost_1_53_0/include -I/usr/local/include/bam/include -I/usr/local/include/Eigen/include -o cufflinks -L/usr/local/lib -L/usr/local/include/bam/lib cufflinks.o libcufflinks.a libgc.a -lboost_thread -lboost_system -lbam -lz
/usr/local/lib/libboost_thread.a(thread.o): In function `__gnu_cxx::__exchange_and_add_dispatch(int*, int) [clone .constprop.241]':
thread.cpp.text.unlikely+0x22): undefined reference to `__atomic_fetch_add_4'


I noticed:
-I/usr/local/boost_1_53_0/include
-I/usr/local/include/bam/include


I noticed that while there is an include subdirectory for Eigen there was none for /boost_1_53_0 or /bam. What I did for the bam subdirectory was to copy my header files to the /usr/local/include/bam directory. I went back to the cufflinks gettign started manual
and read "Copy the samtools binary to some directory in your PATH." Would I be correct in assuming that I should copy the contents of Desktop/samtools-0.1.19 to the /usr/local/ folder ? Would it make sense to create an include folder in the /boost_1_53_0 and /bam directories and fill it with the appropriate files ?

The line that Im still trying to decipher is the

thread.cpp.text.unlikely+0x22): undefined reference to `__atomic_fetch_add_4'

I figure it has something to do with not being able to find the thread.cpp in the library directory which in the connfigure statement I defined as : --with-boost-libdir=/usr/local/lib. did a locate *read.cpp and found the following locations:

/usr/local/boost_1_53_0/libs/thread/example/thread.cpp
/usr/local/boost_1_53_0/libs/thread/src/pthread/thread.cpp
/usr/local/boost_1_53_0/libs/thread/src/win32/thread.cpp

[Dave-bo_Baggins]

Dave,

The extra "//" are there because you used an additional trailing "/" in your "--with-bam=/usr/local/include/bam/ and --with-eigen=/usr/local/include/Eigen/". Omit the trailing slashes on these two directives.

Are there ~200 odd files in the boost/include directory now, indicating successful boost build?

Hey GenoMax,

I re-issued the compile statement this time removing the trailing slashes.
and everything compiles no errors.

./configure --prefix=/home/dave/Desktop/cufflinks-2.1.1 --with-boost=/usr/local/boost_1_53_0 --with-boost-libdir=/usr/local/lib --with-bam=/usr/local/include/bam --with-eigen=/usr/local/include/Eigen

I get similar error when I issue the make command:

g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -march=i686 -O3 -DNDEBUG -pthread -I/usr/local/boost_1_53_0/include -I/usr/local/include/bam/include -I/usr/local/include/Eigen/include -o cufflinks -L/usr/local/lib -L/usr/local/include/bam/lib cufflinks.o libcufflinks.a libgc.a -lboost_thread -lboost_system -lbam -lz
/usr/local/lib/libboost_thread.a(thread.o): In function `__gnu_cxx::__exchange_and_add_dispatch(int*, int) [clone .constprop.241]':
thread.cpp.text.unlikely+0x22): undefined reference to `__atomic_fetch_add_4'
collect2: error: ld returned 1 exit status
make[2]: *** [cufflinks] Error 1
make[2]: Leaving directory `/home/dave/Desktop/cufflinks-2.1.1/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/dave/Desktop/cufflinks-2.1.1'
make: *** [all] Error 2

The include and lib subdirectories were created in the /usr/local/ directory

there are still no include or lib sub directories in the boost subdirectory itself. In the /usr/local/boost subdirectory there are about 150 files all .hpp files

[GenoMax]

Dave,

The extra "//" are there because you used an additional trailing "/" in your "--with-bam=/usr/local/include/bam/ and --with-eigen=/usr/local/include/Eigen/". Omit the trailing slashes on these two directives.

Are there ~200 odd files in the boost/include directory now, indicating successful boost build?

[Dave-bo_Baggins]

Dave,

You were missing a "/" at the beginning of --prefix

In any case were "include" and "lib" created under "/home/mrmary/ngs/applications/"? If you were doing the compilation again I would suggest creating a "boost" directory as so "/home/mrmary/ngs/applications/boost".

I also did not bother to get the svn version. I just downloaded the source tar ball from here.

Genomax

Hope you are doing well. I have been trying to install on my home computer. Today I was back at my work station. I reinstalled boost in the /usr/local all seemed well. When I went to my cufflinks directory to type out the ./configure statement I accidentally hit enter after configure but IT WORKED I retyped and entered the whole thing:

./configure --prefix=/home/dave/Desktop/cufflinks-2.1.1/ --with-boost=/usr/local/boost_1_53_0 --with-boost-libdir=/usr/local/lib --with-bam=/usr/local/include/bam/ --with-eigen=/usr/local/include/Eigen/

-- cufflinks 2.1.1 Configuration Results --
C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -march=i686 -O3 -DNDEBUG -pthread -I/usr/local/boost_1_53_0/include -I/usr/local/include/bam//include -I/usr/local/include/Eigen//include
GCC version: gcc (Ubuntu/Linaro 4.7.3-1ubuntu1) 4.7.3
Host System type: i686-pc-linux-gnu
Install prefix: /home/dave/Desktop/cufflinks-2.1.1/
Install eprefix: ${prefix}

The Make didnt work however and I'm sorting through that.

make all-recursive
make[1]: Entering directory `/home/dave/Desktop/cufflinks-2.1.1'
Making all in src
make[2]: Entering directory `/home/dave/Desktop/cufflinks-2.1.1/src'

g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -march=i686 -O3 -DNDEBUG -pthread -I/usr/local/boost_1_53_0/include -I/usr/local/include/bam//include -I/usr/local/include/Eigen//include -o cufflinks -L/usr/local/lib -L/usr/local/include/bam//lib cufflinks.o libcufflinks.a libgc.a -lboost_thread -lboost_system -lbam -lz
/usr/local/lib/libboost_thread.a(thread.o): In function `__gnu_cxx::__exchange_and_add_dispatch(int*, int) [clone .constprop.241]':
thread.cpp.text.unlikely+0x22): undefined reference to `__atomic_fetch_add_4'
collect2: error: ld returned 1 exit status
make[2]: *** [cufflinks] Error 1
make[2]: Leaving directory `/home/dave/Desktop/cufflinks-2.1.1/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/dave/Desktop/cufflinks-2.1.1'
make: *** [all] Error 2


The // thing strikes my eye esp when I compared it to the code given on the post you linked in your first or one of your first responce http://seqanswers.com/forums/showthread.php?t=19805

I think i burned out my retinas over the last few days

Dave

[GenoMax]

Dave,

You were missing a "/" at the beginning of --prefix

--prefix=/home/mrmary/ngs/applications/

In any case were "include" and "lib" created under "/home/mrmary/ngs/applications/"? If you were doing the compilation again I would suggest creating a "boost" directory as so "/home/mrmary/ngs/applications/boost".

I also did not bother to get the svn version. I just downloaded the source tar ball from here.

[Dave-bo_Baggins]

Dave,

There is a typo in the bjam build command that is included on the cufflinks "getting started" page. The address model directive needs a "-" (hyphen) and not an "_".

Can you try (32 or 64 depending on if you are using 32-bit OS or 64-bit)?

address-model=32 [B]or [/B]address-model=64

Hey GenoMax

Thanks for you responses

I deleted my previous boost installation and stared over again:

./bootstrap.sh --prefix=home/mrmary/ngs/applications/

Building Boost.Build engine with toolset gcc... tools/build/v2/engine/bin.linuxx86/b2
Detecting Python version... 2.7
Detecting Python root... /usr
Unicode/ICU support for Boost.Regex?... /usr
Generating Boost.Build configuration in project-config.jam...

Bootstrapping is done. To build, run:

./b2

bjam --prefix=home/mrmary/ngs/applications/ --toolset=gcc architecture=x86 address-model=32 link=static runtime-link=static stage install

warning: mismatched versions of Boost.Build engine and core
warning: Boost.Build engine (bjam) is 03.1.19
warning: Boost.Build core (at /home/mrmary/ngs/applications/boost_1_53_0/tools/build/v2) is 2011.12-svn
/home/mrmary/ngs/applications/boost_1_53_0/tools/build/v2/util/path.jam:476: in path.makedirs
rule MAKEDIR unknown in module path.
/home/mrmary/ngs/applications/boost_1_53_0/tools/build/v2/build/configure.jam:190: in configure.set-log-file
/home/mrmary/ngs/applications/boost_1_53_0/tools/build/v2/build-system.jam:725: in load
/home/mrmary/ngs/applications/boost_1_53_0/tools/build/v2/kernel/modules.jam:283: in import
/home/mrmary/ngs/applications/boost_1_53_0/tools/build/v2/kernel/bootstrap.jam:142: in boost-build
/home/mrmary/ngs/applications/boost_1_53_0/boost-build.jam:17: in module scope

I tried also:
bjam --prefix=home/mrmary/ngs/applications/ --toolset=gcc architecture=x86 address-model=64 link=static runtime-link=static stage install

I got the same warning but it also started to compile and I saw many lines of course but something that caught my eye were lines like the following:

common.copy home/mrmary/ngs/applications/lib/libboost_serialization.so.1.53.0
common.copy home/mrmary/ngs/applications/include/boost/mpl/aux_/preprocessed/bcc/plus.hpp

I did a locate applications/lib, and a locate applications/include but didnt find anything. From what I am seeing online lines like that indicate a broken libdir configuration. I looked at the project-configure.jam and found the lines:

# These settings are equivivalent to corresponding command-line
# options.
option.set prefix : home/mrmary/ngs/applications/ ;
option.set exec-prefix : home/mrmary/ngs/applications/ ;
option.set libdir : home/mrmary/ngs/applications//lib ;
option.set includedir : home/mrmary/ngs/applications//include ;

Looking at the above bolded parts of the file paths, Im guessing this is why the include and lib files werent built. I think I have to specify the libdir and the includedir, I'm looking that up as we speak

Also when everything finished compiling I got the following:
...failed updating 2 targets...
...skipped 6 targets...
...updated 11046 targets...