[pengchy]

the "--with-boost-libdir=" specify the directory like /path/to/lib/boost_1_47_0/include/
here, the "include" directory contain one directory "boost", and many files suffix *hpp locate at "boost" directory. So the files will like "include/boost/*hpp". If you have installed boost, you will find this directory at /prefix/include/boost/*hpp

[Dave-bo_Baggins]

Dave: Where exactly did you install boost libraries? Are they in "/usr/local" or in your home directory?

You may have already seen the instructions here: http://cufflinks.cbcb.umd.edu/tutorial.html#inst Depending on where you installed the boost libraries add that path using " --with-boost=/path/to/boost"

Here are a couple of threads for reference: http://seqanswers.com/forums/showthread.php?t=19805 and http://seqanswers.com/forums/showthread.php?t=14224

Hello GenoMax

Thanks so much for your feedback. Let me answer your question:

Where exactly did you install boost libraries? Are they in "/usr/local" or in your home directory?

I have Boost installed in the home directory: $HOME/ngs/applications

mrmary@mrmary-Dimension-4600i:~/ngs/applications$ ls -l
drwxrwxr-x 10 mrmary mrmary 4096 May 12 05:58 boost_1_53_0

I also copied my boost installation to /usr/local as well

mrmary@mrmary-Dimension-4600i:/usr/local$ ls -l
drwxr-xr-x 10 root root 4096 May 12 08:20 boost_1_53_0

I will look at the threads you have listed and get back to you tomorrow. The locate libboost command looks very promising avenue to start with tomorrow.

Thanks again for your time, I was at wit's end with this
Dave

[Dave-bo_Baggins]

the "--with-boost-libdir=" specify the directory like /path/to/lib/boost_1_47_0/include/
here, the "include" directory contain one directory "boost", and many files suffix *hpp locate at "boost" directory. So the files will like "include/boost/*hpp". If you have installed boost, you will find this directory at /prefix/include/boost/*hpp

Hello pengchy

Thanks for the reply that cleared up things a lil bit. I have .hpp files at the following locations:

/usr/local/boost_1_53_0/boost
/ngs/applications/boost_1_53_0/boost

when I hit the ls -l command I can see the .hpp files. I have understood correctlythe corrected statement should be:

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

I added that to my configure statement but it didnt work. I went back too at the cufflinks config.log and I found these statements:"

configure:3870: checking for boostlib >= 1.47.0
configure:3929: g++ -c -I/home/mrmary/ngs/applications/boost_1_53_0//include conftest.cc >&5
conftest.cc:25:5: error: #error Boost version is too old
configure:3935: $? = 1
configure: failed program was:
| /* confdefs.h. */

configure:3870: checking for boostlib >= 1.47.0
configure:3929: g++ -c -I/home/mrmary/ngs/applications/boost_1_53_0//include

configure:4059: g++ -c -I/home/mrmary/ngs/applications/boost_1_53_0//include -I/home/mrmary/ngs/applications/boost_1_53_0//include conftest.cc >&5
conftest.cc:25:6: error: #error Boost version is too old

I think this may have to do with the lines I got back when I built boost:

The Boost C++ Libraries were successfully built!
The following directory should be added to compiler include paths:
/home/mrmary/ngs/applications/boost_1_53_0
The following directory should be added to linker library paths:
/home/mrmary/ngs/applications/boost_1_53_0/stage/lib

Im gonna sleep on this and get back to it in a few hours
Dave

[GenoMax]

Hello GenoMax

Thanks so much for your feedback. Let me answer your question:


I have Boost installed in the home directory: $HOME/ngs/applications

mrmary@mrmary-Dimension-4600i:~/ngs/applications$ ls -l
drwxrwxr-x 10 mrmary mrmary 4096 May 12 05:58 boost_1_53_0

I also copied my boost installation to /usr/local as well

mrmary@mrmary-Dimension-4600i:/usr/local$ ls -l
drwxr-xr-x 10 root root 4096 May 12 08:20 boost_1_53_0

I will look at the threads you have listed and get back to you tomorrow. The locate libboost command looks very promising avenue to start with tomorrow.

Thanks again for your time, I was at wit's end with this
Dave

Dave,

"--with-boost=" should point to the top level directory where the "include" and "lib" directories for boost are. In your case if "/usr/local/boost_1_53_0" is that directory then your directive will be

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

[Dave-bo_Baggins]

Dave,

"--with-boost=" should point to the top level directory where the "include" and "lib" directories for boost are. In your case if "/usr/local/boost_1_53_0" is that directory then your directive will be

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

Hello Again GenoMax

I decided to go over my configure statement again, in particularly the boost related commands:
--with-boost=/usr/local/boost_1_53_0/
--with-boost-thread=/usr/lib64/boost141/libboost_thread-mt.so
--with-boost-libdir=/usr/local/boost_1_53_0/boost/
--with-boost-system=/usr/local/boost_1_53_0/stage/lib/

I changed the line: --with-boost-thread=/usr/lib64/boost141/libboost_thread-mt.so to --with-boost-thread=/usr/lib/libboost_thread-mt.so

other than that I don't think the issue is with my statement, at least I dont see one. I am going to try appending the LD_PATH. Will get back to you. I cannot think of what I'm missing at the moment.

Thanks for the replies and your time
Dave

[GenoMax]

Dave,

Do you see the two directories "include" and "lib" under "/usr/local/boost_1_53_0/ " (or /home/mrmary/ngs/applications/boost_1_53_0/) ? If you don't then that means your boost libraries did not build properly. Can you please verify?

If the directories (and their contents) are there then the only --with-boost directive you should need is the one I posted in post 64.

[Dave-bo_Baggins]

Dave,

Do you see the two directories "include" and "lib" under "/usr/local/boost_1_53_0/ " (or /home/mrmary/ngs/applications/boost_1_53_0/) ? If you don't then that means your boost libraries did not build properly. Can you please verify?

If the directories (and their contents) are there then the only --with-boost directive you should need is the one I posted in post 64.

GenoMax

I checked paths and there are no "include" or "lib" directories.(there is a libs directory) I will reinstall and rebuild the boost, and keep an eye out for an errors that may come up during building and report back.

Thanks again
Dave

[GenoMax]

"include --> boost" will have all the "*.hpp" files (I see 214 files) and "lib" will have all "libboost*" files.

[Dave-bo_Baggins]

Dave,

Do you see the two directories "include" and "lib" under "/usr/local/boost_1_53_0/ " (or /home/mrmary/ngs/applications/boost_1_53_0/) ? If you don't then that means your boost libraries did not build properly. Can you please verify?

If the directories (and their contents) are there then the only --with-boost directive you should need is the one I posted in post 64.

"include --> boost" will have all the "*.hpp" files (I see 214 files) and "lib" will have all "libboost*" files.

GenoMax

When I entered the the bjam command I got these warnings:

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

and an error statement

error: Invalid property '<address_model>32': unknown feature 'address_model'.

Im checking around to see what does actually it actually mean. Im figuring this was the reason why the include and the lib directories were not created
before

[GenoMax]

GenoMax

When I entered the the bjam command I got these warnings:

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

and an error statement

error: Invalid property '<address_model>32': unknown feature 'address_model'.

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

[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...

[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,

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,

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,

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