.a files for other operating system #3

nielshanson · 2014-06-04T22:34:55Z

Hey Man,

We'd like to compile the source for other operating system, i.e., Mac OSX, however, we need to know how the archive files were compiled from the boost library in order to create compatible versions.

Specifically these are files in the Src/ folder:

libboost_chrono.a
libboost_serialization.a
libboost_system.a
libboost_thread.a

If you could share how these were made that would be very helpful, as we could then create the equivalent files for our systems.

Thanks,
Niels

Niels Hanson
Bioinformatics PhD Candidate
Hallam Lab
University of British Columbia
Department of Microbiology & Immunology
2552-2350 Health Sciences Mall
Vancouver, BC Canada V6T 1Z3
T: 604-827-4216

The text was updated successfully, but these errors were encountered:

zhaoyanswill · 2014-06-04T22:38:52Z

Hi Niels,

They are compiled from BOOST library (http://www.boost.org/), you can
download the latest version and compile it or use brew tool under OSX to
install it. Please let me know if you have any questions!

Sincerely,
Yongan

On 6/4/2014 6:34 PM, nielshanson wrote:

Hey Man,

We'd like to compile the source for other operating system, i.e., Mac
OSX, however, we need to know how the archive files were compiled from
the boost library in order to create compatible versions.

Specifically these are files in the |Src/| folder:

|libboost_chrono.a
libboost_serialization.a
libboost_system.a
libboost_thread.a
|

If you could share how these were made that would be very helpful, as
we could then create the equivalent files for our systems.

Thanks,
Niels

Niels Hanson
Bioinformatics PhD Candidate
Hallam Lab
University of British Columbia
Department of Microbiology & Immunology
2552-2350 Health Sciences Mall
Vancouver, BC Canada V6T 1Z3
T: 604-827-4216

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#3.

nielshanson · 2014-06-11T23:02:28Z

Thanks Yongan,

We got to the bottom of it on our side. In case anyone wants a play-by-play on how to install for Mac (OS X 10.6.8) (using macports). I've put some installation notes below:

Install a version of gcc:

sudo port install gcc4X

Install the boost libraries:

sudo port install boost

Copy from the macports library directory (usually /opt/local/lib) the relevant libraries for RAPSearch2 into the <RAPSearch2>/Src folder: libboost_chrono-mt.a, libboost_serialization-mt.a, libboost_system-mt.a, and libboost_thread-mt.a. Rename them to match the Makefile.
Make sure that gcc is set as the default compiler for g++
sudo port select --set gcc gcc42
Note: you can list the available compilers in macports with the command: port select --list gcc
Try to run the install shell script: ./install. If it causes an undefined symbols error related to the boost libraries:

$ ./install 

RAPSearch installer
rm -f *.o rapsearch prerapsearch
g++ -c -O3 -w  HashSearch.cpp -o HashSearch.o -I ./
g++ -c -O3 -w  BlastStat.cpp -o BlastStat.o -I ./
g++ -c -O3 -w  Seg.cpp -o Seg.o -I ./
g++ -c -O3 -w  mergeUnit.cpp -o mergeUnit.o -I ./
g++ -O3 -w  -o rapsearch main.cpp HashSearch.o BlastStat.o Seg.o mergeUnit.o -I ./ -L ./ -lboost_serialization -lpthread -lboost_thread -lboost_system -lboost_chrono
Undefined symbols for architecture x86_64:
  "boost::thread::start_thread()", referenced from:
      boost::threadpool::detail::worker_thread<boost::threadpool::detail::pool_core<boost::function0<void>, boost::threadpool::fifo_scheduler, boost::threadpool::static_size, boost::threadpool::resize_controller, boost::threadpool::wait_for_all_tasks> >::create_and_attach(boost::shared_ptr<boost::threadpool::detail::pool_core<boost::function0<void>, boost::threadpool::fifo_scheduler, boost::threadpool::static_size, boost::threadpool::resize_controller, boost::threadpool::wait_for_all_tasks> > const&) in HashSearch.o

try removing the include flag -I from the compilation lines in the Makefile. This seems to solve the problem.

zhaoyanswill · 2014-06-12T04:23:00Z

Thanks a lot!

I'll put it in readme file. Thank you for promoting RAPSearch2!

Sincerely,
Yongan

On 6/11/2014 7:02 PM, nielshanson wrote:

Thanks Yongan,

We got to the bottom of it on our side. In case anyone wants a
play-by-play on how to install for Mac (OS X 10.6.8) (using macports).
I've put some installation notes below:

Install a version of gcc:

|sudo port install gcc4X
|

Install the boost libraries:

|sudo port install boost
|

Copy from the macports library directory (usually
|/opt/local/lib|) the relevant libraries for RAPSearch2 into the
|/Src| folder: |libboost_chrono-mt.a|,
|libboost_serialization-mt.a|, |libboost_system-mt.a|, and
|libboost_thread-mt.a|. You can rename them to match the
|Makefile| if you like

Make sure that gcc is set as the default compiler for |g++| sudo
port select --set gcc gcc42 Note: you can list the available
compilers in macports with the command: |port select --list gcc|

Try to run the |install| shell script: |./install|. If it causes
an |undefined symbols| error related to the boost libraries:

|$ ./install

RAPSearch installer
rm -f *.o rapsearch prerapsearch
g++ -c -O3 -w HashSearch.cpp -o HashSearch.o -I ./
g++ -c -O3 -w BlastStat.cpp -o BlastStat.o -I ./
g++ -c -O3 -w Seg.cpp -o Seg.o -I ./
g++ -c -O3 -w mergeUnit.cpp -o mergeUnit.o -I ./
g++ -O3 -w -o rapsearch main.cpp HashSearch.o BlastStat.o Seg.o mergeUnit.o -I ./ -L ./ -lboost_serialization -lpthread -lboost_thread -lboost_system -lboost_chrono
Undefined symbols for architecture x86_64:
"boost::thread::start_thread()", referenced from:
boost::threadpool::detail::worker_threadboost::threadpool::detail::pool_core<boost::function0<void, boost::threadpool::fifo_scheduler, boost::threadpool::static_size, boost::threadpool::resize_controller, boost::threadpool::wait_for_all_tasks> >::create_and_attach(boost::shared_ptrboost::threadpool::detail::pool_core<boost::function0<void, boost::threadpool::fifo_scheduler, boost::threadpool::static_size, boost::threadpool::resize_controller, boost::threadpool::wait_for_all_tasks> > const&) in HashSearch.o
|

try removing the include flag |-I| from the compilation lines in the
|Makefile|. This seems to solve the problem.

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#3 (comment).

bigsparty · 2014-07-18T08:47:54Z

Hey nielshanson and Yongan,

I am using Mac OSX 10.7.5 and tried to install RAPSearch 2 according to the original instructions and (after being unssuccesful) according to the instructions of nielshanson. However, I get the following error/output:
RAPSearch installer
rm -f .o rapsearch prerapsearch
g++ -c -O3 -w HashSearch.cpp -o HashSearch.o -I ./
g++ -c -O3 -w BlastStat.cpp -o BlastStat.o -I ./
g++ -c -O3 -w Seg.cpp -o Seg.o -I ./
g++ -c -O3 -w mergeUnit.cpp -o mergeUnit.o -I ./
g++ -O3 -w -o rapsearch main.cpp HashSearch.o BlastStat.o Seg.o mergeUnit.o -I ./ -L ./ -lboost_serialization -lpthread -lboost_thread -lboost_system -lboost_chrono -lrt
ld: library not found for -lboost_serialization
collect2: ld returned 1 exit status
make: ** [rapsearch] Error 1
mv: rename Src/rapsearch to bin/rapsearch: No such file or directory
mv: rename Src/prerapsearch to bin/prerapsearch: No such file or directory

Executables are now installed under bin/

If I do not replace the -lboost_serialization -lpthread -lboost_thread -lboost_system -lboost_chrono files in /src I get the same output but with the following ending:
ld: library not found for -lrt
collect2: ld returned 1 exit status
make: *** [rapsearch] Error 1
mv: rename Src/rapsearch to bin/rapsearch: No such file or directory
mv: rename Src/prerapsearch to bin/prerapsearch: No such file or directory

Could you be so kind and help me on this issue?

Sincerely,
Felix

zhaoyanswill · 2014-07-18T13:54:10Z

Hi Felix,

It looks like boost libraries are missed. Did you install boost
libraries (|sudo port install boost|) and copy them to RAPSearch2 src
folder?

Sincerely,
Y. Z.

On 07/18/2014 04:47 AM, bigsparty wrote:

Hey nielshanson and Yongan,

I am using Mac OSX 10.7.5 and tried to install RAPSearch 2 according
to the original instructions and (after being unssuccesful) according
to the instructions of nielshanson. However, I get the following
error/output:
RAPSearch installer
rm -f /.o rapsearch prerapsearch
g++ -c -O3 -w HashSearch.cpp -o HashSearch.o -I ./
g++ -c -O3 -w BlastStat.cpp -o BlastStat.o -I ./
g++ -c -O3 -w Seg.cpp -o Seg.o -I ./
g++ -c -O3 -w mergeUnit.cpp -o mergeUnit.o -I ./
g++ -O3 -w -o rapsearch main.cpp HashSearch.o BlastStat.o Seg.o
mergeUnit.o -I ./ -L ./ -lboost_serialization -lpthread -lboost_thread
-lboost_system -lboost_chrono -lrt
ld: library not found for -lboost_serialization
collect2: ld returned 1 exit status
make: **/ [rapsearch] Error 1
mv: rename Src/rapsearch to bin/rapsearch: No such file or directory
mv: rename Src/prerapsearch to bin/prerapsearch: No such file or directory

Executables are now installed under bin/

Could you be so kind and help me on this issue?

Sincerely,
Felix

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#3 (comment).

bigsparty · 2014-07-18T14:03:20Z

Hey Yongan,

yes, I installed boost and copied the boost libraries into the src folder.

The error message is the 2nd of my post:

rm -f .o rapsearch prerapsearch
g++ -c -O3 -w HashSearch.cpp -o HashSearch.o -I ./
g++ -c -O3 -w BlastStat.cpp -o BlastStat.o -I ./
g++ -c -O3 -w Seg.cpp -o Seg.o -I ./
g++ -c -O3 -w mergeUnit.cpp -o mergeUnit.o -I ./
g++ -O3 -w -o rapsearch main.cpp HashSearch.o BlastStat.o Seg.o mergeUnit.o -I ./ -L ./ -lboost_serialization -lpthread -lboost_thread -lboost_system -lboost_chrono -lrt
ld: library not found for -lrt
collect2: ld returned 1 exit status
make: *** [rapsearch] Error 1
mv: rename Src/rapsearch to bin/rapsearch: No such file or directory
mv: rename Src/prerapsearch to bin/prerapsearch: No such file or directory

Sincerely,
Felix

zhaoyanswill · 2014-07-18T14:07:17Z

Hi Felix,

Could you try to remove '-lrt' in Makefile and re-compile it?

Sincerely,
Y. Z.

On 07/18/2014 10:03 AM, bigsparty wrote:

Hey Yongan,

yes, I installed boost and copied the boost libraries into the src folder.

The error message is the 2nd of my post:

rm -f .o rapsearch prerapsearch
g++ -c -O3 -w HashSearch.cpp -o HashSearch.o -I ./
g++ -c -O3 -w BlastStat.cpp -o BlastStat.o -I ./
g++ -c -O3 -w Seg.cpp -o Seg.o -I ./
g++ -c -O3 -w mergeUnit.cpp -o mergeUnit.o -I ./
g++ -O3 -w -o rapsearch main.cpp HashSearch.o BlastStat.o Seg.o
mergeUnit.o -I ./ -L ./ -lboost_serialization -lpthread -lboost_thread
-lboost_system -lboost_chrono -lrt
ld: library not found for -lrt
collect2: ld returned 1 exit status
make: *** [rapsearch] Error 1
mv: rename Src/rapsearch to bin/rapsearch: No such file or directory
mv: rename Src/prerapsearch to bin/prerapsearch: No such file or directory

Sincerely,
Felix

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#3 (comment).

bigsparty · 2014-07-18T14:20:19Z

Hey Yongan,

I tried to remove the -lrt but got the folloing error message:

RAPSearch installer
rm -f *.o rapsearch prerapsearch
g++ -c -O3 -w HashSearch.cpp -o HashSearch.o -I ./
g++ -c -O3 -w BlastStat.cpp -o BlastStat.o -I ./
g++ -c -O3 -w Seg.cpp -o Seg.o -I ./
g++ -c -O3 -w mergeUnit.cpp -o mergeUnit.o -I ./
g++ -O3 -w -o rapsearch main.cpp HashSearch.o BlastStat.o Seg.o mergeUnit.o -I ./ -L ./ -lboost_serialization -lpthread -lboost_thread -lboost_system -lboost_chrono
Undefined symbols for architecture x86_64:
"boost::system::generic_category()", referenced from:
__static_initialization_and_destruction_0(int, int)in ccfB2xme.o

(.......) extremely long error message

Since nielshanson suggested to remove the -I in the makefile I tried this too but ended up with this error:

rm -f *.o rapsearch prerapsearch
g++ -c -O3 -w HashSearch.cpp -o HashSearch.o ./
In file included from HashSearch.cpp:2:
HashSearch.h:11:35: error: boost/thread/thread.hpp: No such file or directory
In file included from HashSearch.h:14,
from HashSearch.cpp:2:
(.......) extremely long error message

Sincerely,
Felix

zhaoyanswill · 2014-07-18T14:26:50Z

Hi Felix,

It could be lacking boost_system library. Is it in the src folder?
What's its name?

Sincerely,
Y. Z.

On 07/18/2014 10:20 AM, bigsparty wrote:

Hey Yongan,

I tried to remove the -lrt but got the folloing error message:

RAPSearch installer
rm -f *.o rapsearch prerapsearch
g++ -c -O3 -w HashSearch.cpp -o HashSearch.o -I ./
g++ -c -O3 -w BlastStat.cpp -o BlastStat.o -I ./
g++ -c -O3 -w Seg.cpp -o Seg.o -I ./
g++ -c -O3 -w mergeUnit.cpp -o mergeUnit.o -I ./
g++ -O3 -w -o rapsearch main.cpp HashSearch.o BlastStat.o Seg.o
mergeUnit.o -I ./ -L ./ -lboost_serialization -lpthread -lboost_thread
-lboost_system -lboost_chrono
Undefined symbols for architecture x86_64:
"boost::system::generic_category()", referenced from:
__static_initialization_and_destruction_0(int, int)in ccfB2xme.o

(.......) extremely long error message

Since nielshanson suggested to remove the -I in the makefile I tried
this too but ended up with this error:

rm -f *.o rapsearch prerapsearch
g++ -c -O3 -w HashSearch.cpp -o HashSearch.o ./
In file included from HashSearch.cpp:2:
HashSearch.h:11:35: error: boost/thread/thread.hpp: No such file or
directory
In file included from HashSearch.h:14,
from HashSearch.cpp:2:
(.......) extremely long error message

Sincerely,
Felix

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#3 (comment).

bigsparty · 2014-07-18T15:11:00Z

Hey Yongan,

sorry for the delayed answer. No it is not there. Where can I get it? Sorry if the question is stupid (I am new to this) but is it possible for you to upload a package with the necessary libraries?

Sincerely,
Felix

zhaoyanswill · 2014-07-18T15:15:23Z

Hi Felix,

You can install boost libraries (|sudo port install boost|) and then
copy them (|/opt/local/lib|) to RAPSearch2 src folder.

Sincerely,
Y. Z.

On 07/18/2014 11:11 AM, bigsparty wrote:

Hey Yongan,

sorry for the delayed answer. No it is not there. Where can I get it?

Sincerely,
Felix

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#3 (comment).

bigsparty · 2014-07-18T15:32:20Z

Hey Yongan,

thank you for the support on this issue, it is now working for me. Nielshanson's comment lacks the information that -lrt should be removed from the makefile before compiling. Otherwise it can be used as step-by-step instruction.

Maybe you can add this to the Readme.

Thanks,
Felix

zhaoyanswill · 2014-07-18T16:14:09Z

Great! I'll add this!

Sincerely,
Y. Z.

On 07/18/2014 11:32 AM, bigsparty wrote:

Hey Yongan,

thank you for the support on this issue, it is now working for me.
Nielshanson's comment lacks the information that -lrt should be
removed from the makefile before compiling. Otherwise it can be used
as step-by-step instruction.

Maybe you can add this to the Readme.

Thanks,
Felix

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#3 (comment).

snayfach · 2014-09-18T17:23:18Z

I'm currently trying to compile RAPsearch2 for OSX 10.9.4, using the above instructions, and have run into problems. Any help would be greatly appreciated.

Here's what I did:
sudo port install gcc49
sudo port select --set gcc mp-gcc49
sudo port install boost
copied boost libraries from /opt/local/lib to /Src
renamed libraries from <libboost_lib>-mt.a to <libboost_lib>.a
removed -lrt from makefile
commented out the line "INC := -I ./" from the makefile and removed references to $(INC)

Here is the error I am getting:
$ ./install

RAPSearch installer
rm -f .o rapsearch prerapsearch
g++ -c -O3 -w HashSearch.cpp -o HashSearch.o
g++ -c -O3 -w BlastStat.cpp -o BlastStat.o
g++ -c -O3 -w Seg.cpp -o Seg.o
g++ -c -O3 -w mergeUnit.cpp -o mergeUnit.o
g++ -O3 -w -o rapsearch main.cpp HashSearch.o BlastStat.o Seg.o mergeUnit.o -L ./ -lboost_serialization -lpthread -lboost_thread -lboost_system -lboost_chrono
Undefined symbols for architecture x86_64:
...
...
...
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make: ** [rapsearch] Error 1
mv: rename Src/rapsearch to bin/rapsearch: No such file or directory
mv: rename Src/prerapsearch to bin/prerapsearch: No such file or directory

Executables are now installed under bin/

zhaoyanswill · 2014-09-18T17:52:50Z

Hi

It seems that the compiler is not compatible with c++ library after
searching it online. Could you try to replace 'g++' in Makefile with
'clang++'?

Sincerely,
Yongan

On 9/18/2014 1:23 PM, snayfach wrote:

I'm currently trying to compile RAPsearch2 for OSX 10.9.4, using the
above instructions, and have run into problems. Any help would be
greatly appreciated.

Here's what I did:
sudo port install gcc49
sudo port select --set gcc mp-gcc49
sudo port install boost
copied boost libraries from /opt/local/lib to /Src
renamed libraries from -mt.a to .a
removed -lrt from makefile
commented out the line "INC := -I ./" from the makefile and removed
references to $(INC)

Here is the error I am getting:
$ ./install

RAPSearch installer
rm -f /.o rapsearch prerapsearch
g++ -c -O3 -w HashSearch.cpp -o HashSearch.o
g++ -c -O3 -w BlastStat.cpp -o BlastStat.o
g++ -c -O3 -w Seg.cpp -o Seg.o
g++ -c -O3 -w mergeUnit.cpp -o mergeUnit.o
g++ -O3 -w -o rapsearch main.cpp HashSearch.o BlastStat.o Seg.o
mergeUnit.o -L ./ -lboost_serialization -lpthread -lboost_thread
-lboost_system -lboost_chrono
Undefined symbols for architecture x86_64:
...
...
...
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make: **/ [rapsearch] Error 1
mv: rename Src/rapsearch to bin/rapsearch: No such file or directory
mv: rename Src/prerapsearch to bin/prerapsearch: No such file or directory

Executables are now installed under bin/

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#3 (comment).

snayfach · 2014-09-18T18:08:17Z

You say that the compiler I'm using (gcc49) is not compatible with one of the c++ libraries. Is this correct? Is there another gcc I should use?

In any case, I replaced 'g++' in Makefile with 'clang++'. Here's the error I got:

$ ./install

RAPSearch installer
rm -f .o rapsearch prerapsearch
clang++ -c -O3 -w HashSearch.cpp -o HashSearch.o
In file included from HashSearch.cpp:2:
./HashSearch.h:11:10: error: 'boost/thread/thread.hpp' file not found with include; use
"quotes" instead
#include <boost/thread/thread.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~
"boost/thread/thread.hpp"
In file included from HashSearch.cpp:2:
In file included from ./HashSearch.h:11:
./boost/thread/thread.hpp:12:10: fatal error: 'boost/thread/detail/platform.hpp' file not found
#include <boost/thread/detail/platform.hpp>
^
2 errors generated.
make: ** [HashSearch.o] Error 1
mv: rename Src/rapsearch to bin/rapsearch: No such file or directory
mv: rename Src/prerapsearch to bin/prerapsearch: No such file or directory

Executables are now installed under bin/

zhaoyanswill · 2014-09-18T18:19:25Z

Hi,

Is 'boost/thread' in your 'Src' directory?

Sincerely,
Yongan

On 9/18/2014 2:08 PM, snayfach wrote:

You say that the compiler I'm using (gcc49) is not compatible with one
of the c++ libraries. Is this correct? Is there another gcc I should use?

In any case, I replaced 'g++' in Makefile with 'clang++'. Here's the
error I got:

$ ./install

RAPSearch installer
rm -f /.o rapsearch prerapsearch
clang++ -c -O3 -w HashSearch.cpp -o HashSearch.o
In file included from HashSearch.cpp:2:
./HashSearch.h:11:10: error: 'boost/thread/thread.hpp' file not found
with include; use
"quotes" instead
#include
^~~~~~~~~~~~~~~~~~~~~~~~~
"boost/thread/thread.hpp"
In file included from HashSearch.cpp:2:
In file included from ./HashSearch.h:11:
./boost/thread/thread.hpp:12:10: fatal error:
'boost/thread/detail/platform.hpp' file not found
#include
^
2 errors generated.
make: **/ [HashSearch.o] Error 1
mv: rename Src/rapsearch to bin/rapsearch: No such file or directory
mv: rename Src/prerapsearch to bin/prerapsearch: No such file or directory

Executables are now installed under bin/

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#3 (comment).

snayfach · 2014-09-18T18:21:08Z

The file 'libboost_thread.a' is in my /Src directory. Here are the other files:

$ ls
BlastStat.cpp boost mergeUnit.cpp
BlastStat.h cindex.h mergeUnit.h
BuildHash.cpp codon.h n2a.h
HashSearch.cpp libboost_chrono.a paras.h
HashSearch.h libboost_serialization.a sortUnit.h
Makefile libboost_system.a threadpool
Seg.cpp libboost_thread.a threadpool.hpp
Seg.h lnfac.h weight.h
aa.h main.cpp

zhaoyanswill · 2014-09-18T18:39:26Z

Could you check if 'boost/thread' is in your 'Src' directory?

Sincerely,
Yongan

On 9/18/2014 2:08 PM, snayfach wrote:

You say that the compiler I'm using (gcc49) is not compatible with one
of the c++ libraries. Is this correct? Is there another gcc I should use?

In any case, I replaced 'g++' in Makefile with 'clang++'. Here's the
error I got:

$ ./install

RAPSearch installer
rm -f /.o rapsearch prerapsearch
clang++ -c -O3 -w HashSearch.cpp -o HashSearch.o
In file included from HashSearch.cpp:2:
./HashSearch.h:11:10: error: 'boost/thread/thread.hpp' file not found
with include; use
"quotes" instead
#include
^~~~~~~~~~~~~~~~~~~~~~~~~
"boost/thread/thread.hpp"
In file included from HashSearch.cpp:2:
In file included from ./HashSearch.h:11:
./boost/thread/thread.hpp:12:10: fatal error:
'boost/thread/detail/platform.hpp' file not found
#include
^
2 errors generated.
make: **/ [HashSearch.o] Error 1
mv: rename Src/rapsearch to bin/rapsearch: No such file or directory
mv: rename Src/prerapsearch to bin/prerapsearch: No such file or directory

Executables are now installed under bin/

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#3 (comment).

snayfach · 2014-09-18T18:46:38Z

No, there is no boost directory in my RAPsearch Src folder

snayfach · 2014-09-18T18:52:45Z

Sorry, my mistake. Yes, 'boost/thread' is in my 'Src' directory

zhaoyanswill · 2014-09-18T19:07:58Z

What undefinded symbols showed when compiling the program?

Sincerely,
Yongan

On 9/18/2014 2:52 PM, snayfach wrote:

Sorry, my mistake. Yes, 'boost/thread' is in my 'Src' directory

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#3 (comment).

snayfach · 2014-09-18T21:32:24Z

So, I was finally able to compile the software using nielshanson's SOP and my old laptop which was running OSX 10.7.5. Those directions do not work for 10.9.4.

Thankfully, the compiled binaries run on both OSX 10.7.5 and 10.9.4.

zhaoyanswill · 2014-09-18T21:34:10Z

Sound great!

Sincerely,
Yongan

On 9/18/2014 5:32 PM, snayfach wrote:

So, I was finally able to compile the software using nielshanson's SOP
and my old laptop which was running OSX 10.7.5. Those directions do
not work for 10.9.4.

Thankfully, the compiled binaries run on both OSX 10.7.5 and 10.9.4.

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#3 (comment).

QuorumUS · 2014-11-04T20:01:16Z

I recompiled the boost libraries and copied them into Src/ on a Mac (10.9.5); however, when I run ./install (with or without -I and -lrt) I get some form of the following error message: error: unable to open output file 'Src/main-d39381.o': 'Error opening output file 'Src/main-d39381.o': No such file or directory'

Any ideas?

Thank you!

nana-marinbio · 2016-06-24T01:25:01Z

Hey nielshanson and Yongan,

It seems everybody solved the problem with rapsearch2 in a Mac but me.
I am using Mac OSX 10.7.5 and tried all above suggestions.
I checked my gcc version, installed boost libraries, checked if gcc is the default compiler and llvm-gcc42 is selected and active. I copied libboost_chrono-mt.a, libboost_system-mt.a, libboost_serialization-mt.dylib and libboost_thread-mt.dylib. For the latter two there is no .a extension, only .dylig. I replaced them by the ones in the Src folder and renamed to match the Makefile. Then I commented the INC flag and deleted the $(INC).
The error message begins with:
RAPSearch installer
rm -f .o rapsearch prerapsearch
g++ -c -O3 -w HashSearch.cpp -o HashSearch.o
In file included from HashSearch.cpp:2:
HashSearch.h:11:35: error: boost/thread/thread.hpp: No such file or directory … and continues (its very long) until finally:
make: ** [HashSearch.o] Error 1
mv: rename Src/rapsearch to bin/rapsearch: No such file or directory
mv: rename Src/prerapsearch to bin/prerapsearch: No such file or directory

Executables are now installed under bin/

Can anybody help me?
Thank you in advance.
Nana

wookietreiber mentioned this issue Sep 24, 2014

GNU autotools based build #8

Open

Public-Health-Bioinformatics mentioned this issue Jul 30, 2015

Prerapsearch Aborted (core dumped) #19

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.a files for other operating system #3

.a files for other operating system #3

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nielshanson commented Jun 4, 2014

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