R help - Jun 2011 - Porting "unmaintained" packages to post R 2.10.0 era

Hi all,

I am trying to re-compile some "unmaintained" (it seems) packages,
namely rSoNIA
and dynamicnetwork from:
http://csde.washington.edu/~skyebend/rsonia/rsoniaDemo/ 
These packages predates R 2.10.0 so they need to be recompile.

After split the single big file in /man in each packages into a file  for each 
function + some minor fix,  I successfully manage to recompile and load the 
packages

C:\BenSave\R\BuildRPackage>R CMD build --binary dynamicnetwork
--binary is deprecated
* checking for file 'dynamicnetwork/DESCRIPTION' ... OK
* preparing 'dynamicnetwork':
* checking DESCRIPTION meta-information ... OK
* checking whether 'INDEX' is up-to-date ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building binary distribution
* installing *source* package 'dynamicnetwork' ...
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
     Classes for Relational Data
Version      1.6 created on      January 28, 2011.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of Washington
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
For citation information, type citation("network").
Type help("network-package") to get started.
* MD5 sums
packaged installation of 'dynamicnetwork' as dynamicnetwork_0.0-4.zip

* DONE (dynamicnetwork)

I then tried to run the main example, but it seems no function has been built 
(The help for these function is working for some reason).
>fauxDyn <- as.dynamic(fauxSim20, check.renewal=FALSE); 
Error: could not find function "as.dynamic" 
>launchSonia(fauxDyn); 
Error: could not find function "launchSonia" 



Is there a HOWTO/porting guide for packages pre R 2.10.0 to post R 2.10.0?

I have tried googling for it but I must be looking at the wrong place.

What about "--binary is deprecated"? What is the correct way now?

Thanks in advance,

Ben

On 16.06.2011 14:46, Ben Rhelp wrote:
> Hi all,
>
> I am trying to re-compile some "unmaintained" (it seems)
packages, namely rSoNIA
> and dynamicnetwork from:
> http://csde.washington.edu/~skyebend/rsonia/rsoniaDemo/
> These packages predates R 2.10.0 so they need to be recompile.
>
> After split the single big file in /man in each packages into a file  for
each
> function + some minor fix,  I successfully manage to recompile and load the
> packages
>
> C:\BenSave\R\BuildRPackage>R CMD build --binary dynamicnetwork
> --binary is deprecated
> * checking for file 'dynamicnetwork/DESCRIPTION' ... OK
> * preparing 'dynamicnetwork':
> * checking DESCRIPTION meta-information ... OK
> * checking whether 'INDEX' is up-to-date ... OK
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories
> * building binary distribution
> * installing *source* package 'dynamicnetwork' ...
> ** help
> *** installing help indices
> ** building package indices ...
> ** testing if installed package can be loaded
>       Classes for Relational Data
> Version      1.6 created on      January 28, 2011.
> copyright (c) 2005, Carter T. Butts, University of California-Irvine
>                      Mark S. Handcock, University of Washington
>                      David R. Hunter, Penn State University
>                      Martina Morris, University of Washington
> For citation information, type citation("network").
> Type help("network-package") to get started.
> * MD5 sums
> packaged installation of 'dynamicnetwork' as
dynamicnetwork_0.0-4.zip
>
> * DONE (dynamicnetwork)
>
> I then tried to run the main example, but it seems no function has been
built
> (The help for these function is working for some reason).
>
>> fauxDyn<- as.dynamic(fauxSim20, check.renewal=FALSE);
>
> Error: could not find function "as.dynamic"
>
>> launchSonia(fauxDyn);
>
> Error: could not find function "launchSonia"
>
>
>
> Is there a HOWTO/porting guide for packages pre R 2.10.0 to post R 2.10.0?
Actually the main change was the help system for R-2.10.0. The structure 
of R code did not change at all.

> I have tried googling for it but I must be looking at the wrong place.
>
> What about "--binary is deprecated"? What is the correct way now?
See the manual. It tells you

R CMD INSTALL --build

will generate a binary package.

Best,
Uwe Ligges

>
> Thanks in advance,
>
> Ben
>
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

On Thu, 16 Jun 2011, Mr Rhelp wrote:
> Hi all,
>
> I am trying to re-compile some "unmaintained" (it seems)
packages, namely rSoNIA
> and dynamicnetwork from:
> http://csde.washington.edu/~skyebend/rsonia/rsoniaDemo/
> These packages predates R 2.10.0 so they need to be recompile.
Well, re-installed.
> After split the single big file in /man in each packages into a file  for
each
> function + some minor fix,  I successfully manage to recompile and load the
> packages
Sounds like you are doing this on Windows (please do tell us!) and 
trying to start with a Windows binary package.
> C:\BenSave\R\BuildRPackage>R CMD build --binary dynamicnetwork
> --binary is deprecated
> * checking for file 'dynamicnetwork/DESCRIPTION' ... OK
> * preparing 'dynamicnetwork':
> * checking DESCRIPTION meta-information ... OK
> * checking whether 'INDEX' is up-to-date ... OK
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories
> * building binary distribution
> * installing *source* package 'dynamicnetwork' ...
> ** help
> *** installing help indices
> ** building package indices ...
> ** testing if installed package can be loaded
>     Classes for Relational Data
> Version      1.6 created on      January 28, 2011.
> copyright (c) 2005, Carter T. Butts, University of California-Irvine
>                    Mark S. Handcock, University of Washington
>                    David R. Hunter, Penn State University
>                    Martina Morris, University of Washington
> For citation information, type citation("network").
> Type help("network-package") to get started.
> * MD5 sums
> packaged installation of 'dynamicnetwork' as
dynamicnetwork_0.0-4.zip
>
> * DONE (dynamicnetwork)
>
> I then tried to run the main example, but it seems no function has been
built
> (The help for these function is working for some reason).
>
>> fauxDyn <- as.dynamic(fauxSim20, check.renewal=FALSE);
Is that supposed to be R code?  R code lines don't end in semicolons.
> Error: could not find function "as.dynamic"
>
>> launchSonia(fauxDyn);
>
> Error: could not find function "launchSonia"
>
> Is there a HOWTO/porting guide for packages pre R 2.10.0 to post R 2.10.0?
You don't need one.  You start with the package sources, and install 
those.  If you don't have the sources, you ask the author for the 
sources.  But on the page you mention, I see

'unix/macs use the  *.tar.gz version'

by which they mean 'the source package'.

(Note that for GPLed packages such as this one, the sources must be 
made available.)

There are some errors in the format of the Rd files, but both packages 
install in R 2.13.0.  However, you are supposed to get Java components 
from a site which no longer exists, so I think you are going to need 
to ask the author for help.

One advantage of recent R is that to install packages like these from 
the sources you just need R, so there is no reason to distribute 
Windows binary packages (for such packages, with no C/C++/Fortran 
code).
> I have tried googling for it but I must be looking at the wrong place.
>
> What about "--binary is deprecated"? What is the correct way now?
R CMD INSTALL --build is preferred (and always has been on Windows).

But why are you trying to build a binary package before you even have 
it working?  Binary packages are really only useful for 
redistribution.
> Thanks in advance,
>
> Ben
Surname 'Rhelp'

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

----- Original Message ----
> From: Uwe Ligges <ligges at statistik.tu-dortmund.de>
> To: Ben Rhelp <benrhelp at yahoo.co.uk>
> Cc: r-help at r-project.org
> Sent: Thu, 16 June, 2011 14:38:12
> Subject: Re: [R] Porting "unmaintained" packages to post R 2.10.0
era
> 
[...]
> >
> > What about "--binary is  deprecated"? What is the correct
way now?
> 
> See the manual. It tells  you
> 
> R CMD INSTALL --build
> 
> will generate a binary  package.
Hi Uwe,

Thanks a lot for this. I hope Google will rank your reply because it seems I am 
not the only one to make this mistake:

http://www.biostat.wisc.edu/~kbroman/Rintro/Rwinpack.html
http://robjhyndman.com/researchtips/building-r-packages-for-windows/
http://stevemosher.wordpress.com/step-10-build/

Cheers,

Ben

On 17.06.2011 12:04, Ben Rhelp wrote:
> ----- Original Message ----
>
>> From: Uwe Ligges<ligges at statistik.tu-dortmund.de>
>> To: Ben Rhelp<benrhelp at yahoo.co.uk>
>> Cc: r-help at r-project.org
>> Sent: Thu, 16 June, 2011 14:38:12
>> Subject: Re: [R] Porting "unmaintained" packages to post R
2.10.0 era
>>
> [...]
>>>
>>> What about "--binary is  deprecated"? What is the correct
way now?
>>
>> See the manual. It tells  you
>>
>> R CMD INSTALL --build
>>
>> will generate a binary  package.
>
> Hi Uwe,
>
> Thanks a lot for this. I hope Google will rank your reply because it seems
I am
> not the only one to make this mistake:
>
> http://www.biostat.wisc.edu/~kbroman/Rintro/Rwinpack.html
> http://robjhyndman.com/researchtips/building-r-packages-for-windows/
> http://stevemosher.wordpress.com/step-10-build/

We know, and we always ask people to read the recent official manuals 
where this is mentioned rather than any outdated material.

Best,
Uwe Ligges

> Cheers,
>
> Ben

Dear Uwe,
> If you think the relevant section is not sufficient, it's 
> your turn to provide a short and precise suggestion for a 
> change, preferable a diff against the R-devel sources. That 
> way you may be able to convince an R Core member to work on it.
I would be more than happy to rearrange the parts I have identified as hard to
find or under inappropriate headings and add the odd qualification to help folk
find the useful bits; if that's all you need I will do so and send you the
diff.

The caveat is that i) that leaves a comparative amateur hacking about in
'Writing R extensions' and 'R Installation and administration'
and b) I cannot guarantee that the result will represent the best practice you
want people to adopt because only you know that.

Alternatively I will be happy to provide some suggested editorial changes to you
- based on what I've already said - so that you can think about them and
maybe include them together with your own recommendations.

Let me know what you'd like me to do.

Steve E*******************************************************************
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