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zhaoyanswill / RAPSearch2

Reduced Alphabet based Protein similarity Search
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.a files for other operating system #3

Open nielshanson opened 10 years ago

nielshanson commented 10 years ago

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

zhaoyanswill commented 10 years ago

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

— Reply to this email directly or view it on GitHub https://github.com/zhaoyanswill/RAPSearch2/issues/3.

nielshanson commented 10 years ago

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:

sudo port install gcc4X
sudo port install boost
$ ./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 commented 10 years ago

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.

— Reply to this email directly or view it on GitHub https://github.com/zhaoyanswill/RAPSearch2/issues/3#issuecomment-45811482.

bigsparty commented 10 years ago

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 -lboostserialization 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 commented 10 years ago

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

— Reply to this email directly or view it on GitHub https://github.com/zhaoyanswill/RAPSearch2/issues/3#issuecomment-49408702.

bigsparty commented 10 years ago

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 commented 10 years ago

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

— Reply to this email directly or view it on GitHub https://github.com/zhaoyanswill/RAPSearch2/issues/3#issuecomment-49433983.

bigsparty commented 10 years ago

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 commented 10 years ago

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

— Reply to this email directly or view it on GitHub https://github.com/zhaoyanswill/RAPSearch2/issues/3#issuecomment-49435886.

bigsparty commented 10 years ago

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 commented 10 years ago

Hi Felix,

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

Nielshanson's comment: 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|. Rename them to match the |Makefile|.

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

— Reply to this email directly or view it on GitHub https://github.com/zhaoyanswill/RAPSearch2/issues/3#issuecomment-49441926.

bigsparty commented 10 years ago

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 commented 10 years ago

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

— Reply to this email directly or view it on GitHub https://github.com/zhaoyanswill/RAPSearch2/issues/3#issuecomment-49444496.

snayfach commented 10 years ago

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 x8664 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 commented 10 years ago

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/

— Reply to this email directly or view it on GitHub https://github.com/zhaoyanswill/RAPSearch2/issues/3#issuecomment-56072836.

snayfach commented 10 years ago

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 commented 10 years ago

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/

— Reply to this email directly or view it on GitHub https://github.com/zhaoyanswill/RAPSearch2/issues/3#issuecomment-56078966.

snayfach commented 10 years ago

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 commented 10 years ago

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/

— Reply to this email directly or view it on GitHub https://github.com/zhaoyanswill/RAPSearch2/issues/3#issuecomment-56078966.

snayfach commented 10 years ago

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

snayfach commented 10 years ago

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

zhaoyanswill commented 10 years ago

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

— Reply to this email directly or view it on GitHub https://github.com/zhaoyanswill/RAPSearch2/issues/3#issuecomment-56085126.

snayfach commented 10 years ago

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 commented 10 years ago

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.

— Reply to this email directly or view it on GitHub https://github.com/zhaoyanswill/RAPSearch2/issues/3#issuecomment-56106405.

QuorumUS commented 9 years ago

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 commented 8 years ago

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 libboostthread-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