<div dir="ltr">Thanks Mark for pointing those out. Committed <div><br></div><div><div><a href="http://www.admb-project.org/redmine/projects/issues/repository/revisions/1731">http://www.admb-project.org/redmine/projects/issues/repository/revisions/1731</a><br>
</div><div><br></div><div>What permission problem are you having? I can't seem to duplicate those issues.</div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Mar 3, 2014 at 10:02 PM, Mark Payne <span dir="ltr"><<a href="mailto:mpa@aqua.dtu.dk" target="_blank">mpa@aqua.dtu.dk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
Thanks for the tips. It works now following these instructions, although with mods. However, there are a couple of things that I would point out<br>
* there is a tilde missing in the source directory to copy from in step 6. It should read:<br>
[~]$ sudo cp -Rvf ~/admb/build/dist /usr/local/admb<br>
Although the prompt indicates that this command is being run from the home directory there is no suggestion in the text that you need to change accordingly.<br>
* there is a permissions problem created for me (at least) when copying admb/ to /usr/local/admb. By copying as root ie via sudo, all new directories are owned by root, which means that they can't be run by the user. Adding the -p flag to the copy solves this problem<br>
sudo cp -Rvfp ~/admb/build/dist /usr/local/admb<br>
but may not be the cleanest solution ie having files owned by my local user in /usr/local...<br>
* Most importantly, these new build instructions are not reflected in INSTALL.txt!<br>
<br>
Mark<br>
________________________________________<br>
Fra: John Sibert [<a href="mailto:sibert@hawaii.edu">sibert@hawaii.edu</a>]<br>
Sendt: 4. marts 2014 07:12<br>
Til: bigA<br>
Cc: Johnoel Ancheta; Mark Payne; <a href="mailto:users@admb-project.org">users@admb-project.org</a><br>
Emne: Re: [ADMB Users] Build ADMB 11.1<br>
<div class="HOEnZb"><div class="h5"><br>
I'm not convinced that symbolic links are really simpler (because I have<br>
trouble remembering the syntax), so I prefer the environment variable in<br>
most cases. Anyhow it is nice to have the option to do it either way.<br>
<br>
Thanks, Aaron, for preparing the man page. I'm not sure it is consistent<br>
with `admb --help` though. A couple of options seem to be missing.<br>
> $ admb --help<br>
><br>
> Builds AD Model Builder executable or library.<br>
><br>
> Usage: admb [-c] [-d] [-g] [-r] [-f] model [src(s)]<br>
><br>
> Options:<br>
> -c Build only object file(s) (.obj).<br>
> -d Build a shared library (.so).<br>
> -g Build with debug symbols.<br>
> -r Build with Random effects library (ADMB-RE).<br>
> -f Build with Fast optimized mode library (no bounds checking).<br>
> By default, admb script builds with bounds checking.<br>
> model TPL file (ie simple.tpl or the filename simple with no .tpl<br>
> extension)<br>
> src(s) C/C++ Source file(s) containing classes, methods and variables<br>
> that<br>
> are used in model.<br>
<br>
<br>
John Sibert<br>
Emeritus Researcher, SOEST<br>
University of Hawaii at Manoa<br>
Honolulu HI (GMT-10)<br>
<a href="tel:808-294-3842" value="+18082943842">808-294-3842</a><br>
<br>
Visit the ADMB project <a href="http://admb-project.org/" target="_blank">http://admb-project.org/</a><br>
<br>
On 03/03/2014 03:48 PM, bigA wrote:<br>
> In general, fixing the paths and making necessary (or convenient)<br>
> symbolic links is better than asking people to edit their .bashrc .<br>
> Many bash users use their bashrc to configure their working<br>
> environment; admb is just one of countless things I use a shell for.<br>
><br>
> Once again, I have assembled the extant man page; do people think more<br>
> content is needed?<br>
><br>
> <a href="http://www.admb-project.org/developers/packaging/debian/man.pdf/view" target="_blank">http://www.admb-project.org/developers/packaging/debian/man.pdf/view</a><br>
> Cheers!<br>
> Aaron<br>
><br>
><br>
> On Mon, Mar 3, 2014 at 5:27 PM, John Sibert <<a href="mailto:sibert@hawaii.edu">sibert@hawaii.edu</a>> wrote:<br>
>> Why is it preferable to set a symbolic link than to set an environment<br>
>> variable in a .basrc file?<br>
>><br>
>> John Sibert<br>
>> Emeritus Researcher, SOEST<br>
>> University of Hawaii at Manoa<br>
>> Honolulu HI (GMT-10)<br>
>> <a href="tel:808-294-3842" value="+18082943842">808-294-3842</a><br>
>><br>
>> Visit the ADMB project <a href="http://admb-project.org/" target="_blank">http://admb-project.org/</a><br>
>><br>
>><br>
>> On 03/03/2014 08:07 AM, Johnoel Ancheta wrote:<br>
>>> Try<br>
>>><br>
>>> <a href="http://www.admb-project.org/buildbot/documentation/QuickStartUnix.html" target="_blank">http://www.admb-project.org/buildbot/documentation/QuickStartUnix.html</a><br>
>>><br>
>>><br>
>>><br>
>>> On Mon, Mar 3, 2014 at 7:18 AM, Mark Payne <<a href="mailto:mpa@aqua.dtu.dk">mpa@aqua.dtu.dk</a><br>
>>> <mailto:<a href="mailto:mpa@aqua.dtu.dk">mpa@aqua.dtu.dk</a>>> wrote:<br>
>>><br>
>>> Hi,<br>
>>><br>
>>> I am having problems installingADMB 11.1 from the source on the<br>
>>> website ie<br>
>>><br>
>>> <a href="http://admb-project.googlecode.com/files/admb-11.1.zip" target="_blank">http://admb-project.googlecode.com/files/admb-11.1.zip</a><br>
>>><br>
>>> The source appears to build correctly, but fails when trying to<br>
>>> run the simple example. I have RTFM'd to the letter but it seems<br>
>>> that the instructions are incomplete and various items are not<br>
>>> getting picked up in the path.... (see below) What directories<br>
>>> does ADMB need to be in the path?<br>
>>><br>
>>> Mark<br>
>>><br>
>>> admb simple.<br>
>>><br>
>>> *** adlink -s<br>
>>> g++ -o "/home/mpayne/Misc/admb"/contrib/lib/libcontrib.a<br>
>>> "/home/mpayne/Misc/admb"/lib/libadmb.a<br>
>>> /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crt1.o: In<br>
>>> function `_start':<br>
>>> (.text+0x20): undefined reference to `main'<br>
>>> collect2: error: ld returned 1 exit status<br>
>>><br>
>>> Error: Could not build<br>
>>><br>
>>><br>
>>><br>
>>> ------------------------------------------------------------------------<br>
>>> *Fra:* <a href="mailto:users-bounces@admb-project.org">users-bounces@admb-project.org</a><br>
>>> <mailto:<a href="mailto:users-bounces@admb-project.org">users-bounces@admb-project.org</a>><br>
>>> [<a href="mailto:users-bounces@admb-project.org">users-bounces@admb-project.org</a><br>
>>> <mailto:<a href="mailto:users-bounces@admb-project.org">users-bounces@admb-project.org</a>>] pĺ vegne af Johnoel<br>
>>> Ancheta [<a href="mailto:johnoel@hawaii.edu">johnoel@hawaii.edu</a> <mailto:<a href="mailto:johnoel@hawaii.edu">johnoel@hawaii.edu</a>>]<br>
>>> *Sendt:* 21. februar 2014 21:03<br>
>>> *Til:* bigA<br>
>>> *Cc:* <a href="mailto:users@admb-project.org">users@admb-project.org</a> <mailto:<a href="mailto:users@admb-project.org">users@admb-project.org</a>><br>
>>> *Emne:* Re: [ADMB Users] ADMB in standard package formats<br>
>>><br>
>>><br>
>>> The build process has changed. Check the link below.<br>
>>><br>
>>> <a href="http://www.admb-project.org/buildbot/documentation/QuickStartUnix.html" target="_blank">http://www.admb-project.org/buildbot/documentation/QuickStartUnix.html</a><br>
>>><br>
>>> It should be simpler and easier for everyone, but may need some<br>
>>> fine tuning.<br>
>>><br>
>>> Feedback from Barak Pearlmutter was used for the the changes.<br>
>>> Such as the<br>
>>> eliminating the need to set System Variables. Although, it will<br>
>>> still work if they<br>
>>> are set.<br>
>>><br>
>>> If you would like to contribute man pages, please let me know.<br>
>>><br>
>>> Thanks,<br>
>>> Johnoel<br>
>>><br>
>>><br>
>>> On Wed, Feb 19, 2014 at 3:57 AM, bigA <<a href="mailto:jaguar.smart@gmail.com">jaguar.smart@gmail.com</a><br>
>>> <mailto:<a href="mailto:jaguar.smart@gmail.com">jaguar.smart@gmail.com</a>>> wrote:<br>
>>><br>
>>> I can work the man page; I have thus far been responsible for it.<br>
>>> I assume we don't want to write a 5460 line beast of a man page;<br>
>>> however any content that people want included in the man page<br>
>>> shown in<br>
>>> the Debian package.<br>
>>> Honestly, I think that focusing on the standard Linux build<br>
>>> process<br>
>>> and including the man page in the default build process will make<br>
>>> getting admb into the standard linux pipeline.<br>
>>> Barak Pearlmutter is probably a critical resource for this<br>
>>> activity;<br>
>>> however he cannot work on this alone. Has anyone looked at the<br>
>>> patches he has suggested? If the build process needs to be<br>
>>> cleaned up,<br>
>>> who within admb<br>
>>> is willing to work with us on it?<br>
>>><br>
>>> Aaron<br>
>>><br>
>>> On Wed, Feb 19, 2014 at 12:47 AM, Arni Magnusson<br>
>>> <<a href="mailto:arnima@hafro.is">arnima@hafro.is</a> <mailto:<a href="mailto:arnima@hafro.is">arnima@hafro.is</a>>> wrote:<br>
>>> > Our priority should be to release ADMB in standard package<br>
>>> formats: Debian,<br>
>>> > Gentoo, RPM, and Mac.<br>
>>> ><br>
>>> > This will make ADMB much more visible and accessible for<br>
>>> scientists in all<br>
>>> > disciplines. Package repositories are categorized, so ADMB<br>
>>> would be listed<br>
>>> > on autogenerated lists of scientific and statistical<br>
>>> software for Linux, for<br>
>>> > example. These lists are copied to Wikipedia, blogs,<br>
>>> newsletters, etc.<br>
>>> ><br>
>>> > Packaging means adapting the build procedure to Linux<br>
>>> standards (we may be<br>
>>> > there already), writing a short man page, and filling out a<br>
>>> basic template<br>
>>> > file for each package format. Please consider participating<br>
>>> in the ongoing<br>
>>> > effort:<br>
>>> ><br>
>>> > <a href="http://admb-project.org/developers/packaging" target="_blank">http://admb-project.org/developers/packaging</a><br>
>>> ><br>
>>> > Arni<br>
>>> > _______________________________________________<br>
>>> > Users mailing list<br>
>>> > <a href="mailto:Users@admb-project.org">Users@admb-project.org</a> <mailto:<a href="mailto:Users@admb-project.org">Users@admb-project.org</a>><br>
>>><br>
>>> > <a href="http://lists.admb-project.org/mailman/listinfo/users" target="_blank">http://lists.admb-project.org/mailman/listinfo/users</a><br>
>>> _______________________________________________<br>
>>> Users mailing list<br>
>>> <a href="mailto:Users@admb-project.org">Users@admb-project.org</a> <mailto:<a href="mailto:Users@admb-project.org">Users@admb-project.org</a>><br>
>>><br>
>>> <a href="http://lists.admb-project.org/mailman/listinfo/users" target="_blank">http://lists.admb-project.org/mailman/listinfo/users</a><br>
>>><br>
>>><br>
>>><br>
>>> _______________________________________________<br>
>>> Users mailing list<br>
>>> <a href="mailto:Users@admb-project.org">Users@admb-project.org</a> <mailto:<a href="mailto:Users@admb-project.org">Users@admb-project.org</a>><br>
>>><br>
>>> <a href="http://lists.admb-project.org/mailman/listinfo/users" target="_blank">http://lists.admb-project.org/mailman/listinfo/users</a><br>
>>><br>
>>><br>
>>><br>
>>><br>
>>> _______________________________________________<br>
>>> Users mailing list<br>
>>> <a href="mailto:Users@admb-project.org">Users@admb-project.org</a><br>
>>> <a href="http://lists.admb-project.org/mailman/listinfo/users" target="_blank">http://lists.admb-project.org/mailman/listinfo/users</a><br>
>><br>
>><br>
>> _______________________________________________<br>
>> Users mailing list<br>
>> <a href="mailto:Users@admb-project.org">Users@admb-project.org</a><br>
>> <a href="http://lists.admb-project.org/mailman/listinfo/users" target="_blank">http://lists.admb-project.org/mailman/listinfo/users</a><br>
<br>
<br>
</div></div></blockquote></div><br></div>