Re: [R-sig-Geo] install rgdal from source macOS
I finally got back to this. Unfortunately this did not work.
It still doesn't like PKG_CONFIG_PATH and now pcs.csv was not readable. It
did not exist in 'share/gdal' but I found it in miniconda3/pkgs/libgdal* so
I copied it to share/gdal.
> Sys.getenv('PKG_CONFIG_PATH')
[1] "/Users/dosc3612/Applications/miniconda3/envs/rgdal/lib/pkgconfig"
> grep('proj.pc',dir(Sys.getenv('PKG_CONFIG_PATH')))
I'm not sure why it can't find the pkg config
> install.packages('rgdal', repo = 'https://r-forge.r-project.org', type =
"source",
configure.args=c('--with-proj-include=/Users/dosc3612/Applications/miniconda3/envs/rgdal/include',
'--with-proj-lib=/Users/dosc3612/Applications/miniconda3/envs/rgdal/lib',
'--with-gdal-config=/Users/dosc3612/Applications/miniconda3/envs/rgdal/bin/gdal-config','--with-proj-share=/Users/dosc3612/Applications/miniconda3/envs/rgdal/share/proj',
'--with-data-copy=yes'))
trying URL 'https://r-forge.r-project.org/src/contrib/rgdal_1.4-5.tar.gz'
Content type 'application/x-gzip' length 1687877 bytes (1.6 MB)
==
downloaded 1.6 MB
* installing *source* package ‘rgdal’ ...
** using staged installation
configure: R_HOME: /Library/Frameworks/R.framework/Resources
configure: CC: clang
configure: CXX: clang++ -std=gnu++11
configure: C++11 support available
configure: rgdal: 1.4-4
checking for /usr/bin/svnversion... yes
cat: inst/SVN_VERSION: No such file or directory
configure: svn revision:
configure: gdal-config set to
/Users/dosc3612/Applications/miniconda3/envs/rgdal/bin/gdal-config
checking gdal-config exists... yes
checking gdal-config executable... yes
checking gdal-config usability... yes
configure: GDAL: 3.0.0
checking GDAL version >= 1.11.4... yes
checking GDAL version <= 2.5 or >= 3.0... yes
checking gdal: linking with --libs only... yes
checking GDAL: gdal-config data directory readable... yes
checking GDAL:
/Users/dosc3612/Applications/miniconda3/envs/rgdal/share/gdal/pcs.csv
readable... yes
./configure: line 2101: pkg-config: command not found
configure: pkg-config proj not available
set PKG_CONFIG_PATH to the directory containing proj.pc
configure: PROJ version not determined using pkg-config proj
configure: proj CPP flags:
-I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
-I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
checking PROJ header API:... proj_api.h
checking proj_api.h presence and usability... yes
checking PROJ version >= 4.8.0... yes
configure: PROJ_LIB:
/Users/dosc3612/Applications/miniconda3/envs/rgdal/share/proj
dyld: Library not loaded: @rpath/libproj.15.dylib
Referenced from:
/private/var/folders/bb/13z2kq0j01jg5q_0ypjc76grgn/T/RtmpVtyBCi/R.INSTALL76ca8b2ce2d/rgdal/./proj_conf_test2
Reason: image not found
./configure: line 2451: 30994 Abort trap: 6
PROJ_LIB="${proj_share_path}" ./proj_conf_test2
checking PROJ: proj.db found and readable... yes
configure: Copy data for:
configure: PROJ.4:
/Users/dosc3612/Applications/miniconda3/envs/rgdal/share/proj
configure: GDAL:
/Users/dosc3612/Applications/miniconda3/envs/rgdal/share/gdal
configure: Package CPP flags:
-I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
-I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
-DACCEPT_USE_OF_DEPRECATED_PROJ_API_H
configure: Package LIBS:
-L/Users/dosc3612/Applications/miniconda3/envs/rgdal/lib -lgdal
-L/Users/dosc3612/Applications/miniconda3/envs/rgdal/lib -lproj
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include"
-DNDEBUG -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
-I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
-DACCEPT_USE_OF_DEPRECATED_PROJ_API_H
-I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sp/include"
-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-I/usr/local/include -fPIC -Wall -g -O2 -c OGR_write.cpp -o OGR_write.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include"
-DNDEBUG -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
-I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
-DACCEPT_USE_OF_DEPRECATED_PROJ_API_H
-I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sp/include"
-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-I/usr/local/include -fPIC -Wall -g -O2 -c gdal-bindings.cpp -o
gdal-bindings.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
-I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
-DACCEPT_USE_OF_DEPRECATED_PROJ_API_H
-I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sp/include"
-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
Re: [R-sig-Geo] [FORGED] Create a Spatial Weight Matrix based on road distance
Rather than converting an object of class 'SpatialLines' or
'SpatialLinesDataFrame' to the spatstat class 'psp' and then converting it to
the spatstat class 'linnet', it is safer and more efficient to convert the
SpatialLines* object directly to class linnet using
as.linnet.SpatialLinesDataFrame() from the package 'maptools'.
Prof Adrian Baddeley DSc FAA
John Curtin Distinguished Professor
Department of Mathematics and Statistics
Curtin University, Perth, Western Australia
From: Rolf Turner
Sent: Friday, 21 June 2019 10:08 AM
To: Rolando Valdez
Cc: r-sig-geo@r-project.org; Adrian Baddeley; Ege Rubak
Subject: Re: [FORGED] [R-sig-Geo] Create a Spatial Weight Matrix based on road
distance
On 21/06/19 12:26 PM, Rolando Valdez wrote:
> Dear community,
>
> Is there any way to create a spatial weight matrix based on road distance?
> I am trying to use the road distance between two points instead of
> euclidean distance.
>
> I've seen that there is a package named osrm. Can anyone give some advice?
I don't know anything about "osrm". Calculating "road distances" can be
done in the spatstat package reasonably easily, if you take the trouble
to represent your collection of roads as a "linnet" object.
Given that you have done so, suppose that your linnet object is "L" and
that you have vectors "x" and "y" specifying the points on L (i.e. on
your roads) between which you want to know the distances.
Do:
X<- lpp(data.frame(x=x,y=y),L)
dMat <- pairdist(X)
The object "dMat" is a (symmetric) square matrix; dMat[i,j] is the
distance between point i and point j. (Of course the diagonal entries
are all 0.)
If your collection of roads is specified by means of a shapefile,
vignette("shapefiles") will tell you how to turn this collection into a
"psp" ("planar segment pattern") object; the function (method)
as.linnet.psp() can then be used to turn the "psp" object into a
"linnet" object.
HTH
cheers,
Rolf Turner
--
Honorary Research Fellow
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276
[[alternative HTML version deleted]]
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Re: [R-sig-Geo] [FORGED] Create a Spatial Weight Matrix based on road distance
On 21/06/19 12:26 PM, Rolando Valdez wrote:
Dear community,
Is there any way to create a spatial weight matrix based on road distance?
I am trying to use the road distance between two points instead of
euclidean distance.
I've seen that there is a package named osrm. Can anyone give some advice?
I don't know anything about "osrm". Calculating "road distances" can be
done in the spatstat package reasonably easily, if you take the trouble
to represent your collection of roads as a "linnet" object.
Given that you have done so, suppose that your linnet object is "L" and
that you have vectors "x" and "y" specifying the points on L (i.e. on
your roads) between which you want to know the distances.
Do:
X<- lpp(data.frame(x=x,y=y),L)
dMat <- pairdist(X)
The object "dMat" is a (symmetric) square matrix; dMat[i,j] is the
distance between point i and point j. (Of course the diagonal entries
are all 0.)
If your collection of roads is specified by means of a shapefile,
vignette("shapefiles") will tell you how to turn this collection into a
"psp" ("planar segment pattern") object; the function (method)
as.linnet.psp() can then be used to turn the "psp" object into a
"linnet" object.
HTH
cheers,
Rolf Turner
--
Honorary Research Fellow
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276
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[R-sig-Geo] Create a Spatial Weight Matrix based on road distance
Dear community, Is there any way to create a spatial weight matrix based on road distance? I am trying to use the road distance between two points instead of euclidean distance. I've seen that there is a package named osrm. Can anyone give some advice? Thank you in advance. Regards, -- Rol~ [[alternative HTML version deleted]] ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
[R-sig-Geo] Surface Chlorophyll data calculation
Hello, This is my first post to this list. I am a beginner in R and GIS and I work as researcher at Spanish Institute of Oceanography. I have a ncdf file from the Copernicus webpage with monthly primary production data from the Northeastern Atlantic. In my case, the chlorophyll concentration from the following link, http://marine.copernicus.eu/services-portfolio/access-to-products/?option=com_csw=details_id=IBI_REANALYSIS_BIO_005_003 I want to calculate the monthly surface chlorophyll concentration. Unfortunately, after a lot of reading on the issue, I have been unable to come to any understanding. Any indication of tutorials, scripts, sites or packages will be very welcomed. Thanks in advance. Kindest regards, Juan Carlos [[alternative HTML version deleted]] ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Re: [R-sig-Geo] testing a crs string
perfect. Thank you. I thought there must be a function in one of the
packages to check.
-Roy
> On Jun 20, 2019, at 7:42 AM, Edzer Pebesma
> wrote:
>
>
>
> On 6/20/19 4:18 PM, Roy Mendelssohn - NOAA Federal via R-sig-Geo wrote:
>> Hi All:
>>
>> I am extending a package I have to allow users to provide a crs string,
>> which will eventually through some other packages be sent to sf. I like to
>> try and make at least minimal tests that inputs are valid. Is there some
>> existing code that will check if a string is a valid crs string?
>
>> inherits(try(sf::st_crs("+proj=invalid"), silent = TRUE), "try-error")
> [1] TRUE
>> inherits(try(sf::st_crs("+proj=longlat"), silent = TRUE), "try-error")
> [1] FALSE
>
>
>>
>> Thanks,
>>
>> -Roy
>>
>>
>> **
>> "The contents of this message do not reflect any position of the U.S.
>> Government or NOAA."
>> **
>> Roy Mendelssohn
>> Supervisory Operations Research Analyst
>> NOAA/NMFS
>> Environmental Research Division
>> Southwest Fisheries Science Center
>> ***Note new street address***
>> 110 McAllister Way
>> Santa Cruz, CA 95060
>> Phone: (831)-420-3666
>> Fax: (831) 420-3980
>> e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/
>>
>> "Old age and treachery will overcome youth and skill."
>> "From those who have been given much, much will be expected"
>> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
>>
>> ___
>> R-sig-Geo mailing list
>> R-sig-Geo@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>
> --
> Edzer Pebesma
> Institute for Geoinformatics
> Heisenbergstrasse 2, 48151 Muenster, Germany
> Phone: +49 251 8333081
> ___
> R-sig-Geo mailing list
> R-sig-Geo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
**
"The contents of this message do not reflect any position of the U.S.
Government or NOAA."
**
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/
"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
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Re: [R-sig-Geo] testing a crs string
On 6/20/19 4:18 PM, Roy Mendelssohn - NOAA Federal via R-sig-Geo wrote:
> Hi All:
>
> I am extending a package I have to allow users to provide a crs string, which
> will eventually through some other packages be sent to sf. I like to try and
> make at least minimal tests that inputs are valid. Is there some existing
> code that will check if a string is a valid crs string?
> inherits(try(sf::st_crs("+proj=invalid"), silent = TRUE), "try-error")
[1] TRUE
> inherits(try(sf::st_crs("+proj=longlat"), silent = TRUE), "try-error")
[1] FALSE
>
> Thanks,
>
> -Roy
>
>
> **
> "The contents of this message do not reflect any position of the U.S.
> Government or NOAA."
> **
> Roy Mendelssohn
> Supervisory Operations Research Analyst
> NOAA/NMFS
> Environmental Research Division
> Southwest Fisheries Science Center
> ***Note new street address***
> 110 McAllister Way
> Santa Cruz, CA 95060
> Phone: (831)-420-3666
> Fax: (831) 420-3980
> e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/
>
> "Old age and treachery will overcome youth and skill."
> "From those who have been given much, much will be expected"
> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
>
> ___
> R-sig-Geo mailing list
> R-sig-Geo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
--
Edzer Pebesma
Institute for Geoinformatics
Heisenbergstrasse 2, 48151 Muenster, Germany
Phone: +49 251 8333081
pEpkey.asc
Description: application/pgp-keys
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[R-sig-Geo] testing a crs string
Hi All: I am extending a package I have to allow users to provide a crs string, which will eventually through some other packages be sent to sf. I like to try and make at least minimal tests that inputs are valid. Is there some existing code that will check if a string is a valid crs string? Thanks, -Roy ** "The contents of this message do not reflect any position of the U.S. Government or NOAA." ** Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS Environmental Research Division Southwest Fisheries Science Center ***Note new street address*** 110 McAllister Way Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/ "Old age and treachery will overcome youth and skill." "From those who have been given much, much will be expected" "the arc of the moral universe is long, but it bends toward justice" -MLK Jr. ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
