[GRASS-stats] wish: less verbose messages in rgrass7

[Roger Bivand]

On Thu, 10 Sep 2015, Rainer M Krug wrote:

> Markus Neteler <neteler at osgeo.org> writes:
>
>> Hi,
>>
>> today we used "rgrass7" on Windows (and I made some tests on Linux, too).
>
> Hi Markus,
>
> thanks for reporting.
>
>>
>> I was wondering about a few warnings which might be suppressed to avoid
>> user confusion:

Hi,

The confusion is probably coming from the use duality. If a location and 
mapset already exists, the (much) prefered route is to run R inside GRASS 
- start R from the GRASS console or similar. Then GISRC etc. are handled 
in the correct way by GRASS itself.

If there is no location, and the location/mapset will be created on a 
throw-away basis in the R temporary directory or elsewhere outside 
GISDBASE, initGRASS() is a sensible choice, because it gives access to 
GRASS tools - running GRASS inside R.

Here GRASS is being run inside R in relation to an existing 
location/mapset using initGRASS(), which by design doesn't know anything 
about locking etc.; it expects to throw the location away when R exits 
(deleting the temporary directory if owned by R - mileage may vary on 
Windows).

Should we tell users not to do something that isn't very sensible, or 
change initGRASS to know much more about a running GRASS instance?

I prefer the former - for non-advanced users:

1) if the GRASS location/mapset is only a throwaway one, use initGRASS() 
and run GRASS inside R;

2) if you already have a GRASS location/mapset, use R inside GRASS and do 
not use initGRASS().

Advanced users can make their own choices.

Warnings should IMHO never be hidden - I don't agree that not knowing is 
ever helpful.

I don't have time to look at this now, I can look in a couple of weeks' 
time maybe.

Best wishes,

Roger

>>
>>
>> ######## Windows: calling GRASS 7.1 from R session
>>
>>> library(rgrass7)
>> Loading required package: sp
>> Loading required package: XML
>> GRASS GIS interface loaded with GRASS version: (GRASS not running)
>> Warning messages:
>> 1: package ‘rgrass7’ was built under R version 3.2.2
>> 2: package ‘sp’ was built under R version 3.2.2
>> 3: package ‘XML’ was built under R version 3.2.2
>>
>>> initGRASS(gisBase = "C:/OSGeo4W/apps/grass/grass-7.1.svn",
>> + gisDbase = "C:/Users/marissa/GRASSdata/",
>> + location = "CA", mapset = "Aegypti")
>> Error in initGRASS(gisBase = "C:/OSGeo4W/apps/grass/grass-7.1.svn",
>> gisDbase = "C:/Users/marissa/GRASSdata/",  :
>>   A GISRC file already exists; to override, set override=TRUE
>>
>>
>> ==> the last sentence is not quite clear. Perhaps change to
>
> I agree with the first part of the sentence.
>
>>
>> "A GISRC file already exists (the GRASS GIS mapset is already in use); to
>> override, set override=TRUE"
>
> I don't think this is true. I have regularly to use #override=TRUE# even
> though I definitely use the mapset. I rather think that the GISRC is not
> cleaned up after finishing in grass in R.
>
> This raises the question: if GISRC is created, should it be deleted,
> i.e. should there be a function
>
>  closeGRASS()
>
> which is doing the cleanup (or is it done and not working in my cases)?
>
> Rather change it to:
>
> --8<---------------cut here---------------start------------->8--- "A
> GISRC file already exists.
> The GRASS GIS mapset might be already in use or the file has not been
> deleted.
> To override, set override=TRUE"
> --8<---------------cuthere---------------end--------------->8---
>
>
>>
>>
>>> initGRASS(gisBase = "C:/OSGeo4W/apps/grass/grass-7.1.svn",
>> + gisDbase = "C:/Users/marissa/GRASSdata/",
>> + location = "CA", mapset = "Aegypti",
>> + override=TRUE)
>> gisdbase    C:/Users/marissa/GRASSdata/
>> location    CA
>> mapset      Aegypti
>> rows        265
>> columns     230
>> north       452000
>> south       -608000
>> west        -376000
>> east        544000
>> nsres       4000
>> ewres       4000
>> projection  +proj=aea +lat_1=34 +lat_2=40.5 +lat_0=0 +lon_0=-120 +x_0=0
>> +y_0=-4000000 +no_defs +a=6378137 +rf=298.257222101
>> +towgs84=0.000,0.000,0.000 +to_meter=1
>> Warning message:
>> In dir.create(gisDbase) : 'C:\Users\marissa\GRASSdata' already exists
>>
>> ==> the last warning is not clear to me. If I set override=TRUE, I refer to
>> the mapset's gislock, hence the dir.create(gisDbase should not be done at
>> all. Is it a bug?
>
> Strange.
>
> I just looked in the code of initGRASS() and all dir.create(gisDbase) are
> in
>
> ,----
> | if (!file.exists(gisDbase)) dir.create(gisDbase)
> `----
>
> statements. Maybe I am missing something? Could you set
>
> --8<---------------cut here---------------start------------->8---
> option(warn=2)
> --8<---------------cut here---------------end--------------->8---
>
> before running the code again and give a traceback?
>
>
>>
>>
>> ############## Linux
>>
>>> ncdata <- readRAST("elevation")
>> WARNING: 'cellhd/elevation' was found in more mapsets (also found in
>>          <PERMANENT>)
>> WARNING: Using <elevation at user1>
>> WARNING: 'cellhd/elevation' was found in more mapsets (also found in
>>          <PERMANENT>)
>> WARNING: Using <elevation at user1>
>> WARNING: 'cellhd/elevation' was found in more mapsets (also found in
>>          <PERMANENT>)
>> WARNING: Using <elevation at user1>
>>
>> ==> these warning make probably sense in a GRASS session but IMHO here
>> less. They could be suppressed with --q in the respective GRASS module
>> call.
>
> Agreed - but very useful for debugging.
>
> --q could could be added into the options of the rgrass7 package?
>
>>
>>
>> Creating BIL support files...
>> Exporting raster as floating values (bytes=4)
>>  100%
>> Warning messages:
>> 1: In execGRASS("r.info", flags = "g", map = vname[i], intern = TRUE,  :
>>   The command:
>> r.info -g map=elevation
>> produced at least one warning during execution:
>> WARNING: 'cellhd/elevation' was found in more mapsets (also found in
>>          <PERMANENT>)
>> WARNING: Using <elevation at user1>
>> WARNING: 'cellhd/elevation' was found in more mapsets (also found in
>>          <PERMANENT>)
>> WARNING: Using <elevation at user1>
>> WARNING: 'cellhd/elevation' was found in more mapsets (also found in
>>          <PERMANENT>)
>> WARNING: Using <elevation at user1>
>>
>> ==> here it is, I suggest to use r.info --q
>
> This should be optional - for debugging, these warnings might be crucial.
>
>>
>> 2: In execGRASS("r.info", flags = "r", map = vname[i], intern = TRUE,  :
>>   The command:
>> r.info -r map=elevation
>> produced at least one warning during execution:
>> WARNING: 'cellhd/elevation' was found in more mapsets (also found in
>>          <PERMANENT>)
>> WARNING: Using <elevation at user1>
>> WARNING: 'cellhd/elevation' was found in more mapsets (also found in
>>          <PERMANENT>)
>> WARNING: Using <elevation at user1>
>> WARNING: 'cellhd/elevation' was found in more mapsets (also found in
>>          <PERMANENT>)
>> WARNING: Using <elevation at user1>
>>
>> ==> same thing
>
> No - If I use execGRASS() I know grass (hopefully...) and I can specify
> --q if I want it.
> The execGRASS must not add any flags or arguments which make the
> commands differ from the GRASS versions.
>
>>
>> 3: In execGRASS("r.out.bin", flags = rOutBinFlags, input = vname[i],  :
>>   The command:
>> r.out.bin -b -f input=elevation
>> output=/home/neteler/grassdata/nc_spm_08_grass7/user1/.tmp/pgis_north/elevation
>> bytes=4 null=54
>> produced at least one warning during execution:
>> WARNING: 'cellhd/elevation' was found in more mapsets (also found in
>>          <PERMANENT>)
>> WARNING: Using <elevation at user1>
>> WARNING: 'cellhd/elevation' was found in more mapsets (also found in
>>          <PERMANENT>)
>> WARNING: Using <elevation at user1>
>> WARNING: 'cellhd/elevation' was found in more mapsets (also found in
>>          <PERMANENT>)
>> WARNING: Using <elevation at user1>
>>
>> ==> same thing
>
> Should be using a new rgrass7 option for --q.
>
> Cheers,
>
> Rainer
>
>>
>> Creating BIL support files...
>> Exporting raster as floating values (bytes=4)
>>  100%
>>
>> thanks
>> Markus
>> _______________________________________________
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>> grass-stats at lists.osgeo.org
>> http://lists.osgeo.org/mailman/listinfo/grass-stats
>
>

-- 
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; fax +47 55 95 91 00
e-mail: Roger.Bivand at nhh.no