[GRASS-stats] errors on spgrass Yosemite / homebrew
Roger Bivand
Roger.Bivand at nhh.no
Wed Jan 21 00:47:37 PST 2015
Hi,
We are testing against RC1, and some (many) parameter names were changed
between beta3 (2014-08-05) and RC1 (2015-01-14) I think. I believe that
the parameter and flag names have been being simlified and made consistent
across modules.
Roger
On Wed, 21 Jan 2015, Rainer M Krug wrote:
>
> Hi
>
> I tried to run
>
> --8<---------------cut here---------------start------------->8---
> library(spgrass)
> examples(spgrass)
> --8<---------------cut here---------------end--------------->8---
>
> but I got an error - transcript below.
>
> Let me know if I should try something out.
>
> Cheers,
>
> Rainer
>
> ,----
> | 09:30:33 ~$ grass70 ~/Documents/spearfish60_grass7/user1/
> | Cleaning up temporary files...
> | Starting GRASS GIS...
> |
> | __________ ___ __________ _______________
> | / ____/ __ \/ | / ___/ ___/ / ____/ _/ ___/
> | / / __/ /_/ / /| | \__ \\_ \ / / __ / / \__ \
> | / /_/ / _, _/ ___ |___/ /__/ / / /_/ // / ___/ /
> | \____/_/ |_/_/ |_/____/____/ \____/___//____/
> |
> | Welcome to GRASS 7.0.0beta3
> | GRASS homepage: http://grass.osgeo.org
> | This version running through: Bash Shell (/usr/local/bin/bash)
> | Help is available with the command: g.manual -i
> | See the licence terms with: g.version -c
> | Start the GUI with: g.gui wxpython
> | When ready to quit enter: exit
> |
> | GRASS 7.0.0beta3 (spearfish60_grass7):~ > R
> |
> | R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
> | Copyright (C) 2014 The R Foundation for Statistical Computing
> | Platform: x86_64-apple-darwin14.1.0 (64-bit)
> |
> | R is free software and comes with ABSOLUTELY NO WARRANTY.
> | You are welcome to redistribute it under certain conditions.
> | Type 'license()' or 'licence()' for distribution details.
> |
> | Natural language support but running in an English locale
> |
> | R is a collaborative project with many contributors.
> | Type 'contributors()' for more information and
> | 'citation()' on how to cite R or R packages in publications.
> |
> | Type 'demo()' for some demos, 'help()' for on-line help, or
> | 'help.start()' for an HTML browser interface to help.
> | Type 'q()' to quit R.
> |
> | [Previously saved workspace restored]
> |
> | > library(spgrass)
> | Loading required package: sp
> | Loading required package: XML
> | GRASS GIS interface loaded with GRASS version: GRASS 7.0.0beta3 (2014)
> | and location: spearfish60_grass7
> | > example(spgrass)
> |
> | spgrss> if (nchar(Sys.getenv("GISRC")) > 0) {
> | spgrss+ require(rgdal)
> | spgrss+ soilsph <- readRAST("soils.ph", ignore.stderr=TRUE, plugin=FALSE)
> | spgrss+ summary(soilsph)
> | spgrss+ grd <- gmeta2grd(ignore.stderr=TRUE)
> | spgrss+ grd
> | spgrss+ set.seed(1)
> | spgrss+ pts <- spsample(soilsph, 200, "random")
> | spgrss+ smple <- SpatialPointsDataFrame(pts, data=over(pts, soilsph))
> | spgrss+ summary(smple)
> | spgrss+ writeVECT(smple, "sp_dem", v.in.ogr_flags="overwrite", ignore.stderr=TRUE)
> | spgrss+ bugsDF <- readVECT("bugsites", ignore.stderr=TRUE, mapset="PERMANENT")
> | spgrss+ summary(bugsDF)
> | spgrss+ vInfo("streams", ignore.stderr=TRUE)
> | spgrss+ vColumns("streams", ignore.stderr=TRUE)
> | spgrss+ vDataCount("streams", ignore.stderr=TRUE)
> | spgrss+ streams <- readVECT("streams", type="line,boundary",
> | spgrss+ remove.duplicates=FALSE, ignore.stderr=TRUE, plugin=FALSE)
> | spgrss+ summary(streams)
> | spgrss+ }
> | Loading required package: rgdal
> | rgdal: version: 0.9-1, (SVN revision 518)
> | Geospatial Data Abstraction Library extensions to R successfully loaded
> | Loaded GDAL runtime: GDAL 1.11.1, released 2014/09/24
> | Path to GDAL shared files: /usr/local/Cellar/gdal/1.11.1_3/share/gdal
> | Loaded PROJ.4 runtime: Rel. 4.8.0, 6 March 2012, [PJ_VERSION: 480]
> | Path to PROJ.4 shared files: (autodetected)
> | Command: v.in.ogr
> | Description: Imports vector data into a GRASS vector map using OGR library.
> | Keywords: vector, import, OGR
> | Parameters:
> | name: dsn, type: string, required: yes, multiple: no
> | [Examples:
> | ESRI Shapefile: directory containing shapefiles
> | MapInfo File: directory containing mapinfo files]
> | name: layer, type: string, required: no, multiple: yes
> | [Examples:
> | ESRI Shapefile: shapefile name
> | MapInfo File: mapinfo file name]
> | name: output, type: string, required: no, multiple: no
> | keydesc: name, keydesc_count: 1
> | [Name for output vector map]
> | name: spatial, type: float, required: no, multiple: yes
> | keydesc: xmin,ymin,xmax,ymax, keydesc_count: 4
> | [Format: xmin,ymin,xmax,ymax - usually W,S,E,N]
> | name: where, type: string, required: no, multiple: no
> | keydesc: sql_query, keydesc_count: 1
> | [Example: income < 1000 and inhab >= 10000]
> | name: min_area, type: float, required: no, multiple: no
> | default: 0.0001
> | [Smaller areas and islands are ignored. Should be greater than snap^2]
> | name: type, type: string, required: no, multiple: yes
> | default:
> | [Optionally change default input type]
> | name: snap, type: float, required: no, multiple: no
> | default: -1
> | ['-1' for no snap]
> | name: location, type: string, required: no, multiple: no
> | keydesc: name, keydesc_count: 1
> | [Name for new location to create]
> | name: cnames, type: string, required: no, multiple: yes
> | [List of column names to be used instead of original names, first is used for category column]
> | name: encoding, type: string, required: no, multiple: no
> | [Overrides encoding interpretation, useful when importing ESRI Shapefile]
> | name: key, type: string, required: no, multiple: no
> | [If not given, categories are generated as unique values and stored in 'cat' column]
> | Flags:
> | name: f [List supported OGR formats and exit] {TRUE}
> | name: l [List available OGR layers in data source and exit] {TRUE}
> | name: c [Do not clean polygons (not recommended)] {FALSE}
> | name: 2 [Useful if input is 3D but all z coordinates are identical] {FALSE}
> | name: t [Do not create attribute table] {FALSE}
> | name: o [Override dataset projection (use location's projection)] {FALSE}
> | name: r [Limit import to the current region] {FALSE}
> | name: e [Also updates the default region if in the PERMANENT mapset] {FALSE}
> | name: w [Change column names to lowercase characters] {FALSE}
> | name: i [Create the location specified by the "location" parameter and exit. Do not import the vector data.] {FALSE}
> | name: overwrite [Allow output files to overwrite existing files] {FALSE}
> | name: help [Print usage summary] {FALSE}
> | name: verbose [Verbose module output] {FALSE}
> | name: quiet [Quiet module output] {FALSE}
> | Error in insert_required(pcmd = pcmd, parameters = parameters, pt = pt, :
> | required parameters with no defaults missing: dsn
> |
> | > traceback()
> | 10: stop(paste("required parameters with no defaults missing:", paste(nadefnms1,
> | collapse = " ")))
> | 9: insert_required(pcmd = pcmd, parameters = parameters, pt = pt,
> | req = req, suppress_required = suppress_required)
> | 8: doGRASS(cmd, flags = flags, ..., parameters = parameters, echoCmd = echoCmd,
> | legacyExec = legacyExec)
> | 7: execGRASS("v.in.ogr", flags = v.in.ogr_flags, input = GDSN, output = vname,
> | layer = LAYER, ignore.stderr = ignore.stderr)
> | 6: writeVECT(smple, "sp_dem", v.in.ogr_flags = "overwrite", ignore.stderr = TRUE) at Rex5d28289dfd2d#18
> | 5: eval(expr, envir, enclos)
> | 4: eval(ei, envir)
> | 3: withVisible(eval(ei, envir))
> | 2: source(tf, local, echo = echo, prompt.echo = paste0(prompt.prefix,
> | getOption("prompt")), continue.echo = paste0(prompt.prefix,
> | getOption("continue")), verbose = verbose, max.deparse.length = Inf,
> | encoding = "UTF-8", skip.echo = skips, keep.source = TRUE)
> | 1: example(spgrass)
> | > version
> | _
> | platform x86_64-apple-darwin14.1.0
> | arch x86_64
> | os darwin14.1.0
> | system x86_64, darwin14.1.0
> | status
> | major 3
> | minor 1.2
> | year 2014
> | month 10
> | day 31
> | svn rev 66913
> | language R
> | version.string R version 3.1.2 (2014-10-31)
> | nickname Pumpkin Helmet
> | > sessionInfo()
> | R version 3.1.2 (2014-10-31)
> | Platform: x86_64-apple-darwin14.1.0 (64-bit)
> |
> | locale:
> | [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> |
> | attached base packages:
> | [1] stats graphics grDevices utils datasets methods base
> |
> | other attached packages:
> | [1] rgdal_0.9-1 spgrass_0.1-0 XML_3.98-1.1 sp_1.0-16
> |
> | loaded via a namespace (and not attached):
> | [1] grid_3.1.2 lattice_0.20-29 tools_3.1.2
> | >
> `----
>
>
>
>
--
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
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