[GRASS-stats] Some refactoring and fixing

Rainer M Krug Rainer at krugs.de
Thu Jan 29 03:51:13 PST 2015 

Rainer M Krug <Rainer at krugs.de> writes:

> Roger Bivand <Roger.Bivand at nhh.no> writes:
>
>> On Wed, 28 Jan 2015, Rainer M Krug wrote:
>>
>>> OK - the problem seems to be a name conflict. The build system status
>>> report [1] states:
>>>
>>> ,----
>>> | - Package name conflicts:
>>> | ...
>>> | [7] "rspatial: spgrass6"     "spgrass: spgrass6"
>>> `----
>>
>> Right, spgrass6 is still hosted as part of rspatial (it was originally
>> there). I'll try to resolve this by removing it from that project.
>
> Thanks Roger - spgrass6 is now available to be installed via
>
>
> install.packages("spgrass6", repos="http://R-Forge.R-project.org")
>
>
> for windows (source and compiled), linux (source) and Mac (source).
>
> Is there any possibility to remove the spgrass package (which has been
> renamed to spgrass7) from the R Packages listing [1] to avoid confusion?
>
>> The file oChangeLog is the frozen ChangeLog from its original project,
>> so when releasing, we need to run:
>>
>> cd spgrass6 # or 7
>> svn up
>> sh svn2cl.sh # must be on PATH
>> # if formatted too narrowly
>> # fmt < ChangeLog > tmp
>> # mv tmp ChangeLog
>> cat oChangeLog >> ChangeLog
>> cp ChangeLog inst
>> svn commit -m tidy
>> svn up
>> cd ..
>>
>> to build a ChangeLog including all past history.
>
> Concerning changes before release:
>
> 1) I would suggest to create for all functions which have a 6 at the end
> (e.g. redRAST6) an alias without the 6 (e.g. readRAST). By using these
> names without the 6 the switch between GRASS (and related spgrassX)
> versions will require mainly a switch of the library used. For further
> versions of spgrassX I would suggest to drop the numbers completely as,
> even when spgrass6 and spgrass7 are loaded at the same time, specific
> versions can be accessed by using the :: (i.e. spgrass6::readRAST).

Committed (revision 18) - please check!

>
> 2) I will go through the code and remove references (and version checks)
> to GRASS GIS 7 to simplify the code. These checks are not needed anymore as
> the check for the GRASS GIS version is done upon loading (only loads
> when started outside grass session or inside grass 6.x session) and on
> initGRASS() (aborts if gisBase points to grass 6.x installation)

Committed (revision 17) - please check.

The new spgrass6 concludes all examples without error messages and
,----
| R CMD check --as-cran
`----
also without errors.

Thomas - could you please do some testing on this version
(revision 18) - the packages are building at the moment?

Cheers,

Rainer
>
> Otherwise I can't thinkl of any other points before release.
>
> Thanks,
>
> Rainer
>
>>
>> Roger
>>
>>>
>>> So the easiest to install at the moment seems to be to checkout the
>>> sources via
>>>
>>> ,----
>>> | svn checkout svn://r-forge.r-project.org/svnroot/spgrass/
>>> `----
>>>
>>> and then install from the sources.
>>>
>>> Cheers,
>>>
>>> Rainer
>>>
>>> Rainer M Krug <Rainer at krugs.de> writes:
>>>
>>>> Hi Roger
>>>>
>>>> it seems that there is something not as it should be with the builds of
>>>> spgrass6 and spgrass7 - there are at the moment GRASS, spgrass and
>>>> spgrass7 but no spgrass6 - I don't have much experience with r-forge,
>>>> could you please check what is going on?
>>>>
>>>> Thanks,
>>>>
>>>> Rainer
>>>>
>>>> Rainer M Krug <r.m.krug at gmail.com> writes:
>>>>
>>>>> Envoyé de mon iPhone
>>>>>
>>>>>> Le 28 janv. 2015 à 15:55, Thomas Adams <tea3rd at gmail.com> a écrit :
>>>>>>
>>>>>> Rainer,
>>>>>>
>>>>>> Where can I get the new spgrass6 and spgrass7 to do some testing?
>>>>>
>>>>> The repository is on https://r-forge.r-project.org/projects/spgrass/   .
>>>>>
>>>>> It doesn't seem to be build yet so you have to install it from the svn
>>>>> repo or wait a few hours - then you shoud be able to install it via
>>>>>
>>>>>  	R install command: install.packages("spgrass6", repos="http://R-Forge.R-project.org")
>>>>>
>>>>>  	Cheers,
>>>>>
>>>>> Rainer
>>>>>> Thank you,
>>>>>> Tom
>>>>>>
>>>>>>> On Wed, Jan 28, 2015 at 7:23 AM, Rainer M Krug <Rainer at krugs.de> wrote:
>>>>>>> Rainer M Krug <Rainer at krugs.de> writes:
>>>>>>>
>>>>>>>> Roger Bivand <Roger.Bivand-aX1nC9UfZf8 at public.gmane.org> writes:
>>>>>>>>
>>>>>>>>> On Tue, 27 Jan 2015, Rainer M Krug wrote:
>>>>>>>>>
>>>>>>>>>> Hi
>>>>>>>>>>
>>>>>>>>>> I just committed a few of commits which refactor the code of readRAST,
>>>>>>>>>> writeRAST, readVECT & writeVECT by creating internal fi=unctions for
>>>>>>>>>> reading / writing for plugin / non-plugin and moving the default values
>>>>>>>>>> (get...Options()) into the function definitions.
>>>>>>>>>
>>>>>>>>> Good, thanks; I've updated the default values in the help files. It's
>>>>>>>>> easy to check for discrepancies in spgrass/pkg:
>>>>>>>>>
>>>>>>>>> R CMD build spgrass7
>>>>>>>>> R CMD check spgrass7_0.1-0.tar.gz
>>>>>>>>
>>>>>>>> Thanks - haven't thought about about the check - will do the next time.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>> Maybe we could quieten the progress bar in the output from checking?
>>>>>>>>> As in:
>>>>>>>>>
>>>>>>>>> pkg/spgrass7.Rcheck/spgrass7.Rout
>>>>>>>>>
>>>>>>>>> (local file, not added to repository, created by R CMD check if run in
>>>>>>>>> spgrass/pkg).
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Also, I added tryCatch blocks to close open connections and to reset
>>>>>>>>>> echoCmdOption. I ran the examples before each commit and I did not see
>>>>>>>>>> any errors or changed behavior.
>>>>>>>>>>
>>>>>>>>>> Apologies for the typos in the commit messages - I only saw them later.
>>>>>>>>>>
>>>>>>>>>> To stick with consistency, I would recommend to rename the package to
>>>>>>>>>> spgrass7 and to look into the possibility to create a meta-package which
>>>>>>>>>> uses spgrass6 or spgrass7 (I don't know about the GRASS 5 interface -
>>>>>>>>>> haven't used it) depending on the GRASS GIS version set / loaded.
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> I've renamed spgrass as spgrass7 - when you update, the change will
>>>>>>>>> propagate.
>>>>>>>>
>>>>>>>> Thanks - got it.
>>>>>>>>
>>>>>>>>> I'm unsure about a metapackage, maybe block version 7 in
>>>>>>>>> spgrass6 (following the parameter and flag name harmonisation).
>>>>>>>>
>>>>>>>> Yes - spgrass6 for 6.x, spgrass7 for 7.x.
>>>>>>>>
>>>>>>>> Will respnd in more detail tomorrow.
>>>>>>>
>>>>>>> OK - I just committed a blocking mechanism which for spgrass6 and
>>>>>>> spgrass7 so that they
>>>>>>>
>>>>>>> a) when R is started in GRASS, the package can not be loaded if the
>>>>>>> versions are not compatible and
>>>>>>> b) initGRASS raises an error if the GRASS GIS version in gisBase is not
>>>>>>> compatible with the package version
>>>>>>>
>>>>>>> If you think this is the right approach, the help files still need to be
>>>>>>> amended to reflect this change.
>>>>>>>
>>>>>>> I was thinking if it would make sense to introduce an overwrite
>>>>>>> mechanism for these checks to enable "non-standard" use or testing?
>>>>>>>
>>>>>>> I haven't looked at references for GRASS 7.0 in spgrass6 yet.
>>>>>>>
>>>>>>> Cheers,
>>>>>>>
>>>>>>> Rainer
>>>>>>>
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Rainer
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>> Best wishes,
>>>>>>>>>
>>>>>>>>> Roger
>>>>>>>>>
>>>>>>>>>> Cheers,
>>>>>>>>>>
>>>>>>>>>> Rainer
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
>>>>>>>
>>>>>>> Centre of Excellence for Invasion Biology
>>>>>>> Stellenbosch University
>>>>>>> South Africa
>>>>>>>
>>>>>>> Tel :       +33 - (0)9 53 10 27 44
>>>>>>> Cell:       +33 - (0)6 85 62 59 98
>>>>>>> Fax :       +33 - (0)9 58 10 27 44
>>>>>>>
>>>>>>> Fax (D):    +49 - (0)3 21 21 25 22 44
>>>>>>>
>>>>>>> email:      Rainer at krugs.de
>>>>>>>
>>>>>>> Skype:      RMkrug
>>>>>>>
>>>>>>> PGP: 0x0F52F982
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> grass-stats mailing list
>>>>>>> grass-stats at lists.osgeo.org
>>>>>>> http://lists.osgeo.org/mailman/listinfo/grass-stats
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>
>>>
>>> Footnotes:
>>> [1]  http://download.r-forge.r-project.org/STATUS
>>>
>>>
>
>
> Footnotes: 
> [1]  https://r-forge.r-project.org/R/?group_id=2020

-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer at krugs.de

Skype:      RMkrug

PGP: 0x0F52F982
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