PaPaRa compilation issue (tr1/memory and malloc.h files)

[Alicia S. Arroyo]

Hello, 

I downloaded PaPaRa 2.4 from Exelixis Lab web page and tried to build it by using sh build_papara2.sh, I got an error related to boost libraries (1_61) and apparently I installed them correctly, so I have a folder alicia/Software/papara_nt-2.4 and alicia/Software/boost_1_61_0. Then, I changed the path to the boost library in the build_papara2.sh file as follows:

g++ -o papara -O3 -msse4a -I. -I /Users/alicia/Software/boost_1_61_0/boost -I ivy_mike/src/ -I ublasJama-1.0.2.3 papara.cpp pvec.cpp pars_align_seq.cpp (etc...)

When trying again to run sh build_papara.sh, these following errors appear:

In file included from papara.cpp:26:

In file included from ivy_mike/src/ivymike/fasta.h:40:

ivy_mike/src/ivymike/aligned_buffer.h:30:10: fatal error: 'malloc.h' file not found

#include <malloc.h>

         ^

1 error generated.

In file included from pvec.cpp:21:

In file included from ./pvec.h:41:

In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:31:

ivy_mike/src/ivymike/smart_ptr.h:37:10: fatal error: 'tr1/memory' file not found

#include <tr1/memory>

         ^

1 error generated.

In file included from papara2_main.cpp:25:

In file included from ./papara.h:46:

In file included from ./pvec.h:41:

In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:31:

ivy_mike/src/ivymike/smart_ptr.h:37:10: fatal error: 'tr1/memory' file not found

#include <tr1/memory>

         ^

1 error generated.

In file included from blast_partassign.cpp:13:

In file included from ./papara.h:46:

In file included from ./pvec.h:41:

In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:31:

ivy_mike/src/ivymike/smart_ptr.h:37:10: fatal error: 'tr1/memory' file not found

#include <tr1/memory>

         ^

1 error generated.

In file included from ivy_mike/src/tree_parser.cpp:22:

In file included from ivy_mike/src/ivymike/tree_parser.h:37:

ivy_mike/src/ivymike/smart_ptr.h:37:10: fatal error: 'tr1/memory' file not found

#include <tr1/memory>

         ^

1 error generated.

I don't know what I should do to fix that... Any piece of advice?

Thank you very much, 

A. 

[lucas...@h-its.org]

Hi Alicia,

"tr1/memory" is part of boost. Instead of changing the install script, you might want to try to copy or symlink the "boost" directory (part of the boost_version_number directory) to the papara directory and then run the install script.

As for the "malloc" file, I am not sure where this comes from. Maybe this will be resolved at the same time. If not, more investigation will be needed...

So long
Lucas

[Alicia S. Arroyo]

Hi Lucas, 

Thank you for your quick answer. I tried your suggestion, but still the same error. For installing boost libraries I'm doing:  

cd boost_1_61_0/

./bootstrap.sh --prefix=/Users/alicia/Software/papara_nt-2.4

./b2

./b2 install

After the ./b2 step, I get this message:

The Boost C++ Libraries were successfully built!

The following directory should be added to compiler include paths:

    /Users/alicia/Software/boost_1_61_0

The following directory should be added to linker library paths:

    /Users/alicia/Software/boost_1_61_0/stage/lib

So, I guess that I'm doing something wrong around these final steps... 

A.

[lucas...@h-its.org]

Why do you use the papara path as the boost install path prefix?

 > ./bootstrap.sh --prefix=/Users/alicia/Software/papara_nt-2.4

Or was that a typo? In the output, it looks like boost is installed to /Users/alicia/Software/boost_1_61_0 instead, so, without that prefix...

Anyway, the steps look correct. Can you check whether the file

 > /Users/alicia/Software/papara_nt-2.4/boost/tr1/memory.hpp

exists? If not, try this:

> cd /Users/alicia/Software/papara_nt-2.4
> ln -s /Users/alicia/Software/boost_1_61_0/boost boost

and then try to compile papara again.

Lucas

[Alicia S. Arroyo]

Hi Lucas, 

I tried to use the papara path as the boost install path because I checked some "stuckoverflow" suggestions...jejeje. 

Anyway, I did it again without the prefix, and the file memory.hpp in the /boost/tr1/ path is there... And the same errors...

A. 

[Alexey Kozlov]

Hi Alicia,

those issues seem to be Mac-specific, according to:

https://github.com/RIOT-OS/RIOT/issues/2361
https://github.com/cuberite/cuberite/issues/424

So could you please try the following:

1. Edit the ivy_mike/src/ivymike/aligned_buffer.h file and change the line

#include <malloc.h>

to

#include <stdlib.h>

2. Edit the ivy_mike/src/ivymike/smart_ptr.h file and change the line

#include <tr1/memory>

to

#include <memory>

and then cross fingers and re-compile...


Best,
Alexey

> > ln -s/Users/alicia/Software/boost_1_61_0/boost boost

>
> and then try to compile papara again.
>
> Lucas
>

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[Alicia S. Arroyo]

Hi Alexey, 

Unfortunately it doesn't work. I got more errors (attached the error messages that I get). Should I try to install it in Linux instead of Mac if this is the problem?

A. 

[lucas...@h-its.org]

Hi Alicia,

it's hard for us to detect the problem, as all of us are working on Linux systems - so we cannot reproduce the error. Yes, you can try to run it on Linux. Maybe even a Virtual Machine, if your data is not too big. Another option is to try an older version of boost (~1.50), maybe they simply changed some stuff there...

Don't give up ;-)

Lucas

[Alexandros Stamatakis]

Hi Lucas and Alexey,

We do have a MAC in the lab for resolving this kind of issues.

Alicia, the code was written by a PhD student of mine who left the lab
in early 2013 and unfortunately went to industry.

Nontheless, he still helps out from time to time, I'll try to contact him.

All the best,

Alexis

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Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[Alexey Kozlov]

Hi Alicia,

could you please try the new version of papara (attached) ?

Simon (the author of papara) fixed all the issues you identified, so it should now also compile on the Mac.

Best,
Alexey

On 03.06.2016 14:51, Alicia S. Arroyo wrote:
> Hi Alexey,
>
> Unfortunately it doesn't work. I got more errors (attached the error messages that I get). Should I try to install it in
> Linux instead of Mac if this is the problem?
>
> A.
>
> On Thursday, 2 June 2016 13:28:17 UTC+2, Alexey Kozlov wrote:
>
> Hi Alicia,
>
> those issues seem to be Mac-specific, according to:
>

> https://github.com/RIOT-OS/RIOT/issues/2361 <https://github.com/RIOT-OS/RIOT/issues/2361>
> https://github.com/cuberite/cuberite/issues/424 <https://github.com/cuberite/cuberite/issues/424>

> <javascript:>
> > <mailto:raxml+un...@googlegroups.com <javascript:>>.
> > For more options, visit https://groups.google.com/d/optout <https://groups.google.com/d/optout>.

[lucas...@h-its.org]

Hi Alicia,

we just updated PaPaRa and made the set-up process easier. See here: http://sco.h-its.org/exelixis/web/software/papara/index.html

Let us know whether that works for you.

So long
Lucas

[Alicia S. Arroyo]

Hi Lucas, Alexey and Alexis:

It worked!!!! Oh, man, thank you soooooo much!!! 

It was a matter of the version, because v2.5 works great (I had to compile it because the binary didn't work, but it was not a problem). Also, thank you for the web set-up instructions :)

Thank you very very very veeery much!! I'm excited to use it with my new data :D

Alicia

[lucas...@h-its.org]

Glad to hear ;-)

If there are any more issues, just shout. Otherwise, good luck with your analyses!

Lucas