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Updated: 11 min 11 sec ago

Fwd: Fwd: Re: Sf st_read postgis

Thu, 06/14/2018 - 07:22

-------- Doorgestuurd bericht --------
Onderwerp: Re: [R-sig-Geo] Sf st_read postgis
Datum: Thu, 14 Jun 2018 13:48:17 +0200
Van: Peter <[hidden email]>
Aan: Jan Willem van der Lichte <[hidden email]>



Hi Jan Willem,

reading from a pgdatabase seems extremly sensitive for upper/lowercase
column titles and irregularities IN data (like '+'  and '&' signs)

I tested your query string on a db file in my local pgdatabase and  got
the same error  on a data row with a text field with a '+' in the data.

My guess is there is a similair issue in your db.

An easy solution is :
library(sf)
library(tidyverse)

xx = st_read(connz, "vakantie") %>%  slice(,1:3)

(I know, ALL the data is read in first en then the row 1:3 are selected
....)

# also  try this example

library(sf)
library(mapview)
library(tidyverse)
library(RPostgreSQL)

# read package file nc
nc <- st_read(system.file("shape/nc.shp", package="sf"))

# adjust to your local db parameters
ctest = dbConnect(PostgreSQL(), user="usr",dbname = "db")

# write nc file to db
st_write(nc,ctest)

# check if oke
st_read(ctest, "nc")

st_read(ctest,"nc") %>% slice(.,1:3)

st_read(ctest,"nc") %>% mapview(zcol="NAME")

## all oke !


st_read(ctest,  query="select * from nc limit 1") # oke

# this is the example given in
https://r-spatial.github.io/sf/reference/st_read.html
st_read(ctest,  "nc",query="select * from nc limit 1") # not oke!

st_read(ctest,  query="select * from nc  where NAME = 'Surry'") # not oke

st_read(ctest,  query="select * from nc  where name = 'Ashe'") # not oke


st_read(ctest,  query="select * FROM nc  WHERE \"SID79\" = 0") # oke !
st_read(ctest,  query="select * FROM nc  WHERE \"NAME\" = 'Ashe' ") # oke !

# the query string is not R but sql :
#  UPPERCAST column names need to be double quoted
# and  a "\" is needed to protect the " in the string,
# spaces around the = sign are mandatory

dbDisconnect(ctest)


HTH
  Peter van Horssen


Op 14-6-2018 om 11:59 schreef Jan Willem van der Lichte:
> Hi, thx for answering.
> If I follow your suggestion, I get an error. see below.
> > xx = st_read(connz, query = "SELECT * FROM vakantie LIMIT 3;") Error
> in CPL_hex_to_raw(vapply(x, skip0x, USE.NAMES = FALSE, "")) :
> char2int: false character in hex string
> Any other ideas?
> Thanks Jan Willem
> *Sent:* Tuesday, June 12, 2018 at 2:29 PM
> *From:* "Michael DELORME" <[hidden email]>
> *To:* [hidden email]
> *Subject:* Re: [R-sig-Geo] Sf st_read postgis
> Hi
>
> If you use a query you don't have to set a table name, so
>
> xx <- st_read(connz, query="SELECT * FROM vakantie LIMIT 3;")
>
> should work...
>
>
> Le 12/06/2018 12:12, Jan Willem van der Lichte a �crit :
> > Hi list,
> >
> > Can someone help me with a basic sf question.
> >
> > I try to use the sf::st_read function to get some data out of postgis.
> >
> > I set up a connection (connz) to postgis.
> > I checked if the connection was working with
> >
> > dbListTables(connz)
> >
> > The result was ok, I saw all the tables in the database.
> >
> > Next I tried to get some data with the st_read() function, from the
> sf package.
> >
> > I tried to follow the example in the help.
> >
> > xx<- st_read(connz, "vakantie", query="SELECT * FROM vakantie LIMIT 3;")
> >
> > So i replaced the table meuse with vakantie.
> >
> > When I execute this statement, I get a warning
> >
> > Warning message: In st_read.DBIObject(...) : Ignoring query
> argument, only using table.
> >
> > So what's happening, am I doing something wrong? Which is possible,
> cause I'm new to R. :-)
> >
> > Thanks
> > Jan Willem
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > Sent with my iPad
> >
> > _______________________________________________
> > R-sig-Geo mailing list
> > [hidden email]
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >
> >
>
> --
> *Micha�l DELORME*
> Administrateur de donn�es, charg� de projet en g�omatique
> Service r�gional de l'information statistique, �conomique et territoriale
> Direction r�gionale de l'alimentation, de l'agriculture et de la for�t
> Auvergne-Rh�ne-Alpes
> Site de Lyon
> 165 rue Garibaldi � BP 3202 � 69401 LYON cedex 03
> 04 78 63 34 21
>
> Pour �crire au service :
> DRAAF Auvergne-Rh�ne-Alpes � SRISET
> 16B rue Aim� Rudel � BP 45 � 63370 LEMPDES
>
> http://www.draaf.auvergne-rhone-alpes.agriculture.gouv.fr/
>
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*GreenStat* - /Statistical and GIS services for ecological research/

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<http://www.greenstat.nl>

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Re: Sf st_read postgis

Thu, 06/14/2018 - 04:59
  Hi, thx for answering.   If I follow your suggestion, I get an error. see below.   > xx = st_read(connz, query = "SELECT * FROM vakantie LIMIT 3;") Error in CPL_hex_to_raw(vapply(x, skip0x, USE.NAMES = FALSE, "")) : char2int: false character in hex string   Any other ideas?   Thanks Jan Willem     Sent: Tuesday, June 12, 2018 at 2:29 PM
From: "Michael DELORME" <[hidden email]>
To: [hidden email]
Subject: Re: [R-sig-Geo] Sf st_read postgis Hi

If you use a query you don't have to set a table name, so

xx <- st_read(connz, query="SELECT * FROM vakantie LIMIT 3;")

should work...


Le 12/06/2018 12:12, Jan Willem van der Lichte a �crit :
> Hi list,
>
> Can someone help me with a basic sf question.
>
> I try to use the sf::st_read function to get some data out of postgis.
>
> I set up a connection (connz) to postgis.
> I checked if the connection was working with
>
> dbListTables(connz)
>
> The result was ok, I saw all the tables in the database.
>
> Next I tried to get some data with the st_read() function, from the sf package.
>
> I tried to follow the example in the help.
>
> xx<- st_read(connz, "vakantie", query="SELECT * FROM vakantie LIMIT 3;")
>
> So i replaced the table meuse with vakantie.
>
> When I execute this statement, I get a warning
>
> Warning message: In st_read.DBIObject(...) : Ignoring query argument, only using table.
>
> So what's happening, am I doing something wrong? Which is possible, cause I'm new to R. :-)
>
> Thanks
> Jan Willem
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Sent with my iPad
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
>

--
*Micha�l DELORME*
Administrateur de donn�es, charg� de projet en g�omatique
Service r�gional de l'information statistique, �conomique et territoriale
Direction r�gionale de l'alimentation, de l'agriculture et de la for�t
Auvergne-Rh�ne-Alpes
Site de Lyon
165 rue Garibaldi � BP 3202 � 69401 LYON cedex 03
04 78 63 34 21

Pour �crire au service :
DRAAF Auvergne-Rh�ne-Alpes � SRISET
16B rue Aim� Rudel � BP 45 � 63370 LEMPDES

http://www.draaf.auvergne-rhone-alpes.agriculture.gouv.fr/

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Re: Spatio-Temporal objects and kriging

Thu, 06/14/2018 - 03:33
Dear Bruno,

On 14.06.2018 08:40, Bruno Sesti wrote:
> Hi, I have some questions about spatio temporal objects and kriging, I have
> done some research to try to solve this problems but I did not find any
> answer.
> I would Like to know if and, if yes, how could be possible to convert a
> STIDF object to a SpatialPointsDataFrame object.
You can simply coerce it to "Spatial", note that the class of your
projected Spatial-Obj will depend on the class of the spatial slot of
your STIDF-Obj:

library(sp)
library(xts)
library(spacetime)

data("meuse")
coordinates(meuse) <- ~x+y
proj4string(meuse) <- CRS("+init=epsg:28992")

stidf <- STIDF(geometry(meuse), xts(1:length(meuse), Sys.time() -
(1:length(meuse))*24*3600), meuse@data)

spdf <- as(stidf, "Spatial")

spplot(spdf, "copper")

> The second issue is if and how it could be possible to plot the map(s)
> obtained through the function krigeST over an open street map or a Google
> map layer in R environment and/or in other gis environments.
The function stplot re-uses the function spplot, hence you could use the
mechanisms of overlaying base maps with your interpolated values (i.e.
via sp.layout):

data(meuse.riv)
meuse.sr =
SpatialPolygons(list(Polygons(list(Polygon(meuse.riv)),"meuse.riv")))
stplot(stidf[,,"copper"], sp.layout=list("sp.polygons",
fill="lightblue", meuse.sr))

The package plotKML allows to directly plot an STIDF-Obj in Google Earth
including the temporal domain allowing for a quick animation:

library(plotKML)
plotKML(stidf)

Generally, one will have to pick an appropriate (exchange) format that
respects time and is understood by R and your favorite GIS. A slice wise
pure spatial export/plot is of course also an option, i.e. looping
through all relevant timestamps and exporting e.g. a geotiff each or
using the same techniques as in the pure spatial case.

HTH,

  Ben


>
> Kind regards.
>
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>
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Martin-Luther-King-Weg 24
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E-Mail: [hidden email]
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Spatio-Temporal objects and kriging

Thu, 06/14/2018 - 01:40
Hi, I have some questions about spatio temporal objects and kriging, I have
done some research to try to solve this problems but I did not find any
answer.
I would Like to know if and, if yes, how could be possible to convert a
STIDF object to a SpatialPointsDataFrame object.
The second issue is if and how it could be possible to plot the map(s)
obtained through the function krigeST over an open street map or a Google
map layer in R environment and/or in other gis environments.

Kind regards.

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What is the Coordinate Reference System?

Wed, 06/13/2018 - 23:03
Greetings,

I'm want to read NetCDF spatial data from a meteorological model (WRF
model). The NetCDF can have one of these three projections:

Polar stereographic
Lambert conformal
Mercator projection

(See figure
https://user-images.githubusercontent.com/27447280/41389756-ed23f91a-6f68-11e8-961e-6ba901913c54.png
)

What is the  Coordinate Reference System for each case?

Thanks!

Here an example with ncdf4 and raster:

library(ncdf4)
library(raster)
a <- tempfile()
download.file(url = "
http://www.unidata.ucar.edu/software/netcdf/examples/wrfout_v2_Lambert.nc",
              destfile = a) #78 Mb
wrf <- nc_open(a)
paste("The file has",wrf$nvars,"variables")
paste("The file has",names(wrf$var))
lat <- ncvar_get( wrf, "XLAT" )
lon <- ncvar_get( wrf, "XLONG" )
t2 <- ncvar_get( wrf, "T2" ) - 273.15
dim(t2) #73 60 13
#image
image(t2[, , 12])
# raster
rt2 <- raster(t(t2[1:dim(t2)[1],
                   dim(t2)[2]:1,
                   12]),
              xmn = min(lon),
              xmx = max(lon),
              ymn = min(lat),
              ymx = max(lat),
*              crs="+init=epsg:4326") # ???*
spplot(rt2)



--
​Sergio Ibarra Espinosa
Post Doc
PhD in Atmospheric Sciences
Instituto de Astronomia, Geofísica e Ciências Atmosféricas
Universidade de São Paulo
Rua do Matão, 1226
São Paulo-SP - Brasil -
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Re: CRAN releases of sp, rgdal and rgeos

Tue, 06/12/2018 - 16:32


On 06/12/2018 07:49 PM, Vijay Lulla wrote:
> What is the setup that CRAN uses?  Where can I find this information?

The last two links of https://cran.r-project.org/bin/macosx/ point you
to the libraries it statically links to; further info maybe
https://github.com/r-spatial/sf/issues/327 (or search sf issues for "simon")

>
> I install most of the R packages on my mac from source and I will be happy
> to help (mostly with answering questions and sharing my notes about how I
> get packages to compile).
>
> On Tue, Jun 12, 2018 at 12:00 PM, Edzer Pebesma <
> [hidden email]> wrote:
>
>> proj.5 contains new features, but none of these are, or will in the near
>> future be available to R users. All our (= Roger + me) efforts so far
>> have been to get software (rgdal, sf) running with proj.5, not to expose
>> any of its new features.
>> See also https://github.com/r-spatial/sf/issues/545
>>
>> Also: if anyone insists on installing rgdal or sf from source on a Mac
>> but doesn't use the setup CRAN uses for building binaries, neither Roger
>> nor I can assist in case of problems beyond wildly guessing. Of course,
>> any help from anyone else on these kind of issues is highly appreciated.
>>
>> On 06/12/2018 04:41 PM, Vijay Lulla wrote:
>>> Thank you for the explanation of difference between proj.h and proj_api.h
>>> and the recommendation of setting environment variable for pkg-config.  I
>>> had tried using pkg-config by setting env variables but haven't had much
>>> luck getting it to work.
>>> Cordially,
>>> Vijay.
>>>
>>> On Tue, Jun 12, 2018 at 3:11 AM, Roger Bivand <[hidden email]>
>> wrote:
>>>
>>>> On Tue, 12 Jun 2018, Vijay Lulla wrote:
>>>>
>>>> I too use R on a mac but I cannot get rgdal to use proj5 (port info
>> proj).
>>>>> rgdal still uses proj4 even when there is a newer version of proj
>> already
>>>>> on my computer.  Neither of these proj packages (proj4 or proj) use
>>>>> pkg-config mechanism even though there are proj.pc files in both
>> versions
>>>>> of the package.  Maybe using the pkg-config mechanism to detect
>> version of
>>>>> packages during source installation might help?  I don't know whether
>> this
>>>>> is a "proj" or a "macports" issue though.
>>>>>
>>>>>
>>>> Neither sp/rgdal nor sf plan to accomodate the proj.h interface until
>> the
>>>> GDAL barn-raising project is completed. Even then, most software using
>> proj
>>>> will have to support the proj_api.h and the proj.h APIs because many
>>>> platforms are bound to move at the speed of the slowest package using
>> proj.
>>>> The proj_api.h API does use the new mechanisms internally, but it isn't
>>>> obvious how or whether proj.h pipelines should be exposed (GRASS has a
>>>> prototype implementation).
>>>>
>>>> If you work in geodetics and need sub-cm precision, this may matter; in
>>>> which case please follow the GDAL barn-raising project and provide use
>>>> cases where the proj.h API is required. The main difference is that the
>>>> proj_api.h API always transforms to the WGS84 datum first then
>> transforms
>>>> to the target datum (many to one then one to many). When this was chosen
>>>> 1984 was not so long ago; the new proj.h API suggests transforming
>> along a
>>>> pipeline from source to target datum without going through WGS84 (many
>> to
>>>> many).
>>>>
>>>> If your question is about how to install rgdal from source on OSX, you
>> may
>>>> need to ensure that you only have one version of proj installed, or use
>>>> configure arguments and load path modifications on your own
>> responsibility.
>>>>
>>>> From rgdal 1.3-1, the pkg-config mechanism is used if the path to
>> proj.pc
>>>> is set correctly (environment variable), but will fall back on standard
>>>> locations if pkg-config proj fails.
>>>>
>>>> Roger
>>>>
>>>>
>>>>
>>>>> On Mon, Jun 11, 2018 at 7:54 PM, Thiago V. dos Santos via R-sig-Geo <
>>>>> [hidden email]> wrote:
>>>>>
>>>>> Hi Roger, thanks for the follow up. Answering to your comments:
>>>>>>
>>>>>> a) I am using Macports's gdal version 2.3.0.20180523. I am pretty sure
>>>>>> that its source code (i.e. the one that is compiled on my machine) is
>>>>>> downloaded from OSGEO (at least according to https://github.com/
>>>>>> macports/macports-ports/blob/master/gis/gdal/Portfile);
>>>>>>
>>>>>> b) I do have more than one libproj installed on my system (as QGIS for
>>>>>> macOS requires its own gdal and proj stuff), but only the Macports
>> one is
>>>>>> on my path;
>>>>>>
>>>>>>
>>>>>> c) I tried running:
>>>>>> tools::testInstalledPackage("rgdal", outDir=tempdir())list.files(
>>>>>> tempdir())file.show(file.path(tempdir(), "rgdal-Ex.Rout"))
>>>>>>
>>>>>> but it unexpectedly returned "Error in library("rgdal") : there is no
>>>>>> package called ‘rgdal’. Execution halted".
>>>>>>
>>>>>> It looks weird but so far I am able to normally load and use at least
>> a
>>>>>> couple of rgdal's functions.
>>>>>>
>>>>>> I will keep monitoring it though, and report any other issue.
>>>>>>
>>>>>> Cheers,
>>>>>>  -- Thiago V. dos Santos
>>>>>> Postdoctoral Research FellowDepartment of Climate and Space Science
>> and
>>>>>> EngineeringUniversity of Michigan
>>>>>>
>>>>>>     On Sunday, June 10, 2018, 4:46:04 AM EDT, Roger Bivand <
>>>>>> [hidden email]> wrote:
>>>>>>
>>>>>>  Thanks for reporting, comments inline below (note that I have no OSX
>>>>>> access at all):
>>>>>>
>>>>>> On Sat, 9 Jun 2018, Thiago V. dos Santos wrote:
>>>>>>
>>>>>> Dear Roger,
>>>>>>> Thank you very much for the excellent work done with those packages.
>>>>>>> Today I update both rgeos and rgdal on my system - macOS 10.13.5 with
>>>>>>> all dependencies installed via MacPorts. I had updated sp a few days
>>>>>>> earlier. The dependencies versions on my system are gdal
>>>>>>> @2.3.0.20180523_0+grib+hdf4+hdf5+jasper+mpich+netcdf and proj
>> @5.1.0_0.
>>>>>>> Rgeos's update went flawlessly, but I got a few errors while updating
>>>>>>> rgdal. It still compiled successfully, but I am concerned that some
>>>>>>> functionality might be compromised due to the errors.
>>>>>>> This is what I got (I have to manually specify the location of proj
>> or
>>>>>>> rgdal won't find it):> install.packages('rgdal', type = "source",
>>>>>>> configure.args=c(
>>>>>>> +    '--with-proj-include=/opt/local/lib/proj5/include',
>>>>>>> +    '--with-proj-lib=/opt/local/lib/proj5/lib'))
>>>>>>> Installing package into ‘/Users/thiago/Documents/R-packages’
>>>>>>> (as ‘lib’ is unspecified)
>>>>>>> trying URL 'https://cran.r-project.org/
>> src/contrib/rgdal_1.3-2.tar.gz'
>>>>>>> Content type 'application/x-gzip' length 1667049 bytes (1.6 MB)
>>>>>>> ==================================================
>>>>>>> downloaded 1.6 MB
>>>>>>>
>>>>>>> * installing *source* package ‘rgdal’ ...
>>>>>>> ** package ‘rgdal’ successfully unpacked and MD5 sums checked
>>>>>>> configure: CC: /usr/bin/clang
>>>>>>> configure: CXX: /usr/bin/clang++
>>>>>>> configure: rgdal: 1.3-2
>>>>>>> checking for /usr/bin/svnversion... yes
>>>>>>> configure: svn revision: 755
>>>>>>> checking whether the C++ compiler works... yes
>>>>>>> checking for C++ compiler default output file name... a.out
>>>>>>> checking for suffix of executables...
>>>>>>> checking whether we are cross compiling... no
>>>>>>> checking for suffix of object files... o
>>>>>>> checking whether we are using the GNU C++ compiler... yes
>>>>>>> checking whether /usr/bin/clang++ accepts -g... yes
>>>>>>> checking whether /usr/bin/clang++ supports C++11 features by
>> default...
>>>>>>>
>>>>>> no
>>>>>>
>>>>>>> checking whether /usr/bin/clang++ supports C++11 features with
>>>>>>>
>>>>>> -std=gnu++11... yes
>>>>>>
>>>>>>> configure: C++11 support available
>>>>>>> checking for gdal-config... /opt/local/bin/gdal-config
>>>>>>> checking gdal-config usability... yes
>>>>>>> configure: GDAL: 2.4.0
>>>>>>>
>>>>>>
>>>>>> All OK up to the GDAL version returned by gdal-config - are you using
>> the
>>>>>> released GDAL 2.3.0 (probably not) or master?
>>>>>>
>>>>>> checking C++11 support for GDAL >= 2.3.0... yes
>>>>>>> checking GDAL version >= 1.11.4... yes
>>>>>>> checking gdal: linking with --libs only... yes
>>>>>>> checking GDAL: /opt/local/share/gdal/pcs.csv readable... yes
>>>>>>> checking proj_api.h presence and usability... yes
>>>>>>> ./configure: line 3395: test: =: unary operator expected
>>>>>>>
>>>>>>
>>>>>> Will check, that line is:
>>>>>>
>>>>>> if test ${PROJ_VERSION} = "" ; then
>>>>>>
>>>>>> from configure.ac line 305. Possibly a shell dialect issue.
>>>>>>
>>>>>> checking PROJ version >= 4.8.0... yes
>>>>>>> checking projects.h presence and usability... yes
>>>>>>>
>>>>>>
>>>>>> These relate to configure.ac lines 376-419, and the outcome: epsg
>> found
>>>>>> and readable is OK - could there be two libproj on your system (maybe
>> for
>>>>>> different architectures)?
>>>>>>
>>>>>> Undefined symbols for architecture x86_64:
>>>>>>>  "_pj_ctx_fclose", referenced from:
>>>>>>>      _main in proj_conf_test2-06fe7d.o
>>>>>>>  "_pj_get_default_ctx", referenced from:
>>>>>>>      _main in proj_conf_test2-06fe7d.o
>>>>>>>  "_pj_open_lib", referenced from:
>>>>>>>      _main in proj_conf_test2-06fe7d.o
>>>>>>> ld: symbol(s) not found for architecture x86_64
>>>>>>> clang: error: linker command failed with exit code 1 (use -v to see
>>>>>>>
>>>>>> invocation)
>>>>>>
>>>>>>> ./configure: line 3511: ./proj_conf_test2: No such file or directory
>>>>>>> checking PROJ.4: epsg found and readable... yes
>>>>>>>
>>>>>>
>>>>>> Same here for next block in configure.ac; conus found and readable.
>>>>>>
>>>>>> Undefined symbols for architecture x86_64:
>>>>>>>  "_pj_ctx_fclose", referenced from:
>>>>>>>      _main in proj_conf_test3-3b7aa2.o
>>>>>>>  "_pj_get_default_ctx", referenced from:
>>>>>>>      _main in proj_conf_test3-3b7aa2.o
>>>>>>>  "_pj_open_lib", referenced from:
>>>>>>>      _main in proj_conf_test3-3b7aa2.o
>>>>>>> ld: symbol(s) not found for architecture x86_64
>>>>>>> clang: error: linker command failed with exit code 1 (use -v to see
>>>>>>>
>>>>>> invocation)
>>>>>>
>>>>>>> ./configure: line 3570: ./proj_conf_test3: No such file or directory
>>>>>>> checking PROJ.4: conus found and readable... yes
>>>>>>> configure: Package CPP flags:  -I/opt/local/include
>>>>>>>
>>>>>> -I/opt/local/lib/proj5/include
>>>>>>
>>>>>>> configure: Package LIBS:  -L/opt/local/lib -lgdal
>>>>>>>
>>>>>> -L/opt/local/lib/proj5/lib -lproj
>>>>>>
>>>>>>> configure: creating ./config.status
>>>>>>> config.status: creating src/Makevars
>>>>>>> ** libs
>>>>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
>>>>>>> work/Resources/include"
>>>>>>>
>>>>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>>>>> -I"/Users/thiago/Documents/R-packages/sp/include"
>> -I/usr/local/include
>>>>>> -fPIC  -Wall -g -O2 -c OGR_write.cpp -o OGR_write.o
>>>>>>
>>>>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
>>>>>>> work/Resources/include"
>>>>>>>
>>>>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>>>>> -I"/Users/thiago/Documents/R-packages/sp/include"
>> -I/usr/local/include
>>>>>> -fPIC  -Wall -g -O2 -c gdal-bindings.cpp -o gdal-bindings.o
>>>>>>
>>>>>>> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
>>>>>>>
>>>>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>>>>> -I"/Users/thiago/Documents/R-packages/sp/include"
>> -I/usr/local/include
>>>>>> -fPIC  -Wall -g -O2  -c init.c -o init.o
>>>>>>
>>>>>>> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
>>>>>>>
>>>>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>>>>> -I"/Users/thiago/Documents/R-packages/sp/include"
>> -I/usr/local/include
>>>>>> -fPIC  -Wall -g -O2  -c inverser.c -o inverser.o
>>>>>>
>>>>>>> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
>>>>>>>
>>>>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>>>>> -I"/Users/thiago/Documents/R-packages/sp/include"
>> -I/usr/local/include
>>>>>> -fPIC  -Wall -g -O2  -c local_stubs.c -o local_stubs.o
>>>>>>
>>>>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
>>>>>>> work/Resources/include"
>>>>>>>
>>>>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>>>>> -I"/Users/thiago/Documents/R-packages/sp/include"
>> -I/usr/local/include
>>>>>> -fPIC  -Wall -g -O2 -c ogr_geom.cpp -o ogr_geom.o
>>>>>>
>>>>>>> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
>>>>>>>
>>>>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>>>>> -I"/Users/thiago/Documents/R-packages/sp/include"
>> -I/usr/local/include
>>>>>> -fPIC  -Wall -g -O2  -c ogr_polygons.c -o ogr_polygons.o
>>>>>>
>>>>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
>>>>>>> work/Resources/include"
>>>>>>>
>>>>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>>>>> -I"/Users/thiago/Documents/R-packages/sp/include"
>> -I/usr/local/include
>>>>>> -fPIC  -Wall -g -O2 -c ogr_proj.cpp -o ogr_proj.o
>>>>>>
>>>>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
>>>>>>> work/Resources/include"
>>>>>>>
>>>>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>>>>> -I"/Users/thiago/Documents/R-packages/sp/include"
>> -I/usr/local/include
>>>>>> -fPIC  -Wall -g -O2 -c ogrdrivers.cpp -o ogrdrivers.o
>>>>>>
>>>>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
>>>>>>> work/Resources/include"
>>>>>>>
>>>>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>>>>> -I"/Users/thiago/Documents/R-packages/sp/include"
>> -I/usr/local/include
>>>>>> -fPIC  -Wall -g -O2 -c ogrsource.cpp -o ogrsource.o
>>>>>>
>>>>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
>>>>>>> work/Resources/include"
>>>>>>>
>>>>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>>>>> -I"/Users/thiago/Documents/R-packages/sp/include"
>> -I/usr/local/include
>>>>>> -fPIC  -Wall -g -O2 -c projectit.cpp -o projectit.o
>>>>>>
>>>>>>> clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names
>>>>>>>
>>>>>> -undefined dynamic_lookup -single_module -multiply_defined suppress
>>>>>> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
>>>>>> rgdal.so OGR_write.o gdal-bindings.o init.o inverser.o local_stubs.o
>>>>>> ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o
>> projectit.o
>>>>>> -L/opt/local/lib -lgdal -L/opt/local/lib/proj5/lib -lproj
>>>>>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>>>>>> -Wl,CoreFoundation
>>>>>>
>>>>>>> installing to /Users/thiago/Documents/R-packages/rgdal/libs
>>>>>>> ** R
>>>>>>> ** data
>>>>>>> ** inst
>>>>>>> ** byte-compile and prepare package for lazy loading
>>>>>>> ** help
>>>>>>> *** installing help indices
>>>>>>> ** building package indices
>>>>>>> ** installing vignettes
>>>>>>> ** testing if installed package can be loaded
>>>>>>> * DONE (rgdal)
>>>>>>>
>>>>>>> The downloaded source packages are in
>>>>>>>
>>>>>>> ‘/private/var/folders/_z/01gg71zs19g816v6m2dddt8w0000gn
>>>>>>>
>>>>>> /T/Rtmp5K6lt8/downloaded_packages’
>>>>>>
>>>>>>> ​Is this something that needs to be investigated, or I can just
>> safely
>>>>>>> ignore those messages?
>>>>>>>
>>>>>>
>>>>>> Please try to run:
>>>>>>
>>>>>> tools::testInstalledPackage("rgdal", outDir=tempdir())
>>>>>> list.files(tempdir())
>>>>>> file.show(file.path(tempdir(), "rgdal-Ex.Rout"))
>>>>>>
>>>>>> and if the outcomes are as expected, you should be OK, please let us
>>>>>> know.
>>>>>>
>>>>>> If any OSX users installing from source can contribute, that would be
>>>>>> useful. It will take a little while before the CRAN OSX binaries
>> catch up
>>>>>> with new PROJ and GDAL.
>>>>>>
>>>>>> Again thanks for reporting!
>>>>>>
>>>>>> Roger
>>>>>>
>>>>>> Many thanks, -- Thiago V. dos Santos
>>>>>>> Postdoctoral Research FellowDepartment of Climate and Space Science
>> and
>>>>>>>
>>>>>> EngineeringUniversity of Michigan
>>>>>>
>>>>>>>
>>>>>>>    On Friday, June 8, 2018, 2:15:43 PM EDT, Roger Bivand <
>>>>>>>
>>>>>> [hidden email]> wrote:
>>>>>>
>>>>>>>
>>>>>>> There are new releases of sp, rgdal and rgeos on CRAN. Please
>> install sp
>>>>>>> first, then the other two, which link to the installed sp. They all
>>>>>>> address so-called rchk issues, which have not so far been a problem,
>> but
>>>>>>> might have become more fragile as R's internal memory management is
>> made
>>>>>>> even more efficient. This involves compiled code using memory
>> allocated
>>>>>>>
>>>>>> by
>>>>>>
>>>>>>> R to be freed by R's garbage collector, which has to know if an
>> object
>>>>>>> is
>>>>>>> still being used. Tomas Kalibera, the author of rchk, helped resolve
>> and
>>>>>>> explain the issues encountered - what was good coding practice
>> fifteen
>>>>>>> years ago isn't always still good practice.
>>>>>>>
>>>>>>> In addition, the earliest versions of GDAL and PROJ with which rgdal
>>>>>>> will
>>>>>>> work have been updated, and set to PROJ 4.8.0 and GDAL 1.11.4. The
>>>>>>>
>>>>>> current
>>>>>>
>>>>>>> released versions of PROJ and GDAL are to be prefered, as bugs have
>> been
>>>>>>> fixed and new features and drivers introduced. A check has been put
>>>>>>> in place to trap attempts to install rgdal without a C++11-capable
>>>>>>> compiler when the GDAL version is >=2.3.0 - which requires C++11.
>> rgeos
>>>>>>>
>>>>>> is
>>>>>>
>>>>>>> ready for the forthcoming version of GEOS.
>>>>>>>
>>>>>>> The CRAN team has also been very supportive of our efforts to bring
>>>>>>> compiled code in these packages into rchk compliance.
>>>>>>>
>>>>>>> Please get in touch if you see any loose ends in these releases.
>>>>>>>
>>>>>>> Roger
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> --
>>>>>> Roger Bivand
>>>>>> Department of Economics, Norwegian School of Economics,
>>>>>> Helleveien 30, N-5045 Bergen, Norway.
>>>>>> voice: +47 55 95 93 55; e-mail: [hidden email]
>>>>>> http://orcid.org/0000-0003-2392-6140
>>>>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>>>>>         [[alternative HTML version deleted]]
>>>>>>
>>>>>> _______________________________________________
>>>>>> R-sig-Geo mailing list
>>>>>> [hidden email]
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>> --
>>>> Roger Bivand
>>>> Department of Economics, Norwegian School of Economics,
>>>> Helleveien 30, N-5045 Bergen, Norway.
>>>> voice: +47 55 95 93 55; e-mail: [hidden email]
>>>> http://orcid.org/0000-0003-2392-6140
>>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>>>
>>>
>>>
>>>
>>
>> --
>> Edzer Pebesma
>> Institute for Geoinformatics
>> Heisenbergstrasse 2, 48151 Muenster, Germany
>> Phone: +49 251 8333081
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> [hidden email]
>> 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
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo

Re: CRAN releases of sp, rgdal and rgeos

Tue, 06/12/2018 - 12:49
What is the setup that CRAN uses?  Where can I find this information?

I install most of the R packages on my mac from source and I will be happy
to help (mostly with answering questions and sharing my notes about how I
get packages to compile).

On Tue, Jun 12, 2018 at 12:00 PM, Edzer Pebesma <
[hidden email]> wrote:

> proj.5 contains new features, but none of these are, or will in the near
> future be available to R users. All our (= Roger + me) efforts so far
> have been to get software (rgdal, sf) running with proj.5, not to expose
> any of its new features.
> See also https://github.com/r-spatial/sf/issues/545
>
> Also: if anyone insists on installing rgdal or sf from source on a Mac
> but doesn't use the setup CRAN uses for building binaries, neither Roger
> nor I can assist in case of problems beyond wildly guessing. Of course,
> any help from anyone else on these kind of issues is highly appreciated.
>
> On 06/12/2018 04:41 PM, Vijay Lulla wrote:
> > Thank you for the explanation of difference between proj.h and proj_api.h
> > and the recommendation of setting environment variable for pkg-config.  I
> > had tried using pkg-config by setting env variables but haven't had much
> > luck getting it to work.
> > Cordially,
> > Vijay.
> >
> > On Tue, Jun 12, 2018 at 3:11 AM, Roger Bivand <[hidden email]>
> wrote:
> >
> >> On Tue, 12 Jun 2018, Vijay Lulla wrote:
> >>
> >> I too use R on a mac but I cannot get rgdal to use proj5 (port info
> proj).
> >>> rgdal still uses proj4 even when there is a newer version of proj
> already
> >>> on my computer.  Neither of these proj packages (proj4 or proj) use
> >>> pkg-config mechanism even though there are proj.pc files in both
> versions
> >>> of the package.  Maybe using the pkg-config mechanism to detect
> version of
> >>> packages during source installation might help?  I don't know whether
> this
> >>> is a "proj" or a "macports" issue though.
> >>>
> >>>
> >> Neither sp/rgdal nor sf plan to accomodate the proj.h interface until
> the
> >> GDAL barn-raising project is completed. Even then, most software using
> proj
> >> will have to support the proj_api.h and the proj.h APIs because many
> >> platforms are bound to move at the speed of the slowest package using
> proj.
> >> The proj_api.h API does use the new mechanisms internally, but it isn't
> >> obvious how or whether proj.h pipelines should be exposed (GRASS has a
> >> prototype implementation).
> >>
> >> If you work in geodetics and need sub-cm precision, this may matter; in
> >> which case please follow the GDAL barn-raising project and provide use
> >> cases where the proj.h API is required. The main difference is that the
> >> proj_api.h API always transforms to the WGS84 datum first then
> transforms
> >> to the target datum (many to one then one to many). When this was chosen
> >> 1984 was not so long ago; the new proj.h API suggests transforming
> along a
> >> pipeline from source to target datum without going through WGS84 (many
> to
> >> many).
> >>
> >> If your question is about how to install rgdal from source on OSX, you
> may
> >> need to ensure that you only have one version of proj installed, or use
> >> configure arguments and load path modifications on your own
> responsibility.
> >>
> >> From rgdal 1.3-1, the pkg-config mechanism is used if the path to
> proj.pc
> >> is set correctly (environment variable), but will fall back on standard
> >> locations if pkg-config proj fails.
> >>
> >> Roger
> >>
> >>
> >>
> >>> On Mon, Jun 11, 2018 at 7:54 PM, Thiago V. dos Santos via R-sig-Geo <
> >>> [hidden email]> wrote:
> >>>
> >>> Hi Roger, thanks for the follow up. Answering to your comments:
> >>>>
> >>>> a) I am using Macports's gdal version 2.3.0.20180523. I am pretty sure
> >>>> that its source code (i.e. the one that is compiled on my machine) is
> >>>> downloaded from OSGEO (at least according to https://github.com/
> >>>> macports/macports-ports/blob/master/gis/gdal/Portfile);
> >>>>
> >>>> b) I do have more than one libproj installed on my system (as QGIS for
> >>>> macOS requires its own gdal and proj stuff), but only the Macports
> one is
> >>>> on my path;
> >>>>
> >>>>
> >>>> c) I tried running:
> >>>> tools::testInstalledPackage("rgdal", outDir=tempdir())list.files(
> >>>> tempdir())file.show(file.path(tempdir(), "rgdal-Ex.Rout"))
> >>>>
> >>>> but it unexpectedly returned "Error in library("rgdal") : there is no
> >>>> package called ‘rgdal’. Execution halted".
> >>>>
> >>>> It looks weird but so far I am able to normally load and use at least
> a
> >>>> couple of rgdal's functions.
> >>>>
> >>>> I will keep monitoring it though, and report any other issue.
> >>>>
> >>>> Cheers,
> >>>>  -- Thiago V. dos Santos
> >>>> Postdoctoral Research FellowDepartment of Climate and Space Science
> and
> >>>> EngineeringUniversity of Michigan
> >>>>
> >>>>     On Sunday, June 10, 2018, 4:46:04 AM EDT, Roger Bivand <
> >>>> [hidden email]> wrote:
> >>>>
> >>>>  Thanks for reporting, comments inline below (note that I have no OSX
> >>>> access at all):
> >>>>
> >>>> On Sat, 9 Jun 2018, Thiago V. dos Santos wrote:
> >>>>
> >>>> Dear Roger,
> >>>>> Thank you very much for the excellent work done with those packages.
> >>>>> Today I update both rgeos and rgdal on my system - macOS 10.13.5 with
> >>>>> all dependencies installed via MacPorts. I had updated sp a few days
> >>>>> earlier. The dependencies versions on my system are gdal
> >>>>> @2.3.0.20180523_0+grib+hdf4+hdf5+jasper+mpich+netcdf and proj
> @5.1.0_0.
> >>>>> Rgeos's update went flawlessly, but I got a few errors while updating
> >>>>> rgdal. It still compiled successfully, but I am concerned that some
> >>>>> functionality might be compromised due to the errors.
> >>>>> This is what I got (I have to manually specify the location of proj
> or
> >>>>> rgdal won't find it):> install.packages('rgdal', type = "source",
> >>>>> configure.args=c(
> >>>>> +    '--with-proj-include=/opt/local/lib/proj5/include',
> >>>>> +    '--with-proj-lib=/opt/local/lib/proj5/lib'))
> >>>>> Installing package into ‘/Users/thiago/Documents/R-packages’
> >>>>> (as ‘lib’ is unspecified)
> >>>>> trying URL 'https://cran.r-project.org/
> src/contrib/rgdal_1.3-2.tar.gz'
> >>>>> Content type 'application/x-gzip' length 1667049 bytes (1.6 MB)
> >>>>> ==================================================
> >>>>> downloaded 1.6 MB
> >>>>>
> >>>>> * installing *source* package ‘rgdal’ ...
> >>>>> ** package ‘rgdal’ successfully unpacked and MD5 sums checked
> >>>>> configure: CC: /usr/bin/clang
> >>>>> configure: CXX: /usr/bin/clang++
> >>>>> configure: rgdal: 1.3-2
> >>>>> checking for /usr/bin/svnversion... yes
> >>>>> configure: svn revision: 755
> >>>>> checking whether the C++ compiler works... yes
> >>>>> checking for C++ compiler default output file name... a.out
> >>>>> checking for suffix of executables...
> >>>>> checking whether we are cross compiling... no
> >>>>> checking for suffix of object files... o
> >>>>> checking whether we are using the GNU C++ compiler... yes
> >>>>> checking whether /usr/bin/clang++ accepts -g... yes
> >>>>> checking whether /usr/bin/clang++ supports C++11 features by
> default...
> >>>>>
> >>>> no
> >>>>
> >>>>> checking whether /usr/bin/clang++ supports C++11 features with
> >>>>>
> >>>> -std=gnu++11... yes
> >>>>
> >>>>> configure: C++11 support available
> >>>>> checking for gdal-config... /opt/local/bin/gdal-config
> >>>>> checking gdal-config usability... yes
> >>>>> configure: GDAL: 2.4.0
> >>>>>
> >>>>
> >>>> All OK up to the GDAL version returned by gdal-config - are you using
> the
> >>>> released GDAL 2.3.0 (probably not) or master?
> >>>>
> >>>> checking C++11 support for GDAL >= 2.3.0... yes
> >>>>> checking GDAL version >= 1.11.4... yes
> >>>>> checking gdal: linking with --libs only... yes
> >>>>> checking GDAL: /opt/local/share/gdal/pcs.csv readable... yes
> >>>>> checking proj_api.h presence and usability... yes
> >>>>> ./configure: line 3395: test: =: unary operator expected
> >>>>>
> >>>>
> >>>> Will check, that line is:
> >>>>
> >>>> if test ${PROJ_VERSION} = "" ; then
> >>>>
> >>>> from configure.ac line 305. Possibly a shell dialect issue.
> >>>>
> >>>> checking PROJ version >= 4.8.0... yes
> >>>>> checking projects.h presence and usability... yes
> >>>>>
> >>>>
> >>>> These relate to configure.ac lines 376-419, and the outcome: epsg
> found
> >>>> and readable is OK - could there be two libproj on your system (maybe
> for
> >>>> different architectures)?
> >>>>
> >>>> Undefined symbols for architecture x86_64:
> >>>>>  "_pj_ctx_fclose", referenced from:
> >>>>>      _main in proj_conf_test2-06fe7d.o
> >>>>>  "_pj_get_default_ctx", referenced from:
> >>>>>      _main in proj_conf_test2-06fe7d.o
> >>>>>  "_pj_open_lib", referenced from:
> >>>>>      _main in proj_conf_test2-06fe7d.o
> >>>>> ld: symbol(s) not found for architecture x86_64
> >>>>> clang: error: linker command failed with exit code 1 (use -v to see
> >>>>>
> >>>> invocation)
> >>>>
> >>>>> ./configure: line 3511: ./proj_conf_test2: No such file or directory
> >>>>> checking PROJ.4: epsg found and readable... yes
> >>>>>
> >>>>
> >>>> Same here for next block in configure.ac; conus found and readable.
> >>>>
> >>>> Undefined symbols for architecture x86_64:
> >>>>>  "_pj_ctx_fclose", referenced from:
> >>>>>      _main in proj_conf_test3-3b7aa2.o
> >>>>>  "_pj_get_default_ctx", referenced from:
> >>>>>      _main in proj_conf_test3-3b7aa2.o
> >>>>>  "_pj_open_lib", referenced from:
> >>>>>      _main in proj_conf_test3-3b7aa2.o
> >>>>> ld: symbol(s) not found for architecture x86_64
> >>>>> clang: error: linker command failed with exit code 1 (use -v to see
> >>>>>
> >>>> invocation)
> >>>>
> >>>>> ./configure: line 3570: ./proj_conf_test3: No such file or directory
> >>>>> checking PROJ.4: conus found and readable... yes
> >>>>> configure: Package CPP flags:  -I/opt/local/include
> >>>>>
> >>>> -I/opt/local/lib/proj5/include
> >>>>
> >>>>> configure: Package LIBS:  -L/opt/local/lib -lgdal
> >>>>>
> >>>> -L/opt/local/lib/proj5/lib -lproj
> >>>>
> >>>>> configure: creating ./config.status
> >>>>> config.status: creating src/Makevars
> >>>>> ** libs
> >>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
> >>>>> work/Resources/include"
> >>>>>
> >>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
> >>>> -I"/Users/thiago/Documents/R-packages/sp/include"
> -I/usr/local/include
> >>>> -fPIC  -Wall -g -O2 -c OGR_write.cpp -o OGR_write.o
> >>>>
> >>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
> >>>>> work/Resources/include"
> >>>>>
> >>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
> >>>> -I"/Users/thiago/Documents/R-packages/sp/include"
> -I/usr/local/include
> >>>> -fPIC  -Wall -g -O2 -c gdal-bindings.cpp -o gdal-bindings.o
> >>>>
> >>>>> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
> >>>>>
> >>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
> >>>> -I"/Users/thiago/Documents/R-packages/sp/include"
> -I/usr/local/include
> >>>> -fPIC  -Wall -g -O2  -c init.c -o init.o
> >>>>
> >>>>> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
> >>>>>
> >>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
> >>>> -I"/Users/thiago/Documents/R-packages/sp/include"
> -I/usr/local/include
> >>>> -fPIC  -Wall -g -O2  -c inverser.c -o inverser.o
> >>>>
> >>>>> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
> >>>>>
> >>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
> >>>> -I"/Users/thiago/Documents/R-packages/sp/include"
> -I/usr/local/include
> >>>> -fPIC  -Wall -g -O2  -c local_stubs.c -o local_stubs.o
> >>>>
> >>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
> >>>>> work/Resources/include"
> >>>>>
> >>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
> >>>> -I"/Users/thiago/Documents/R-packages/sp/include"
> -I/usr/local/include
> >>>> -fPIC  -Wall -g -O2 -c ogr_geom.cpp -o ogr_geom.o
> >>>>
> >>>>> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
> >>>>>
> >>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
> >>>> -I"/Users/thiago/Documents/R-packages/sp/include"
> -I/usr/local/include
> >>>> -fPIC  -Wall -g -O2  -c ogr_polygons.c -o ogr_polygons.o
> >>>>
> >>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
> >>>>> work/Resources/include"
> >>>>>
> >>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
> >>>> -I"/Users/thiago/Documents/R-packages/sp/include"
> -I/usr/local/include
> >>>> -fPIC  -Wall -g -O2 -c ogr_proj.cpp -o ogr_proj.o
> >>>>
> >>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
> >>>>> work/Resources/include"
> >>>>>
> >>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
> >>>> -I"/Users/thiago/Documents/R-packages/sp/include"
> -I/usr/local/include
> >>>> -fPIC  -Wall -g -O2 -c ogrdrivers.cpp -o ogrdrivers.o
> >>>>
> >>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
> >>>>> work/Resources/include"
> >>>>>
> >>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
> >>>> -I"/Users/thiago/Documents/R-packages/sp/include"
> -I/usr/local/include
> >>>> -fPIC  -Wall -g -O2 -c ogrsource.cpp -o ogrsource.o
> >>>>
> >>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
> >>>>> work/Resources/include"
> >>>>>
> >>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
> >>>> -I"/Users/thiago/Documents/R-packages/sp/include"
> -I/usr/local/include
> >>>> -fPIC  -Wall -g -O2 -c projectit.cpp -o projectit.o
> >>>>
> >>>>> clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names
> >>>>>
> >>>> -undefined dynamic_lookup -single_module -multiply_defined suppress
> >>>> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
> >>>> rgdal.so OGR_write.o gdal-bindings.o init.o inverser.o local_stubs.o
> >>>> ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o
> projectit.o
> >>>> -L/opt/local/lib -lgdal -L/opt/local/lib/proj5/lib -lproj
> >>>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
> >>>> -Wl,CoreFoundation
> >>>>
> >>>>> installing to /Users/thiago/Documents/R-packages/rgdal/libs
> >>>>> ** R
> >>>>> ** data
> >>>>> ** inst
> >>>>> ** byte-compile and prepare package for lazy loading
> >>>>> ** help
> >>>>> *** installing help indices
> >>>>> ** building package indices
> >>>>> ** installing vignettes
> >>>>> ** testing if installed package can be loaded
> >>>>> * DONE (rgdal)
> >>>>>
> >>>>> The downloaded source packages are in
> >>>>>
> >>>>> ‘/private/var/folders/_z/01gg71zs19g816v6m2dddt8w0000gn
> >>>>>
> >>>> /T/Rtmp5K6lt8/downloaded_packages’
> >>>>
> >>>>> ​Is this something that needs to be investigated, or I can just
> safely
> >>>>> ignore those messages?
> >>>>>
> >>>>
> >>>> Please try to run:
> >>>>
> >>>> tools::testInstalledPackage("rgdal", outDir=tempdir())
> >>>> list.files(tempdir())
> >>>> file.show(file.path(tempdir(), "rgdal-Ex.Rout"))
> >>>>
> >>>> and if the outcomes are as expected, you should be OK, please let us
> >>>> know.
> >>>>
> >>>> If any OSX users installing from source can contribute, that would be
> >>>> useful. It will take a little while before the CRAN OSX binaries
> catch up
> >>>> with new PROJ and GDAL.
> >>>>
> >>>> Again thanks for reporting!
> >>>>
> >>>> Roger
> >>>>
> >>>> Many thanks, -- Thiago V. dos Santos
> >>>>> Postdoctoral Research FellowDepartment of Climate and Space Science
> and
> >>>>>
> >>>> EngineeringUniversity of Michigan
> >>>>
> >>>>>
> >>>>>    On Friday, June 8, 2018, 2:15:43 PM EDT, Roger Bivand <
> >>>>>
> >>>> [hidden email]> wrote:
> >>>>
> >>>>>
> >>>>> There are new releases of sp, rgdal and rgeos on CRAN. Please
> install sp
> >>>>> first, then the other two, which link to the installed sp. They all
> >>>>> address so-called rchk issues, which have not so far been a problem,
> but
> >>>>> might have become more fragile as R's internal memory management is
> made
> >>>>> even more efficient. This involves compiled code using memory
> allocated
> >>>>>
> >>>> by
> >>>>
> >>>>> R to be freed by R's garbage collector, which has to know if an
> object
> >>>>> is
> >>>>> still being used. Tomas Kalibera, the author of rchk, helped resolve
> and
> >>>>> explain the issues encountered - what was good coding practice
> fifteen
> >>>>> years ago isn't always still good practice.
> >>>>>
> >>>>> In addition, the earliest versions of GDAL and PROJ with which rgdal
> >>>>> will
> >>>>> work have been updated, and set to PROJ 4.8.0 and GDAL 1.11.4. The
> >>>>>
> >>>> current
> >>>>
> >>>>> released versions of PROJ and GDAL are to be prefered, as bugs have
> been
> >>>>> fixed and new features and drivers introduced. A check has been put
> >>>>> in place to trap attempts to install rgdal without a C++11-capable
> >>>>> compiler when the GDAL version is >=2.3.0 - which requires C++11.
> rgeos
> >>>>>
> >>>> is
> >>>>
> >>>>> ready for the forthcoming version of GEOS.
> >>>>>
> >>>>> The CRAN team has also been very supportive of our efforts to bring
> >>>>> compiled code in these packages into rchk compliance.
> >>>>>
> >>>>> Please get in touch if you see any loose ends in these releases.
> >>>>>
> >>>>> Roger
> >>>>>
> >>>>>
> >>>>>
> >>>> --
> >>>> Roger Bivand
> >>>> Department of Economics, Norwegian School of Economics,
> >>>> Helleveien 30, N-5045 Bergen, Norway.
> >>>> voice: +47 55 95 93 55; e-mail: [hidden email]
> >>>> http://orcid.org/0000-0003-2392-6140
> >>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
> >>>>         [[alternative HTML version deleted]]
> >>>>
> >>>> _______________________________________________
> >>>> R-sig-Geo mailing list
> >>>> [hidden email]
> >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >>>>
> >>>>
> >>>
> >>>
> >>>
> >>>
> >> --
> >> Roger Bivand
> >> Department of Economics, Norwegian School of Economics,
> >> Helleveien 30, N-5045 Bergen, Norway.
> >> voice: +47 55 95 93 55; e-mail: [hidden email]
> >> http://orcid.org/0000-0003-2392-6140
> >> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
> >>
> >
> >
> >
>
> --
> Edzer Pebesma
> Institute for Geoinformatics
> Heisenbergstrasse 2, 48151 Muenster, Germany
> Phone: +49 251 8333081
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>


--
Vijay Lulla

Assistant Professor,
Dept. of Geography, IUPUI
425 University Blvd, CA-207C.
Indianapolis, IN-46202
[hidden email]
ORCID: https://orcid.org/0000-0002-0823-2522
Webpage: http://vijaylulla.com

        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo

Re: CRAN releases of sp, rgdal and rgeos

Tue, 06/12/2018 - 11:00
proj.5 contains new features, but none of these are, or will in the near
future be available to R users. All our (= Roger + me) efforts so far
have been to get software (rgdal, sf) running with proj.5, not to expose
any of its new features.
See also https://github.com/r-spatial/sf/issues/545

Also: if anyone insists on installing rgdal or sf from source on a Mac
but doesn't use the setup CRAN uses for building binaries, neither Roger
nor I can assist in case of problems beyond wildly guessing. Of course,
any help from anyone else on these kind of issues is highly appreciated.

On 06/12/2018 04:41 PM, Vijay Lulla wrote:
> Thank you for the explanation of difference between proj.h and proj_api.h
> and the recommendation of setting environment variable for pkg-config.  I
> had tried using pkg-config by setting env variables but haven't had much
> luck getting it to work.
> Cordially,
> Vijay.
>
> On Tue, Jun 12, 2018 at 3:11 AM, Roger Bivand <[hidden email]> wrote:
>
>> On Tue, 12 Jun 2018, Vijay Lulla wrote:
>>
>> I too use R on a mac but I cannot get rgdal to use proj5 (port info proj).
>>> rgdal still uses proj4 even when there is a newer version of proj already
>>> on my computer.  Neither of these proj packages (proj4 or proj) use
>>> pkg-config mechanism even though there are proj.pc files in both versions
>>> of the package.  Maybe using the pkg-config mechanism to detect version of
>>> packages during source installation might help?  I don't know whether this
>>> is a "proj" or a "macports" issue though.
>>>
>>>
>> Neither sp/rgdal nor sf plan to accomodate the proj.h interface until the
>> GDAL barn-raising project is completed. Even then, most software using proj
>> will have to support the proj_api.h and the proj.h APIs because many
>> platforms are bound to move at the speed of the slowest package using proj.
>> The proj_api.h API does use the new mechanisms internally, but it isn't
>> obvious how or whether proj.h pipelines should be exposed (GRASS has a
>> prototype implementation).
>>
>> If you work in geodetics and need sub-cm precision, this may matter; in
>> which case please follow the GDAL barn-raising project and provide use
>> cases where the proj.h API is required. The main difference is that the
>> proj_api.h API always transforms to the WGS84 datum first then transforms
>> to the target datum (many to one then one to many). When this was chosen
>> 1984 was not so long ago; the new proj.h API suggests transforming along a
>> pipeline from source to target datum without going through WGS84 (many to
>> many).
>>
>> If your question is about how to install rgdal from source on OSX, you may
>> need to ensure that you only have one version of proj installed, or use
>> configure arguments and load path modifications on your own responsibility.
>>
>> From rgdal 1.3-1, the pkg-config mechanism is used if the path to proj.pc
>> is set correctly (environment variable), but will fall back on standard
>> locations if pkg-config proj fails.
>>
>> Roger
>>
>>
>>
>>> On Mon, Jun 11, 2018 at 7:54 PM, Thiago V. dos Santos via R-sig-Geo <
>>> [hidden email]> wrote:
>>>
>>> Hi Roger, thanks for the follow up. Answering to your comments:
>>>>
>>>> a) I am using Macports's gdal version 2.3.0.20180523. I am pretty sure
>>>> that its source code (i.e. the one that is compiled on my machine) is
>>>> downloaded from OSGEO (at least according to https://github.com/
>>>> macports/macports-ports/blob/master/gis/gdal/Portfile);
>>>>
>>>> b) I do have more than one libproj installed on my system (as QGIS for
>>>> macOS requires its own gdal and proj stuff), but only the Macports one is
>>>> on my path;
>>>>
>>>>
>>>> c) I tried running:
>>>> tools::testInstalledPackage("rgdal", outDir=tempdir())list.files(
>>>> tempdir())file.show(file.path(tempdir(), "rgdal-Ex.Rout"))
>>>>
>>>> but it unexpectedly returned "Error in library("rgdal") : there is no
>>>> package called ‘rgdal’. Execution halted".
>>>>
>>>> It looks weird but so far I am able to normally load and use at least a
>>>> couple of rgdal's functions.
>>>>
>>>> I will keep monitoring it though, and report any other issue.
>>>>
>>>> Cheers,
>>>>  -- Thiago V. dos Santos
>>>> Postdoctoral Research FellowDepartment of Climate and Space Science and
>>>> EngineeringUniversity of Michigan
>>>>
>>>>     On Sunday, June 10, 2018, 4:46:04 AM EDT, Roger Bivand <
>>>> [hidden email]> wrote:
>>>>
>>>>  Thanks for reporting, comments inline below (note that I have no OSX
>>>> access at all):
>>>>
>>>> On Sat, 9 Jun 2018, Thiago V. dos Santos wrote:
>>>>
>>>> Dear Roger,
>>>>> Thank you very much for the excellent work done with those packages.
>>>>> Today I update both rgeos and rgdal on my system - macOS 10.13.5 with
>>>>> all dependencies installed via MacPorts. I had updated sp a few days
>>>>> earlier. The dependencies versions on my system are gdal
>>>>> @2.3.0.20180523_0+grib+hdf4+hdf5+jasper+mpich+netcdf and proj @5.1.0_0.
>>>>> Rgeos's update went flawlessly, but I got a few errors while updating
>>>>> rgdal. It still compiled successfully, but I am concerned that some
>>>>> functionality might be compromised due to the errors.
>>>>> This is what I got (I have to manually specify the location of proj or
>>>>> rgdal won't find it):> install.packages('rgdal', type = "source",
>>>>> configure.args=c(
>>>>> +    '--with-proj-include=/opt/local/lib/proj5/include',
>>>>> +    '--with-proj-lib=/opt/local/lib/proj5/lib'))
>>>>> Installing package into ‘/Users/thiago/Documents/R-packages’
>>>>> (as ‘lib’ is unspecified)
>>>>> trying URL 'https://cran.r-project.org/src/contrib/rgdal_1.3-2.tar.gz'
>>>>> Content type 'application/x-gzip' length 1667049 bytes (1.6 MB)
>>>>> ==================================================
>>>>> downloaded 1.6 MB
>>>>>
>>>>> * installing *source* package ‘rgdal’ ...
>>>>> ** package ‘rgdal’ successfully unpacked and MD5 sums checked
>>>>> configure: CC: /usr/bin/clang
>>>>> configure: CXX: /usr/bin/clang++
>>>>> configure: rgdal: 1.3-2
>>>>> checking for /usr/bin/svnversion... yes
>>>>> configure: svn revision: 755
>>>>> checking whether the C++ compiler works... yes
>>>>> checking for C++ compiler default output file name... a.out
>>>>> checking for suffix of executables...
>>>>> checking whether we are cross compiling... no
>>>>> checking for suffix of object files... o
>>>>> checking whether we are using the GNU C++ compiler... yes
>>>>> checking whether /usr/bin/clang++ accepts -g... yes
>>>>> checking whether /usr/bin/clang++ supports C++11 features by default...
>>>>>
>>>> no
>>>>
>>>>> checking whether /usr/bin/clang++ supports C++11 features with
>>>>>
>>>> -std=gnu++11... yes
>>>>
>>>>> configure: C++11 support available
>>>>> checking for gdal-config... /opt/local/bin/gdal-config
>>>>> checking gdal-config usability... yes
>>>>> configure: GDAL: 2.4.0
>>>>>
>>>>
>>>> All OK up to the GDAL version returned by gdal-config - are you using the
>>>> released GDAL 2.3.0 (probably not) or master?
>>>>
>>>> checking C++11 support for GDAL >= 2.3.0... yes
>>>>> checking GDAL version >= 1.11.4... yes
>>>>> checking gdal: linking with --libs only... yes
>>>>> checking GDAL: /opt/local/share/gdal/pcs.csv readable... yes
>>>>> checking proj_api.h presence and usability... yes
>>>>> ./configure: line 3395: test: =: unary operator expected
>>>>>
>>>>
>>>> Will check, that line is:
>>>>
>>>> if test ${PROJ_VERSION} = "" ; then
>>>>
>>>> from configure.ac line 305. Possibly a shell dialect issue.
>>>>
>>>> checking PROJ version >= 4.8.0... yes
>>>>> checking projects.h presence and usability... yes
>>>>>
>>>>
>>>> These relate to configure.ac lines 376-419, and the outcome: epsg found
>>>> and readable is OK - could there be two libproj on your system (maybe for
>>>> different architectures)?
>>>>
>>>> Undefined symbols for architecture x86_64:
>>>>>  "_pj_ctx_fclose", referenced from:
>>>>>      _main in proj_conf_test2-06fe7d.o
>>>>>  "_pj_get_default_ctx", referenced from:
>>>>>      _main in proj_conf_test2-06fe7d.o
>>>>>  "_pj_open_lib", referenced from:
>>>>>      _main in proj_conf_test2-06fe7d.o
>>>>> ld: symbol(s) not found for architecture x86_64
>>>>> clang: error: linker command failed with exit code 1 (use -v to see
>>>>>
>>>> invocation)
>>>>
>>>>> ./configure: line 3511: ./proj_conf_test2: No such file or directory
>>>>> checking PROJ.4: epsg found and readable... yes
>>>>>
>>>>
>>>> Same here for next block in configure.ac; conus found and readable.
>>>>
>>>> Undefined symbols for architecture x86_64:
>>>>>  "_pj_ctx_fclose", referenced from:
>>>>>      _main in proj_conf_test3-3b7aa2.o
>>>>>  "_pj_get_default_ctx", referenced from:
>>>>>      _main in proj_conf_test3-3b7aa2.o
>>>>>  "_pj_open_lib", referenced from:
>>>>>      _main in proj_conf_test3-3b7aa2.o
>>>>> ld: symbol(s) not found for architecture x86_64
>>>>> clang: error: linker command failed with exit code 1 (use -v to see
>>>>>
>>>> invocation)
>>>>
>>>>> ./configure: line 3570: ./proj_conf_test3: No such file or directory
>>>>> checking PROJ.4: conus found and readable... yes
>>>>> configure: Package CPP flags:  -I/opt/local/include
>>>>>
>>>> -I/opt/local/lib/proj5/include
>>>>
>>>>> configure: Package LIBS:  -L/opt/local/lib -lgdal
>>>>>
>>>> -L/opt/local/lib/proj5/lib -lproj
>>>>
>>>>> configure: creating ./config.status
>>>>> config.status: creating src/Makevars
>>>>> ** libs
>>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
>>>>> work/Resources/include"
>>>>>
>>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>>>> -fPIC  -Wall -g -O2 -c OGR_write.cpp -o OGR_write.o
>>>>
>>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
>>>>> work/Resources/include"
>>>>>
>>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>>>> -fPIC  -Wall -g -O2 -c gdal-bindings.cpp -o gdal-bindings.o
>>>>
>>>>> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
>>>>>
>>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>>>> -fPIC  -Wall -g -O2  -c init.c -o init.o
>>>>
>>>>> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
>>>>>
>>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>>>> -fPIC  -Wall -g -O2  -c inverser.c -o inverser.o
>>>>
>>>>> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
>>>>>
>>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>>>> -fPIC  -Wall -g -O2  -c local_stubs.c -o local_stubs.o
>>>>
>>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
>>>>> work/Resources/include"
>>>>>
>>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>>>> -fPIC  -Wall -g -O2 -c ogr_geom.cpp -o ogr_geom.o
>>>>
>>>>> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
>>>>>
>>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>>>> -fPIC  -Wall -g -O2  -c ogr_polygons.c -o ogr_polygons.o
>>>>
>>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
>>>>> work/Resources/include"
>>>>>
>>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>>>> -fPIC  -Wall -g -O2 -c ogr_proj.cpp -o ogr_proj.o
>>>>
>>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
>>>>> work/Resources/include"
>>>>>
>>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>>>> -fPIC  -Wall -g -O2 -c ogrdrivers.cpp -o ogrdrivers.o
>>>>
>>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
>>>>> work/Resources/include"
>>>>>
>>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>>>> -fPIC  -Wall -g -O2 -c ogrsource.cpp -o ogrsource.o
>>>>
>>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
>>>>> work/Resources/include"
>>>>>
>>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>>>> -fPIC  -Wall -g -O2 -c projectit.cpp -o projectit.o
>>>>
>>>>> clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names
>>>>>
>>>> -undefined dynamic_lookup -single_module -multiply_defined suppress
>>>> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
>>>> rgdal.so OGR_write.o gdal-bindings.o init.o inverser.o local_stubs.o
>>>> ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o
>>>> -L/opt/local/lib -lgdal -L/opt/local/lib/proj5/lib -lproj
>>>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>>>> -Wl,CoreFoundation
>>>>
>>>>> installing to /Users/thiago/Documents/R-packages/rgdal/libs
>>>>> ** R
>>>>> ** data
>>>>> ** inst
>>>>> ** byte-compile and prepare package for lazy loading
>>>>> ** help
>>>>> *** installing help indices
>>>>> ** building package indices
>>>>> ** installing vignettes
>>>>> ** testing if installed package can be loaded
>>>>> * DONE (rgdal)
>>>>>
>>>>> The downloaded source packages are in
>>>>>
>>>>> ‘/private/var/folders/_z/01gg71zs19g816v6m2dddt8w0000gn
>>>>>
>>>> /T/Rtmp5K6lt8/downloaded_packages’
>>>>
>>>>> ​Is this something that needs to be investigated, or I can just safely
>>>>> ignore those messages?
>>>>>
>>>>
>>>> Please try to run:
>>>>
>>>> tools::testInstalledPackage("rgdal", outDir=tempdir())
>>>> list.files(tempdir())
>>>> file.show(file.path(tempdir(), "rgdal-Ex.Rout"))
>>>>
>>>> and if the outcomes are as expected, you should be OK, please let us
>>>> know.
>>>>
>>>> If any OSX users installing from source can contribute, that would be
>>>> useful. It will take a little while before the CRAN OSX binaries catch up
>>>> with new PROJ and GDAL.
>>>>
>>>> Again thanks for reporting!
>>>>
>>>> Roger
>>>>
>>>> Many thanks, -- Thiago V. dos Santos
>>>>> Postdoctoral Research FellowDepartment of Climate and Space Science and
>>>>>
>>>> EngineeringUniversity of Michigan
>>>>
>>>>>
>>>>>    On Friday, June 8, 2018, 2:15:43 PM EDT, Roger Bivand <
>>>>>
>>>> [hidden email]> wrote:
>>>>
>>>>>
>>>>> There are new releases of sp, rgdal and rgeos on CRAN. Please install sp
>>>>> first, then the other two, which link to the installed sp. They all
>>>>> address so-called rchk issues, which have not so far been a problem, but
>>>>> might have become more fragile as R's internal memory management is made
>>>>> even more efficient. This involves compiled code using memory allocated
>>>>>
>>>> by
>>>>
>>>>> R to be freed by R's garbage collector, which has to know if an object
>>>>> is
>>>>> still being used. Tomas Kalibera, the author of rchk, helped resolve and
>>>>> explain the issues encountered - what was good coding practice fifteen
>>>>> years ago isn't always still good practice.
>>>>>
>>>>> In addition, the earliest versions of GDAL and PROJ with which rgdal
>>>>> will
>>>>> work have been updated, and set to PROJ 4.8.0 and GDAL 1.11.4. The
>>>>>
>>>> current
>>>>
>>>>> released versions of PROJ and GDAL are to be prefered, as bugs have been
>>>>> fixed and new features and drivers introduced. A check has been put
>>>>> in place to trap attempts to install rgdal without a C++11-capable
>>>>> compiler when the GDAL version is >=2.3.0 - which requires C++11. rgeos
>>>>>
>>>> is
>>>>
>>>>> ready for the forthcoming version of GEOS.
>>>>>
>>>>> The CRAN team has also been very supportive of our efforts to bring
>>>>> compiled code in these packages into rchk compliance.
>>>>>
>>>>> Please get in touch if you see any loose ends in these releases.
>>>>>
>>>>> Roger
>>>>>
>>>>>
>>>>>
>>>> --
>>>> Roger Bivand
>>>> Department of Economics, Norwegian School of Economics,
>>>> Helleveien 30, N-5045 Bergen, Norway.
>>>> voice: +47 55 95 93 55; e-mail: [hidden email]
>>>> http://orcid.org/0000-0003-2392-6140
>>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>>>         [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
>>>> R-sig-Geo mailing list
>>>> [hidden email]
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>
>>>>
>>>
>>>
>>>
>>>
>> --
>> Roger Bivand
>> Department of Economics, Norwegian School of Economics,
>> Helleveien 30, N-5045 Bergen, Norway.
>> voice: +47 55 95 93 55; e-mail: [hidden email]
>> http://orcid.org/0000-0003-2392-6140
>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>
>
>
>
--
Edzer Pebesma
Institute for Geoinformatics
Heisenbergstrasse 2, 48151 Muenster, Germany
Phone: +49 251 8333081

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Re: CRAN releases of sp, rgdal and rgeos

Tue, 06/12/2018 - 09:41
Thank you for the explanation of difference between proj.h and proj_api.h
and the recommendation of setting environment variable for pkg-config.  I
had tried using pkg-config by setting env variables but haven't had much
luck getting it to work.
Cordially,
Vijay.

On Tue, Jun 12, 2018 at 3:11 AM, Roger Bivand <[hidden email]> wrote:

> On Tue, 12 Jun 2018, Vijay Lulla wrote:
>
> I too use R on a mac but I cannot get rgdal to use proj5 (port info proj).
>> rgdal still uses proj4 even when there is a newer version of proj already
>> on my computer.  Neither of these proj packages (proj4 or proj) use
>> pkg-config mechanism even though there are proj.pc files in both versions
>> of the package.  Maybe using the pkg-config mechanism to detect version of
>> packages during source installation might help?  I don't know whether this
>> is a "proj" or a "macports" issue though.
>>
>>
> Neither sp/rgdal nor sf plan to accomodate the proj.h interface until the
> GDAL barn-raising project is completed. Even then, most software using proj
> will have to support the proj_api.h and the proj.h APIs because many
> platforms are bound to move at the speed of the slowest package using proj.
> The proj_api.h API does use the new mechanisms internally, but it isn't
> obvious how or whether proj.h pipelines should be exposed (GRASS has a
> prototype implementation).
>
> If you work in geodetics and need sub-cm precision, this may matter; in
> which case please follow the GDAL barn-raising project and provide use
> cases where the proj.h API is required. The main difference is that the
> proj_api.h API always transforms to the WGS84 datum first then transforms
> to the target datum (many to one then one to many). When this was chosen
> 1984 was not so long ago; the new proj.h API suggests transforming along a
> pipeline from source to target datum without going through WGS84 (many to
> many).
>
> If your question is about how to install rgdal from source on OSX, you may
> need to ensure that you only have one version of proj installed, or use
> configure arguments and load path modifications on your own responsibility.
>
> From rgdal 1.3-1, the pkg-config mechanism is used if the path to proj.pc
> is set correctly (environment variable), but will fall back on standard
> locations if pkg-config proj fails.
>
> Roger
>
>
>
>> On Mon, Jun 11, 2018 at 7:54 PM, Thiago V. dos Santos via R-sig-Geo <
>> [hidden email]> wrote:
>>
>> Hi Roger, thanks for the follow up. Answering to your comments:
>>>
>>> a) I am using Macports's gdal version 2.3.0.20180523. I am pretty sure
>>> that its source code (i.e. the one that is compiled on my machine) is
>>> downloaded from OSGEO (at least according to https://github.com/
>>> macports/macports-ports/blob/master/gis/gdal/Portfile);
>>>
>>> b) I do have more than one libproj installed on my system (as QGIS for
>>> macOS requires its own gdal and proj stuff), but only the Macports one is
>>> on my path;
>>>
>>>
>>> c) I tried running:
>>> tools::testInstalledPackage("rgdal", outDir=tempdir())list.files(
>>> tempdir())file.show(file.path(tempdir(), "rgdal-Ex.Rout"))
>>>
>>> but it unexpectedly returned "Error in library("rgdal") : there is no
>>> package called ‘rgdal’. Execution halted".
>>>
>>> It looks weird but so far I am able to normally load and use at least a
>>> couple of rgdal's functions.
>>>
>>> I will keep monitoring it though, and report any other issue.
>>>
>>> Cheers,
>>>  -- Thiago V. dos Santos
>>> Postdoctoral Research FellowDepartment of Climate and Space Science and
>>> EngineeringUniversity of Michigan
>>>
>>>     On Sunday, June 10, 2018, 4:46:04 AM EDT, Roger Bivand <
>>> [hidden email]> wrote:
>>>
>>>  Thanks for reporting, comments inline below (note that I have no OSX
>>> access at all):
>>>
>>> On Sat, 9 Jun 2018, Thiago V. dos Santos wrote:
>>>
>>> Dear Roger,
>>>> Thank you very much for the excellent work done with those packages.
>>>> Today I update both rgeos and rgdal on my system - macOS 10.13.5 with
>>>> all dependencies installed via MacPorts. I had updated sp a few days
>>>> earlier. The dependencies versions on my system are gdal
>>>> @2.3.0.20180523_0+grib+hdf4+hdf5+jasper+mpich+netcdf and proj @5.1.0_0.
>>>> Rgeos's update went flawlessly, but I got a few errors while updating
>>>> rgdal. It still compiled successfully, but I am concerned that some
>>>> functionality might be compromised due to the errors.
>>>> This is what I got (I have to manually specify the location of proj or
>>>> rgdal won't find it):> install.packages('rgdal', type = "source",
>>>> configure.args=c(
>>>> +    '--with-proj-include=/opt/local/lib/proj5/include',
>>>> +    '--with-proj-lib=/opt/local/lib/proj5/lib'))
>>>> Installing package into ‘/Users/thiago/Documents/R-packages’
>>>> (as ‘lib’ is unspecified)
>>>> trying URL 'https://cran.r-project.org/src/contrib/rgdal_1.3-2.tar.gz'
>>>> Content type 'application/x-gzip' length 1667049 bytes (1.6 MB)
>>>> ==================================================
>>>> downloaded 1.6 MB
>>>>
>>>> * installing *source* package ‘rgdal’ ...
>>>> ** package ‘rgdal’ successfully unpacked and MD5 sums checked
>>>> configure: CC: /usr/bin/clang
>>>> configure: CXX: /usr/bin/clang++
>>>> configure: rgdal: 1.3-2
>>>> checking for /usr/bin/svnversion... yes
>>>> configure: svn revision: 755
>>>> checking whether the C++ compiler works... yes
>>>> checking for C++ compiler default output file name... a.out
>>>> checking for suffix of executables...
>>>> checking whether we are cross compiling... no
>>>> checking for suffix of object files... o
>>>> checking whether we are using the GNU C++ compiler... yes
>>>> checking whether /usr/bin/clang++ accepts -g... yes
>>>> checking whether /usr/bin/clang++ supports C++11 features by default...
>>>>
>>> no
>>>
>>>> checking whether /usr/bin/clang++ supports C++11 features with
>>>>
>>> -std=gnu++11... yes
>>>
>>>> configure: C++11 support available
>>>> checking for gdal-config... /opt/local/bin/gdal-config
>>>> checking gdal-config usability... yes
>>>> configure: GDAL: 2.4.0
>>>>
>>>
>>> All OK up to the GDAL version returned by gdal-config - are you using the
>>> released GDAL 2.3.0 (probably not) or master?
>>>
>>> checking C++11 support for GDAL >= 2.3.0... yes
>>>> checking GDAL version >= 1.11.4... yes
>>>> checking gdal: linking with --libs only... yes
>>>> checking GDAL: /opt/local/share/gdal/pcs.csv readable... yes
>>>> checking proj_api.h presence and usability... yes
>>>> ./configure: line 3395: test: =: unary operator expected
>>>>
>>>
>>> Will check, that line is:
>>>
>>> if test ${PROJ_VERSION} = "" ; then
>>>
>>> from configure.ac line 305. Possibly a shell dialect issue.
>>>
>>> checking PROJ version >= 4.8.0... yes
>>>> checking projects.h presence and usability... yes
>>>>
>>>
>>> These relate to configure.ac lines 376-419, and the outcome: epsg found
>>> and readable is OK - could there be two libproj on your system (maybe for
>>> different architectures)?
>>>
>>> Undefined symbols for architecture x86_64:
>>>>  "_pj_ctx_fclose", referenced from:
>>>>      _main in proj_conf_test2-06fe7d.o
>>>>  "_pj_get_default_ctx", referenced from:
>>>>      _main in proj_conf_test2-06fe7d.o
>>>>  "_pj_open_lib", referenced from:
>>>>      _main in proj_conf_test2-06fe7d.o
>>>> ld: symbol(s) not found for architecture x86_64
>>>> clang: error: linker command failed with exit code 1 (use -v to see
>>>>
>>> invocation)
>>>
>>>> ./configure: line 3511: ./proj_conf_test2: No such file or directory
>>>> checking PROJ.4: epsg found and readable... yes
>>>>
>>>
>>> Same here for next block in configure.ac; conus found and readable.
>>>
>>> Undefined symbols for architecture x86_64:
>>>>  "_pj_ctx_fclose", referenced from:
>>>>      _main in proj_conf_test3-3b7aa2.o
>>>>  "_pj_get_default_ctx", referenced from:
>>>>      _main in proj_conf_test3-3b7aa2.o
>>>>  "_pj_open_lib", referenced from:
>>>>      _main in proj_conf_test3-3b7aa2.o
>>>> ld: symbol(s) not found for architecture x86_64
>>>> clang: error: linker command failed with exit code 1 (use -v to see
>>>>
>>> invocation)
>>>
>>>> ./configure: line 3570: ./proj_conf_test3: No such file or directory
>>>> checking PROJ.4: conus found and readable... yes
>>>> configure: Package CPP flags:  -I/opt/local/include
>>>>
>>> -I/opt/local/lib/proj5/include
>>>
>>>> configure: Package LIBS:  -L/opt/local/lib -lgdal
>>>>
>>> -L/opt/local/lib/proj5/lib -lproj
>>>
>>>> configure: creating ./config.status
>>>> config.status: creating src/Makevars
>>>> ** libs
>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
>>>> work/Resources/include"
>>>>
>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>>> -fPIC  -Wall -g -O2 -c OGR_write.cpp -o OGR_write.o
>>>
>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
>>>> work/Resources/include"
>>>>
>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>>> -fPIC  -Wall -g -O2 -c gdal-bindings.cpp -o gdal-bindings.o
>>>
>>>> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
>>>>
>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>>> -fPIC  -Wall -g -O2  -c init.c -o init.o
>>>
>>>> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
>>>>
>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>>> -fPIC  -Wall -g -O2  -c inverser.c -o inverser.o
>>>
>>>> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
>>>>
>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>>> -fPIC  -Wall -g -O2  -c local_stubs.c -o local_stubs.o
>>>
>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
>>>> work/Resources/include"
>>>>
>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>>> -fPIC  -Wall -g -O2 -c ogr_geom.cpp -o ogr_geom.o
>>>
>>>> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
>>>>
>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>>> -fPIC  -Wall -g -O2  -c ogr_polygons.c -o ogr_polygons.o
>>>
>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
>>>> work/Resources/include"
>>>>
>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>>> -fPIC  -Wall -g -O2 -c ogr_proj.cpp -o ogr_proj.o
>>>
>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
>>>> work/Resources/include"
>>>>
>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>>> -fPIC  -Wall -g -O2 -c ogrdrivers.cpp -o ogrdrivers.o
>>>
>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
>>>> work/Resources/include"
>>>>
>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>>> -fPIC  -Wall -g -O2 -c ogrsource.cpp -o ogrsource.o
>>>
>>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.frame
>>>> work/Resources/include"
>>>>
>>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>>> -fPIC  -Wall -g -O2 -c projectit.cpp -o projectit.o
>>>
>>>> clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names
>>>>
>>> -undefined dynamic_lookup -single_module -multiply_defined suppress
>>> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
>>> rgdal.so OGR_write.o gdal-bindings.o init.o inverser.o local_stubs.o
>>> ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o
>>> -L/opt/local/lib -lgdal -L/opt/local/lib/proj5/lib -lproj
>>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>>> -Wl,CoreFoundation
>>>
>>>> installing to /Users/thiago/Documents/R-packages/rgdal/libs
>>>> ** R
>>>> ** data
>>>> ** inst
>>>> ** byte-compile and prepare package for lazy loading
>>>> ** help
>>>> *** installing help indices
>>>> ** building package indices
>>>> ** installing vignettes
>>>> ** testing if installed package can be loaded
>>>> * DONE (rgdal)
>>>>
>>>> The downloaded source packages are in
>>>>
>>>> ‘/private/var/folders/_z/01gg71zs19g816v6m2dddt8w0000gn
>>>>
>>> /T/Rtmp5K6lt8/downloaded_packages’
>>>
>>>> ​Is this something that needs to be investigated, or I can just safely
>>>> ignore those messages?
>>>>
>>>
>>> Please try to run:
>>>
>>> tools::testInstalledPackage("rgdal", outDir=tempdir())
>>> list.files(tempdir())
>>> file.show(file.path(tempdir(), "rgdal-Ex.Rout"))
>>>
>>> and if the outcomes are as expected, you should be OK, please let us
>>> know.
>>>
>>> If any OSX users installing from source can contribute, that would be
>>> useful. It will take a little while before the CRAN OSX binaries catch up
>>> with new PROJ and GDAL.
>>>
>>> Again thanks for reporting!
>>>
>>> Roger
>>>
>>> Many thanks, -- Thiago V. dos Santos
>>>> Postdoctoral Research FellowDepartment of Climate and Space Science and
>>>>
>>> EngineeringUniversity of Michigan
>>>
>>>>
>>>>    On Friday, June 8, 2018, 2:15:43 PM EDT, Roger Bivand <
>>>>
>>> [hidden email]> wrote:
>>>
>>>>
>>>> There are new releases of sp, rgdal and rgeos on CRAN. Please install sp
>>>> first, then the other two, which link to the installed sp. They all
>>>> address so-called rchk issues, which have not so far been a problem, but
>>>> might have become more fragile as R's internal memory management is made
>>>> even more efficient. This involves compiled code using memory allocated
>>>>
>>> by
>>>
>>>> R to be freed by R's garbage collector, which has to know if an object
>>>> is
>>>> still being used. Tomas Kalibera, the author of rchk, helped resolve and
>>>> explain the issues encountered - what was good coding practice fifteen
>>>> years ago isn't always still good practice.
>>>>
>>>> In addition, the earliest versions of GDAL and PROJ with which rgdal
>>>> will
>>>> work have been updated, and set to PROJ 4.8.0 and GDAL 1.11.4. The
>>>>
>>> current
>>>
>>>> released versions of PROJ and GDAL are to be prefered, as bugs have been
>>>> fixed and new features and drivers introduced. A check has been put
>>>> in place to trap attempts to install rgdal without a C++11-capable
>>>> compiler when the GDAL version is >=2.3.0 - which requires C++11. rgeos
>>>>
>>> is
>>>
>>>> ready for the forthcoming version of GEOS.
>>>>
>>>> The CRAN team has also been very supportive of our efforts to bring
>>>> compiled code in these packages into rchk compliance.
>>>>
>>>> Please get in touch if you see any loose ends in these releases.
>>>>
>>>> Roger
>>>>
>>>>
>>>>
>>> --
>>> Roger Bivand
>>> Department of Economics, Norwegian School of Economics,
>>> Helleveien 30, N-5045 Bergen, Norway.
>>> voice: +47 55 95 93 55; e-mail: [hidden email]
>>> http://orcid.org/0000-0003-2392-6140
>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>>         [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>> [hidden email]
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>>
>>
>>
>>
>>
> --
> Roger Bivand
> Department of Economics, Norwegian School of Economics,
> Helleveien 30, N-5045 Bergen, Norway.
> voice: +47 55 95 93 55; e-mail: [hidden email]
> http://orcid.org/0000-0003-2392-6140
> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>


--
Vijay Lulla

Assistant Professor,
Dept. of Geography, IUPUI
425 University Blvd, CA-207C.
Indianapolis, IN-46202
[hidden email]
ORCID: https://orcid.org/0000-0002-0823-2522
Webpage: http://vijaylulla.com

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Re: Sf st_read postgis

Tue, 06/12/2018 - 07:29
Hi

If you use a query you don't have to set a table name, so

xx <- st_read(connz, query="SELECT * FROM vakantie LIMIT 3;")

should work...


Le 12/06/2018 12:12, Jan Willem van der Lichte a �crit :
> Hi list,
>
> Can someone help me with a basic sf question.
>
> I try to use the sf::st_read function to get some data out of postgis.
>
> I set up a connection (connz) to postgis.
> I checked if the connection was working with
>
> dbListTables(connz)
>
> The result was ok, I saw all the tables in the database.
>
> Next I tried to get some data with the st_read() function, from the sf package.
>
> I tried to follow the example in the help.
>
> xx<- st_read(connz, "vakantie", query="SELECT * FROM vakantie LIMIT 3;")
>
> So i replaced the table meuse with vakantie.
>
> When I execute this statement, I get a warning
>
> Warning message: In st_read.DBIObject(...) : Ignoring query argument, only using table.
>
> So what's happening, am I doing something wrong? Which is possible, cause I'm new to R. :-)
>
> Thanks
> Jan Willem
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Sent with my iPad
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
> --
*Micha�l DELORME*
Administrateur de donn�es, charg� de projet en g�omatique
Service r�gional de l'information statistique, �conomique et territoriale
Direction r�gionale de l'alimentation, de l'agriculture et de la for�t
Auvergne-Rh�ne-Alpes
Site de Lyon
165 rue Garibaldi � BP 3202 � 69401 LYON cedex 03
04 78 63 34 21

Pour �crire au service :
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Sf st_read postgis

Tue, 06/12/2018 - 05:12

Hi list,

Can someone help me with a basic sf question.

I try to use the sf::st_read function to get some data out of postgis.

I set up a connection (connz) to postgis.
I checked if the connection was working with

dbListTables(connz)

The result was ok, I saw all the tables in the database.

Next I tried to get some data with the st_read() function, from the sf package.

I tried to follow the example in the help.

xx<- st_read(connz, "vakantie", query="SELECT * FROM vakantie LIMIT 3;")

So i replaced the table meuse with vakantie.

When I execute this statement, I get a warning

Warning message: In st_read.DBIObject(...) : Ignoring query argument, only using table.

So what's happening, am I doing something wrong? Which is possible, cause I'm new to R. :-)

Thanks
Jan Willem














Sent with my iPad

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Re: CRAN releases of sp, rgdal and rgeos

Tue, 06/12/2018 - 02:11
On Tue, 12 Jun 2018, Vijay Lulla wrote:

> I too use R on a mac but I cannot get rgdal to use proj5 (port info proj).
> rgdal still uses proj4 even when there is a newer version of proj already
> on my computer.  Neither of these proj packages (proj4 or proj) use
> pkg-config mechanism even though there are proj.pc files in both versions
> of the package.  Maybe using the pkg-config mechanism to detect version of
> packages during source installation might help?  I don't know whether this
> is a "proj" or a "macports" issue though.
>

Neither sp/rgdal nor sf plan to accomodate the proj.h interface until the
GDAL barn-raising project is completed. Even then, most software using
proj will have to support the proj_api.h and the proj.h APIs because many
platforms are bound to move at the speed of the slowest package using
proj. The proj_api.h API does use the new mechanisms internally, but it
isn't obvious how or whether proj.h pipelines should be exposed (GRASS has
a prototype implementation).

If you work in geodetics and need sub-cm precision, this may matter; in
which case please follow the GDAL barn-raising project and provide use
cases where the proj.h API is required. The main difference is that the
proj_api.h API always transforms to the WGS84 datum first then transforms
to the target datum (many to one then one to many). When this was chosen
1984 was not so long ago; the new proj.h API suggests transforming along a
pipeline from source to target datum without going through WGS84 (many to
many).

If your question is about how to install rgdal from source on OSX, you may
need to ensure that you only have one version of proj installed, or use
configure arguments and load path modifications on your own
responsibility.

From rgdal 1.3-1, the pkg-config mechanism is used if the path to proj.pc
is set correctly (environment variable), but will fall back on standard
locations if pkg-config proj fails.

Roger

>
> On Mon, Jun 11, 2018 at 7:54 PM, Thiago V. dos Santos via R-sig-Geo <
> [hidden email]> wrote:
>
>> Hi Roger, thanks for the follow up. Answering to your comments:
>>
>> a) I am using Macports's gdal version 2.3.0.20180523. I am pretty sure
>> that its source code (i.e. the one that is compiled on my machine) is
>> downloaded from OSGEO (at least according to https://github.com/
>> macports/macports-ports/blob/master/gis/gdal/Portfile);
>>
>> b) I do have more than one libproj installed on my system (as QGIS for
>> macOS requires its own gdal and proj stuff), but only the Macports one is
>> on my path;
>>
>>
>> c) I tried running:
>> tools::testInstalledPackage("rgdal", outDir=tempdir())list.files(
>> tempdir())file.show(file.path(tempdir(), "rgdal-Ex.Rout"))
>>
>> but it unexpectedly returned "Error in library("rgdal") : there is no
>> package called ‘rgdal’. Execution halted".
>>
>> It looks weird but so far I am able to normally load and use at least a
>> couple of rgdal's functions.
>>
>> I will keep monitoring it though, and report any other issue.
>>
>> Cheers,
>>  -- Thiago V. dos Santos
>> Postdoctoral Research FellowDepartment of Climate and Space Science and
>> EngineeringUniversity of Michigan
>>
>>     On Sunday, June 10, 2018, 4:46:04 AM EDT, Roger Bivand <
>> [hidden email]> wrote:
>>
>>  Thanks for reporting, comments inline below (note that I have no OSX
>> access at all):
>>
>> On Sat, 9 Jun 2018, Thiago V. dos Santos wrote:
>>
>>> Dear Roger,
>>> Thank you very much for the excellent work done with those packages.
>>> Today I update both rgeos and rgdal on my system - macOS 10.13.5 with
>>> all dependencies installed via MacPorts. I had updated sp a few days
>>> earlier. The dependencies versions on my system are gdal
>>> @2.3.0.20180523_0+grib+hdf4+hdf5+jasper+mpich+netcdf and proj @5.1.0_0.
>>> Rgeos's update went flawlessly, but I got a few errors while updating
>>> rgdal. It still compiled successfully, but I am concerned that some
>>> functionality might be compromised due to the errors.
>>> This is what I got (I have to manually specify the location of proj or
>>> rgdal won't find it):> install.packages('rgdal', type = "source",
>>> configure.args=c(
>>> +    '--with-proj-include=/opt/local/lib/proj5/include',
>>> +    '--with-proj-lib=/opt/local/lib/proj5/lib'))
>>> Installing package into ‘/Users/thiago/Documents/R-packages’
>>> (as ‘lib’ is unspecified)
>>> trying URL 'https://cran.r-project.org/src/contrib/rgdal_1.3-2.tar.gz'
>>> Content type 'application/x-gzip' length 1667049 bytes (1.6 MB)
>>> ==================================================
>>> downloaded 1.6 MB
>>>
>>> * installing *source* package ‘rgdal’ ...
>>> ** package ‘rgdal’ successfully unpacked and MD5 sums checked
>>> configure: CC: /usr/bin/clang
>>> configure: CXX: /usr/bin/clang++
>>> configure: rgdal: 1.3-2
>>> checking for /usr/bin/svnversion... yes
>>> configure: svn revision: 755
>>> checking whether the C++ compiler works... yes
>>> checking for C++ compiler default output file name... a.out
>>> checking for suffix of executables...
>>> checking whether we are cross compiling... no
>>> checking for suffix of object files... o
>>> checking whether we are using the GNU C++ compiler... yes
>>> checking whether /usr/bin/clang++ accepts -g... yes
>>> checking whether /usr/bin/clang++ supports C++11 features by default...
>> no
>>> checking whether /usr/bin/clang++ supports C++11 features with
>> -std=gnu++11... yes
>>> configure: C++11 support available
>>> checking for gdal-config... /opt/local/bin/gdal-config
>>> checking gdal-config usability... yes
>>> configure: GDAL: 2.4.0
>>
>> All OK up to the GDAL version returned by gdal-config - are you using the
>> released GDAL 2.3.0 (probably not) or master?
>>
>>> checking C++11 support for GDAL >= 2.3.0... yes
>>> checking GDAL version >= 1.11.4... yes
>>> checking gdal: linking with --libs only... yes
>>> checking GDAL: /opt/local/share/gdal/pcs.csv readable... yes
>>> checking proj_api.h presence and usability... yes
>>> ./configure: line 3395: test: =: unary operator expected
>>
>> Will check, that line is:
>>
>> if test ${PROJ_VERSION} = "" ; then
>>
>> from configure.ac line 305. Possibly a shell dialect issue.
>>
>>> checking PROJ version >= 4.8.0... yes
>>> checking projects.h presence and usability... yes
>>
>> These relate to configure.ac lines 376-419, and the outcome: epsg found
>> and readable is OK - could there be two libproj on your system (maybe for
>> different architectures)?
>>
>>> Undefined symbols for architecture x86_64:
>>>  "_pj_ctx_fclose", referenced from:
>>>      _main in proj_conf_test2-06fe7d.o
>>>  "_pj_get_default_ctx", referenced from:
>>>      _main in proj_conf_test2-06fe7d.o
>>>  "_pj_open_lib", referenced from:
>>>      _main in proj_conf_test2-06fe7d.o
>>> ld: symbol(s) not found for architecture x86_64
>>> clang: error: linker command failed with exit code 1 (use -v to see
>> invocation)
>>> ./configure: line 3511: ./proj_conf_test2: No such file or directory
>>> checking PROJ.4: epsg found and readable... yes
>>
>> Same here for next block in configure.ac; conus found and readable.
>>
>>> Undefined symbols for architecture x86_64:
>>>  "_pj_ctx_fclose", referenced from:
>>>      _main in proj_conf_test3-3b7aa2.o
>>>  "_pj_get_default_ctx", referenced from:
>>>      _main in proj_conf_test3-3b7aa2.o
>>>  "_pj_open_lib", referenced from:
>>>      _main in proj_conf_test3-3b7aa2.o
>>> ld: symbol(s) not found for architecture x86_64
>>> clang: error: linker command failed with exit code 1 (use -v to see
>> invocation)
>>> ./configure: line 3570: ./proj_conf_test3: No such file or directory
>>> checking PROJ.4: conus found and readable... yes
>>> configure: Package CPP flags:  -I/opt/local/include
>> -I/opt/local/lib/proj5/include
>>> configure: Package LIBS:  -L/opt/local/lib -lgdal
>> -L/opt/local/lib/proj5/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/opt/local/include -I/opt/local/lib/proj5/include
>> -I"/Users/thiago/Documents/R-packages/sp/include" -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/opt/local/include -I/opt/local/lib/proj5/include
>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>> -fPIC  -Wall -g -O2 -c gdal-bindings.cpp -o gdal-bindings.o
>>> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>> -fPIC  -Wall -g -O2  -c init.c -o init.o
>>> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>> -fPIC  -Wall -g -O2  -c inverser.c -o inverser.o
>>> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>> -fPIC  -Wall -g -O2  -c local_stubs.c -o local_stubs.o
>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include"
>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>> -fPIC  -Wall -g -O2 -c ogr_geom.cpp -o ogr_geom.o
>>> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>> -fPIC  -Wall -g -O2  -c ogr_polygons.c -o ogr_polygons.o
>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include"
>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>> -fPIC  -Wall -g -O2 -c ogr_proj.cpp -o ogr_proj.o
>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include"
>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>> -fPIC  -Wall -g -O2 -c ogrdrivers.cpp -o ogrdrivers.o
>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include"
>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>> -fPIC  -Wall -g -O2 -c ogrsource.cpp -o ogrsource.o
>>> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include"
>> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
>> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
>> -fPIC  -Wall -g -O2 -c projectit.cpp -o projectit.o
>>> clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names
>> -undefined dynamic_lookup -single_module -multiply_defined suppress
>> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
>> rgdal.so OGR_write.o gdal-bindings.o init.o inverser.o local_stubs.o
>> ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o
>> -L/opt/local/lib -lgdal -L/opt/local/lib/proj5/lib -lproj
>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>> -Wl,CoreFoundation
>>> installing to /Users/thiago/Documents/R-packages/rgdal/libs
>>> ** R
>>> ** data
>>> ** inst
>>> ** byte-compile and prepare package for lazy loading
>>> ** help
>>> *** installing help indices
>>> ** building package indices
>>> ** installing vignettes
>>> ** testing if installed package can be loaded
>>> * DONE (rgdal)
>>>
>>> The downloaded source packages are in
>>>
>>> ‘/private/var/folders/_z/01gg71zs19g816v6m2dddt8w0000gn
>> /T/Rtmp5K6lt8/downloaded_packages’
>>> ​Is this something that needs to be investigated, or I can just safely
>>> ignore those messages?
>>
>> Please try to run:
>>
>> tools::testInstalledPackage("rgdal", outDir=tempdir())
>> list.files(tempdir())
>> file.show(file.path(tempdir(), "rgdal-Ex.Rout"))
>>
>> and if the outcomes are as expected, you should be OK, please let us know.
>>
>> If any OSX users installing from source can contribute, that would be
>> useful. It will take a little while before the CRAN OSX binaries catch up
>> with new PROJ and GDAL.
>>
>> Again thanks for reporting!
>>
>> Roger
>>
>>> Many thanks, -- Thiago V. dos Santos
>>> Postdoctoral Research FellowDepartment of Climate and Space Science and
>> EngineeringUniversity of Michigan
>>>
>>>    On Friday, June 8, 2018, 2:15:43 PM EDT, Roger Bivand <
>> [hidden email]> wrote:
>>>
>>> There are new releases of sp, rgdal and rgeos on CRAN. Please install sp
>>> first, then the other two, which link to the installed sp. They all
>>> address so-called rchk issues, which have not so far been a problem, but
>>> might have become more fragile as R's internal memory management is made
>>> even more efficient. This involves compiled code using memory allocated
>> by
>>> R to be freed by R's garbage collector, which has to know if an object is
>>> still being used. Tomas Kalibera, the author of rchk, helped resolve and
>>> explain the issues encountered - what was good coding practice fifteen
>>> years ago isn't always still good practice.
>>>
>>> In addition, the earliest versions of GDAL and PROJ with which rgdal will
>>> work have been updated, and set to PROJ 4.8.0 and GDAL 1.11.4. The
>> current
>>> released versions of PROJ and GDAL are to be prefered, as bugs have been
>>> fixed and new features and drivers introduced. A check has been put
>>> in place to trap attempts to install rgdal without a C++11-capable
>>> compiler when the GDAL version is >=2.3.0 - which requires C++11. rgeos
>> is
>>> ready for the forthcoming version of GEOS.
>>>
>>> The CRAN team has also been very supportive of our efforts to bring
>>> compiled code in these packages into rchk compliance.
>>>
>>> Please get in touch if you see any loose ends in these releases.
>>>
>>> Roger
>>>
>>>
>>
>> --
>> Roger Bivand
>> Department of Economics, Norwegian School of Economics,
>> Helleveien 30, N-5045 Bergen, Norway.
>> voice: +47 55 95 93 55; e-mail: [hidden email]
>> http://orcid.org/0000-0003-2392-6140
>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> [hidden email]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>
>
>
> --
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: [hidden email]
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Roger Bivand
Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway

Re: CRAN releases of sp, rgdal and rgeos

Mon, 06/11/2018 - 20:16
I too use R on a mac but I cannot get rgdal to use proj5 (port info proj).
rgdal still uses proj4 even when there is a newer version of proj already
on my computer.  Neither of these proj packages (proj4 or proj) use
pkg-config mechanism even though there are proj.pc files in both versions
of the package.  Maybe using the pkg-config mechanism to detect version of
packages during source installation might help?  I don't know whether this
is a "proj" or a "macports" issue though.


On Mon, Jun 11, 2018 at 7:54 PM, Thiago V. dos Santos via R-sig-Geo <
[hidden email]> wrote:

> Hi Roger, thanks for the follow up. Answering to your comments:
>
> a) I am using Macports's gdal version 2.3.0.20180523. I am pretty sure
> that its source code (i.e. the one that is compiled on my machine) is
> downloaded from OSGEO (at least according to https://github.com/
> macports/macports-ports/blob/master/gis/gdal/Portfile);
>
> b) I do have more than one libproj installed on my system (as QGIS for
> macOS requires its own gdal and proj stuff), but only the Macports one is
> on my path;
>
>
> c) I tried running:
> tools::testInstalledPackage("rgdal", outDir=tempdir())list.files(
> tempdir())file.show(file.path(tempdir(), "rgdal-Ex.Rout"))
>
> but it unexpectedly returned "Error in library("rgdal") : there is no
> package called ‘rgdal’. Execution halted".
>
> It looks weird but so far I am able to normally load and use at least a
> couple of rgdal's functions.
>
> I will keep monitoring it though, and report any other issue.
>
> Cheers,
>  -- Thiago V. dos Santos
> Postdoctoral Research FellowDepartment of Climate and Space Science and
> EngineeringUniversity of Michigan
>
>     On Sunday, June 10, 2018, 4:46:04 AM EDT, Roger Bivand <
> [hidden email]> wrote:
>
>  Thanks for reporting, comments inline below (note that I have no OSX
> access at all):
>
> On Sat, 9 Jun 2018, Thiago V. dos Santos wrote:
>
> > Dear Roger,
> > Thank you very much for the excellent work done with those packages.
> > Today I update both rgeos and rgdal on my system - macOS 10.13.5 with
> > all dependencies installed via MacPorts. I had updated sp a few days
> > earlier. The dependencies versions on my system are gdal
> > @2.3.0.20180523_0+grib+hdf4+hdf5+jasper+mpich+netcdf and proj @5.1.0_0.
> > Rgeos's update went flawlessly, but I got a few errors while updating
> > rgdal. It still compiled successfully, but I am concerned that some
> > functionality might be compromised due to the errors.
> > This is what I got (I have to manually specify the location of proj or
> > rgdal won't find it):> install.packages('rgdal', type = "source",
> > configure.args=c(
> > +    '--with-proj-include=/opt/local/lib/proj5/include',
> > +    '--with-proj-lib=/opt/local/lib/proj5/lib'))
> > Installing package into ‘/Users/thiago/Documents/R-packages’
> > (as ‘lib’ is unspecified)
> > trying URL 'https://cran.r-project.org/src/contrib/rgdal_1.3-2.tar.gz'
> > Content type 'application/x-gzip' length 1667049 bytes (1.6 MB)
> > ==================================================
> > downloaded 1.6 MB
> >
> > * installing *source* package ‘rgdal’ ...
> > ** package ‘rgdal’ successfully unpacked and MD5 sums checked
> > configure: CC: /usr/bin/clang
> > configure: CXX: /usr/bin/clang++
> > configure: rgdal: 1.3-2
> > checking for /usr/bin/svnversion... yes
> > configure: svn revision: 755
> > checking whether the C++ compiler works... yes
> > checking for C++ compiler default output file name... a.out
> > checking for suffix of executables...
> > checking whether we are cross compiling... no
> > checking for suffix of object files... o
> > checking whether we are using the GNU C++ compiler... yes
> > checking whether /usr/bin/clang++ accepts -g... yes
> > checking whether /usr/bin/clang++ supports C++11 features by default...
> no
> > checking whether /usr/bin/clang++ supports C++11 features with
> -std=gnu++11... yes
> > configure: C++11 support available
> > checking for gdal-config... /opt/local/bin/gdal-config
> > checking gdal-config usability... yes
> > configure: GDAL: 2.4.0
>
> All OK up to the GDAL version returned by gdal-config - are you using the
> released GDAL 2.3.0 (probably not) or master?
>
> > checking C++11 support for GDAL >= 2.3.0... yes
> > checking GDAL version >= 1.11.4... yes
> > checking gdal: linking with --libs only... yes
> > checking GDAL: /opt/local/share/gdal/pcs.csv readable... yes
> > checking proj_api.h presence and usability... yes
> > ./configure: line 3395: test: =: unary operator expected
>
> Will check, that line is:
>
> if test ${PROJ_VERSION} = "" ; then
>
> from configure.ac line 305. Possibly a shell dialect issue.
>
> > checking PROJ version >= 4.8.0... yes
> > checking projects.h presence and usability... yes
>
> These relate to configure.ac lines 376-419, and the outcome: epsg found
> and readable is OK - could there be two libproj on your system (maybe for
> different architectures)?
>
> > Undefined symbols for architecture x86_64:
> >  "_pj_ctx_fclose", referenced from:
> >      _main in proj_conf_test2-06fe7d.o
> >  "_pj_get_default_ctx", referenced from:
> >      _main in proj_conf_test2-06fe7d.o
> >  "_pj_open_lib", referenced from:
> >      _main in proj_conf_test2-06fe7d.o
> > ld: symbol(s) not found for architecture x86_64
> > clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> > ./configure: line 3511: ./proj_conf_test2: No such file or directory
> > checking PROJ.4: epsg found and readable... yes
>
> Same here for next block in configure.ac; conus found and readable.
>
> > Undefined symbols for architecture x86_64:
> >  "_pj_ctx_fclose", referenced from:
> >      _main in proj_conf_test3-3b7aa2.o
> >  "_pj_get_default_ctx", referenced from:
> >      _main in proj_conf_test3-3b7aa2.o
> >  "_pj_open_lib", referenced from:
> >      _main in proj_conf_test3-3b7aa2.o
> > ld: symbol(s) not found for architecture x86_64
> > clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> > ./configure: line 3570: ./proj_conf_test3: No such file or directory
> > checking PROJ.4: conus found and readable... yes
> > configure: Package CPP flags:  -I/opt/local/include
> -I/opt/local/lib/proj5/include
> > configure: Package LIBS:  -L/opt/local/lib -lgdal
> -L/opt/local/lib/proj5/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/opt/local/include -I/opt/local/lib/proj5/include
> -I"/Users/thiago/Documents/R-packages/sp/include" -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/opt/local/include -I/opt/local/lib/proj5/include
> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
> -fPIC  -Wall -g -O2 -c gdal-bindings.cpp -o gdal-bindings.o
> > /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
> -fPIC  -Wall -g -O2  -c init.c -o init.o
> > /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
> -fPIC  -Wall -g -O2  -c inverser.c -o inverser.o
> > /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
> -fPIC  -Wall -g -O2  -c local_stubs.c -o local_stubs.o
> > clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include"
> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
> -fPIC  -Wall -g -O2 -c ogr_geom.cpp -o ogr_geom.o
> > /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include"
> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
> -fPIC  -Wall -g -O2  -c ogr_polygons.c -o ogr_polygons.o
> > clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include"
> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
> -fPIC  -Wall -g -O2 -c ogr_proj.cpp -o ogr_proj.o
> > clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include"
> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
> -fPIC  -Wall -g -O2 -c ogrdrivers.cpp -o ogrdrivers.o
> > clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include"
> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
> -fPIC  -Wall -g -O2 -c ogrsource.cpp -o ogrsource.o
> > clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include"
> -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include
> -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include
> -fPIC  -Wall -g -O2 -c projectit.cpp -o projectit.o
> > clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names
> -undefined dynamic_lookup -single_module -multiply_defined suppress
> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
> rgdal.so OGR_write.o gdal-bindings.o init.o inverser.o local_stubs.o
> ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o
> -L/opt/local/lib -lgdal -L/opt/local/lib/proj5/lib -lproj
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
> -Wl,CoreFoundation
> > installing to /Users/thiago/Documents/R-packages/rgdal/libs
> > ** R
> > ** data
> > ** inst
> > ** byte-compile and prepare package for lazy loading
> > ** help
> > *** installing help indices
> > ** building package indices
> > ** installing vignettes
> > ** testing if installed package can be loaded
> > * DONE (rgdal)
> >
> > The downloaded source packages are in
> >
> > ‘/private/var/folders/_z/01gg71zs19g816v6m2dddt8w0000gn
> /T/Rtmp5K6lt8/downloaded_packages’
> > ​Is this something that needs to be investigated, or I can just safely
> > ignore those messages?
>
> Please try to run:
>
> tools::testInstalledPackage("rgdal", outDir=tempdir())
> list.files(tempdir())
> file.show(file.path(tempdir(), "rgdal-Ex.Rout"))
>
> and if the outcomes are as expected, you should be OK, please let us know.
>
> If any OSX users installing from source can contribute, that would be
> useful. It will take a little while before the CRAN OSX binaries catch up
> with new PROJ and GDAL.
>
> Again thanks for reporting!
>
> Roger
>
> > Many thanks, -- Thiago V. dos Santos
> > Postdoctoral Research FellowDepartment of Climate and Space Science and
> EngineeringUniversity of Michigan
> >
> >    On Friday, June 8, 2018, 2:15:43 PM EDT, Roger Bivand <
> [hidden email]> wrote:
> >
> > There are new releases of sp, rgdal and rgeos on CRAN. Please install sp
> > first, then the other two, which link to the installed sp. They all
> > address so-called rchk issues, which have not so far been a problem, but
> > might have become more fragile as R's internal memory management is made
> > even more efficient. This involves compiled code using memory allocated
> by
> > R to be freed by R's garbage collector, which has to know if an object is
> > still being used. Tomas Kalibera, the author of rchk, helped resolve and
> > explain the issues encountered - what was good coding practice fifteen
> > years ago isn't always still good practice.
> >
> > In addition, the earliest versions of GDAL and PROJ with which rgdal will
> > work have been updated, and set to PROJ 4.8.0 and GDAL 1.11.4. The
> current
> > released versions of PROJ and GDAL are to be prefered, as bugs have been
> > fixed and new features and drivers introduced. A check has been put
> > in place to trap attempts to install rgdal without a C++11-capable
> > compiler when the GDAL version is >=2.3.0 - which requires C++11. rgeos
> is
> > ready for the forthcoming version of GEOS.
> >
> > The CRAN team has also been very supportive of our efforts to bring
> > compiled code in these packages into rchk compliance.
> >
> > Please get in touch if you see any loose ends in these releases.
> >
> > Roger
> >
> >
>
> --
> Roger Bivand
> Department of Economics, Norwegian School of Economics,
> Helleveien 30, N-5045 Bergen, Norway.
> voice: +47 55 95 93 55; e-mail: [hidden email]
> http://orcid.org/0000-0003-2392-6140
> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>


--
Vijay Lulla

Assistant Professor,
Dept. of Geography, IUPUI
425 University Blvd, CA-207C.
Indianapolis, IN-46202
[hidden email]
ORCID: https://orcid.org/0000-0002-0823-2522
Webpage: http://vijaylulla.com

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Re: CRAN releases of sp, rgdal and rgeos

Mon, 06/11/2018 - 18:54
Hi Roger, thanks for the follow up. Answering to your comments:

a) I am using Macports's gdal version 2.3.0.20180523. I am pretty sure that its source code (i.e. the one that is compiled on my machine) is downloaded from OSGEO (at least according to https://github.com/macports/macports-ports/blob/master/gis/gdal/Portfile);

b) I do have more than one libproj installed on my system (as QGIS for macOS requires its own gdal and proj stuff), but only the Macports one is on my path;


c) I tried running:
tools::testInstalledPackage("rgdal", outDir=tempdir())list.files(tempdir())file.show(file.path(tempdir(), "rgdal-Ex.Rout"))

but it unexpectedly returned "Error in library("rgdal") : there is no package called ‘rgdal’. Execution halted".

It looks weird but so far I am able to normally load and use at least a couple of rgdal's functions.

I will keep monitoring it though, and report any other issue.

Cheers,
 -- Thiago V. dos Santos
Postdoctoral Research FellowDepartment of Climate and Space Science and EngineeringUniversity of Michigan

    On Sunday, June 10, 2018, 4:46:04 AM EDT, Roger Bivand <[hidden email]> wrote:  
 
 Thanks for reporting, comments inline below (note that I have no OSX
access at all):

On Sat, 9 Jun 2018, Thiago V. dos Santos wrote:

> Dear Roger,
> Thank you very much for the excellent work done with those packages.
> Today I update both rgeos and rgdal on my system - macOS 10.13.5 with
> all dependencies installed via MacPorts. I had updated sp a few days
> earlier. The dependencies versions on my system are gdal
> @2.3.0.20180523_0+grib+hdf4+hdf5+jasper+mpich+netcdf and proj @5.1.0_0.
> Rgeos's update went flawlessly, but I got a few errors while updating
> rgdal. It still compiled successfully, but I am concerned that some
> functionality might be compromised due to the errors.
> This is what I got (I have to manually specify the location of proj or
> rgdal won't find it):> install.packages('rgdal', type = "source",
> configure.args=c(
> +    '--with-proj-include=/opt/local/lib/proj5/include',
> +    '--with-proj-lib=/opt/local/lib/proj5/lib'))
> Installing package into ‘/Users/thiago/Documents/R-packages’
> (as ‘lib’ is unspecified)
> trying URL 'https://cran.r-project.org/src/contrib/rgdal_1.3-2.tar.gz'
> Content type 'application/x-gzip' length 1667049 bytes (1.6 MB)
> ==================================================
> downloaded 1.6 MB
>
> * installing *source* package ‘rgdal’ ...
> ** package ‘rgdal’ successfully unpacked and MD5 sums checked
> configure: CC: /usr/bin/clang
> configure: CXX: /usr/bin/clang++
> configure: rgdal: 1.3-2
> checking for /usr/bin/svnversion... yes
> configure: svn revision: 755
> checking whether the C++ compiler works... yes
> checking for C++ compiler default output file name... a.out
> checking for suffix of executables...
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether we are using the GNU C++ compiler... yes
> checking whether /usr/bin/clang++ accepts -g... yes
> checking whether /usr/bin/clang++ supports C++11 features by default... no
> checking whether /usr/bin/clang++ supports C++11 features with -std=gnu++11... yes
> configure: C++11 support available
> checking for gdal-config... /opt/local/bin/gdal-config
> checking gdal-config usability... yes
> configure: GDAL: 2.4.0
All OK up to the GDAL version returned by gdal-config - are you using the
released GDAL 2.3.0 (probably not) or master?

> checking C++11 support for GDAL >= 2.3.0... yes
> checking GDAL version >= 1.11.4... yes
> checking gdal: linking with --libs only... yes
> checking GDAL: /opt/local/share/gdal/pcs.csv readable... yes
> checking proj_api.h presence and usability... yes
> ./configure: line 3395: test: =: unary operator expected

Will check, that line is:

if test ${PROJ_VERSION} = "" ; then

from configure.ac line 305. Possibly a shell dialect issue.

> checking PROJ version >= 4.8.0... yes
> checking projects.h presence and usability... yes

These relate to configure.ac lines 376-419, and the outcome: epsg found
and readable is OK - could there be two libproj on your system (maybe for
different architectures)?

> Undefined symbols for architecture x86_64:
>  "_pj_ctx_fclose", referenced from:
>      _main in proj_conf_test2-06fe7d.o
>  "_pj_get_default_ctx", referenced from:
>      _main in proj_conf_test2-06fe7d.o
>  "_pj_open_lib", referenced from:
>      _main in proj_conf_test2-06fe7d.o
> ld: symbol(s) not found for architecture x86_64
> clang: error: linker command failed with exit code 1 (use -v to see invocation)
> ./configure: line 3511: ./proj_conf_test2: No such file or directory
> checking PROJ.4: epsg found and readable... yes
Same here for next block in configure.ac; conus found and readable.

> Undefined symbols for architecture x86_64:
>  "_pj_ctx_fclose", referenced from:
>      _main in proj_conf_test3-3b7aa2.o
>  "_pj_get_default_ctx", referenced from:
>      _main in proj_conf_test3-3b7aa2.o
>  "_pj_open_lib", referenced from:
>      _main in proj_conf_test3-3b7aa2.o
> ld: symbol(s) not found for architecture x86_64
> clang: error: linker command failed with exit code 1 (use -v to see invocation)
> ./configure: line 3570: ./proj_conf_test3: No such file or directory
> checking PROJ.4: conus found and readable... yes
> configure: Package CPP flags:  -I/opt/local/include -I/opt/local/lib/proj5/include
> configure: Package LIBS:  -L/opt/local/lib -lgdal -L/opt/local/lib/proj5/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/opt/local/include -I/opt/local/lib/proj5/include -I"/Users/thiago/Documents/R-packages/sp/include" -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/opt/local/include -I/opt/local/lib/proj5/include -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include  -fPIC  -Wall -g -O2 -c gdal-bindings.cpp -o gdal-bindings.o
> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c init.c -o init.o
> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c inverser.c -o inverser.o
> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c local_stubs.c -o local_stubs.o
> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include  -fPIC  -Wall -g -O2 -c ogr_geom.cpp -o ogr_geom.o
> /usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c ogr_polygons.c -o ogr_polygons.o
> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include  -fPIC  -Wall -g -O2 -c ogr_proj.cpp -o ogr_proj.o
> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include  -fPIC  -Wall -g -O2 -c ogrdrivers.cpp -o ogrdrivers.o
> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include  -fPIC  -Wall -g -O2 -c ogrsource.cpp -o ogrsource.o
> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/include -I/opt/local/lib/proj5/include -I"/Users/thiago/Documents/R-packages/sp/include" -I/usr/local/include  -fPIC  -Wall -g -O2 -c projectit.cpp -o projectit.o
> clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rgdal.so OGR_write.o gdal-bindings.o init.o inverser.o local_stubs.o ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o -L/opt/local/lib -lgdal -L/opt/local/lib/proj5/lib -lproj -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
> installing to /Users/thiago/Documents/R-packages/rgdal/libs
> ** R
> ** data
> ** inst
> ** byte-compile and prepare package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> * DONE (rgdal)
>
> The downloaded source packages are in
>
> ‘/private/var/folders/_z/01gg71zs19g816v6m2dddt8w0000gn/T/Rtmp5K6lt8/downloaded_packages’
> ​Is this something that needs to be investigated, or I can just safely
> ignore those messages?
Please try to run:

tools::testInstalledPackage("rgdal", outDir=tempdir())
list.files(tempdir())
file.show(file.path(tempdir(), "rgdal-Ex.Rout"))

and if the outcomes are as expected, you should be OK, please let us know.

If any OSX users installing from source can contribute, that would be
useful. It will take a little while before the CRAN OSX binaries catch up
with new PROJ and GDAL.

Again thanks for reporting!

Roger

> Many thanks, -- Thiago V. dos Santos
> Postdoctoral Research FellowDepartment of Climate and Space Science and EngineeringUniversity of Michigan
>
>    On Friday, June 8, 2018, 2:15:43 PM EDT, Roger Bivand <[hidden email]> wrote:
>
> There are new releases of sp, rgdal and rgeos on CRAN. Please install sp
> first, then the other two, which link to the installed sp. They all
> address so-called rchk issues, which have not so far been a problem, but
> might have become more fragile as R's internal memory management is made
> even more efficient. This involves compiled code using memory allocated by
> R to be freed by R's garbage collector, which has to know if an object is
> still being used. Tomas Kalibera, the author of rchk, helped resolve and
> explain the issues encountered - what was good coding practice fifteen
> years ago isn't always still good practice.
>
> In addition, the earliest versions of GDAL and PROJ with which rgdal will
> work have been updated, and set to PROJ 4.8.0 and GDAL 1.11.4. The current
> released versions of PROJ and GDAL are to be prefered, as bugs have been
> fixed and new features and drivers introduced. A check has been put
> in place to trap attempts to install rgdal without a C++11-capable
> compiler when the GDAL version is >=2.3.0 - which requires C++11. rgeos is
> ready for the forthcoming version of GEOS.
>
> The CRAN team has also been very supportive of our efforts to bring
> compiled code in these packages into rchk compliance.
>
> Please get in touch if you see any loose ends in these releases.
>
> Roger
>
>
--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: [hidden email]
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en 
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Re: CRAN releases of sp, rgdal and rgeos

Mon, 06/11/2018 - 15:06
It's quite a selection of drivers, but my driver world has a short horizon.

> gdalDrivers()
               name                                                long_name create  copy isRaster
1           AAIGrid                                      Arc/Info ASCII Grid  FALSE  TRUE     TRUE
2              ACE2                                                     ACE2  FALSE FALSE     TRUE
3              ADRG                            ARC Digitized Raster Graphics   TRUE FALSE     TRUE
4               AIG                                     Arc/Info Binary Grid  FALSE FALSE     TRUE
5            AirSAR                                AirSAR Polarimetric Image  FALSE FALSE     TRUE
6               ARG                                Azavea Raster Grid format  FALSE  TRUE     TRUE
7               BAG                               Bathymetry Attributed Grid  FALSE FALSE     TRUE
8            BIGGIF                       Graphics Interchange Format (.gif)  FALSE FALSE     TRUE
9               BLX                                     Magellan topo (.blx)  FALSE  TRUE     TRUE
10              BMP                     MS Windows Device Independent Bitmap   TRUE FALSE     TRUE
11              BSB                              Maptech BSB Nautical Charts  FALSE FALSE     TRUE
12               BT                      VTP .bt (Binary Terrain) 1.3 Format   TRUE FALSE     TRUE
13             CALS                                            CALS (Type 1)  FALSE  TRUE     TRUE
14             CEOS                                               CEOS Image  FALSE FALSE     TRUE
15            COASP                          DRDC COASP SAR Processor Raster  FALSE FALSE     TRUE
16            COSAR               COSAR Annotated Binary Matrix (TerraSAR-X)  FALSE FALSE     TRUE
17              CPG                                          Convair PolGASP  FALSE FALSE     TRUE
18          CTable2                                 CTable2 Datum Grid Shift   TRUE FALSE     TRUE
19              CTG                           USGS LULC Composite Theme Grid  FALSE FALSE     TRUE
20            DIMAP                                               SPOT DIMAP  FALSE FALSE     TRUE
21            DIPEx                                                    DIPEx  FALSE FALSE     TRUE
22             DOQ1                                     USGS DOQ (Old Style)  FALSE FALSE     TRUE
23             DOQ2                                     USGS DOQ (New Style)  FALSE FALSE     TRUE
24             DTED                                    DTED Elevation Raster  FALSE  TRUE     TRUE
25          E00GRID                                 Arc/Info Export E00 GRID  FALSE FALSE     TRUE
26          ECRGTOC                                          ECRG TOC format  FALSE FALSE     TRUE
27             EHdr                                       ESRI .hdr Labelled   TRUE  TRUE     TRUE
28              EIR                                        Erdas Imagine Raw  FALSE FALSE     TRUE
29             ELAS                                                     ELAS   TRUE FALSE     TRUE
30             ENVI                                       ENVI .hdr Labelled   TRUE FALSE     TRUE
31              ERS                                   ERMapper .ers Labelled   TRUE FALSE     TRUE
32             ESAT                                     Envisat Image Format  FALSE FALSE     TRUE
33             FAST                                        EOSAT FAST Format  FALSE FALSE     TRUE
34              FIT                                                FIT Image  FALSE  TRUE     TRUE
35          FujiBAS                                   Fuji BAS Scanner Image  FALSE FALSE     TRUE
36           GenBin                           Generic Binary (.hdr Labelled)  FALSE FALSE     TRUE
37              GFF Ground-based SAR Applications Testbed File Format (.gff)  FALSE FALSE     TRUE
38              GIF                       Graphics Interchange Format (.gif)  FALSE  TRUE     TRUE
39              GMT                                   GMT NetCDF Grid Format  FALSE  TRUE     TRUE
40             GPKG                                               GeoPackage   TRUE  TRUE     TRUE
41   GRASSASCIIGrid                                         GRASS ASCII Grid  FALSE FALSE     TRUE
42             GRIB                                    GRIdded Binary (.grb)  FALSE FALSE     TRUE
43            GS7BG                     Golden Software 7 Binary Grid (.grd)   TRUE  TRUE     TRUE
44             GSAG                        Golden Software ASCII Grid (.grd)  FALSE  TRUE     TRUE
45             GSBG                       Golden Software Binary Grid (.grd)   TRUE  TRUE     TRUE
46              GSC                                              GSC Geogrid  FALSE FALSE     TRUE
47            GTiff                                                  GeoTIFF   TRUE  TRUE     TRUE
48              GTX                                 NOAA Vertical Datum .GTX   TRUE FALSE     TRUE
49              GXF                             GeoSoft Grid Exchange Format  FALSE FALSE     TRUE
50             HDF5                       Hierarchical Data Format Release 5  FALSE FALSE     TRUE
51        HDF5Image                                             HDF5 Dataset  FALSE FALSE     TRUE
52              HF2                               HF2/HFZ heightfield raster  FALSE  TRUE     TRUE
53              HFA                              Erdas Imagine Images (.img)   TRUE  TRUE     TRUE
54             HTTP                                    HTTP Fetching Wrapper  FALSE FALSE     TRUE
55              IDA                                  Image Data and Analysis   TRUE FALSE     TRUE
56            ILWIS                                         ILWIS Raster Map   TRUE  TRUE     TRUE
57             INGR                                        Intergraph Raster   TRUE  TRUE     TRUE
58             IRIS                             IRIS data (.PPI, .CAPPi etc)  FALSE FALSE     TRUE
59             ISCE                                              ISCE raster   TRUE FALSE     TRUE
60            ISIS2                  USGS Astrogeology ISIS cube (Version 2)   TRUE FALSE     TRUE
61            ISIS3                  USGS Astrogeology ISIS cube (Version 3)  FALSE FALSE     TRUE
62       JAXAPALSAR               JAXA PALSAR Product Reader (Level 1.1/1.5)  FALSE FALSE     TRUE
63             JDEM                                      Japanese DEM (.mem)  FALSE FALSE     TRUE
64             JPEG                                                JPEG JFIF  FALSE  TRUE     TRUE
65  KMLSUPEROVERLAY                                        Kml Super Overlay  FALSE  TRUE     TRUE
66              KRO                                                KOLOR Raw   TRUE FALSE     TRUE
67              L1B                     NOAA Polar Orbiter Level 1b Data Set  FALSE FALSE     TRUE
68              LAN                                          Erdas .LAN/.GIS   TRUE FALSE     TRUE
69              LCP                        FARSITE v.4 Landscape File (.lcp)  FALSE  TRUE     TRUE
70         Leveller                                     Leveller heightfield   TRUE FALSE     TRUE
71           LOSLAS                        NADCON .los/.las Datum Grid Shift  FALSE FALSE     TRUE
72              MAP                                         OziExplorer .MAP  FALSE FALSE     TRUE
73          MBTiles                                                  MBTiles   TRUE  TRUE     TRUE
74              MEM                                         In Memory Raster   TRUE FALSE     TRUE
75              MFF                                        Vexcel MFF Raster   TRUE  TRUE     TRUE
76             MFF2                                 Vexcel MFF2 (HKV) Raster   TRUE  TRUE     TRUE
77              MRF                                       Meta Raster Format   TRUE  TRUE     TRUE
78             MSGN                           EUMETSAT Archive native (.nat)  FALSE FALSE     TRUE
79              NDF                                        NLAPS Data Format  FALSE FALSE     TRUE
80           netCDF                               Network Common Data Format   TRUE  TRUE     TRUE
81         NGSGEOID                              NOAA NGS Geoid Height Grids  FALSE FALSE     TRUE
82             NITF                     National Imagery Transmission Format   TRUE  TRUE     TRUE
83             NTv2                                    NTv2 Datum Grid Shift   TRUE FALSE     TRUE
84          NWT_GRC               Northwood Classified Grid Format .grc/.tab  FALSE FALSE     TRUE
85          NWT_GRD                  Northwood Numeric Grid Format .grd/.tab  FALSE FALSE     TRUE
86              OZI                                   OziExplorer Image File  FALSE FALSE     TRUE
87             PAux                                        PCI .aux Labelled   TRUE FALSE     TRUE
88           PCIDSK                                     PCIDSK Database File   TRUE FALSE     TRUE
89         PCRaster                                     PCRaster Raster File   TRUE  TRUE     TRUE
90              PDF                                           Geospatial PDF   TRUE  TRUE     TRUE
91              PDS                               NASA Planetary Data System  FALSE FALSE     TRUE
92         PLMOSAIC                                  Planet Labs Mosaics API  FALSE FALSE     TRUE
93         PLSCENES                                   Planet Labs Scenes API  FALSE FALSE     TRUE
94              PNG                                Portable Network Graphics  FALSE  TRUE     TRUE
95              PNM                          Portable Pixmap Format (netpbm)   TRUE FALSE     TRUE
96                R                                      R Object Data Store  FALSE  TRUE     TRUE
97       Rasterlite                                               Rasterlite  FALSE  TRUE     TRUE
98              RIK                                  Swedish Grid RIK (.rik)  FALSE FALSE     TRUE
99              RMF                                     Raster Matrix Format   TRUE FALSE     TRUE
100         ROI_PAC                                           ROI_PAC raster   TRUE FALSE     TRUE
101          RPFTOC                         Raster Product Format TOC format  FALSE FALSE     TRUE
102             RS2                                   RadarSat 2 XML Product  FALSE FALSE     TRUE
103             RST                                        Idrisi Raster A.1   TRUE  TRUE     TRUE
104            SAFE                              Sentinel-1 SAR SAFE Product  FALSE FALSE     TRUE
105            SAGA                             SAGA GIS Binary Grid (.sdat)   TRUE  TRUE     TRUE
106        SAR_CEOS                                           CEOS SAR Image  FALSE FALSE     TRUE
107            SDTS                                              SDTS Raster  FALSE FALSE     TRUE
108       SENTINEL2                                               Sentinel 2  FALSE FALSE     TRUE
109             SGI                                SGI Image File Format 1.0   TRUE FALSE     TRUE
110          SNODAS                            Snow Data Assimilation System  FALSE FALSE     TRUE
111             SRP                      Standard Raster Product (ASRP/USRP)  FALSE FALSE     TRUE
112         SRTMHGT                                      SRTMHGT File Format  FALSE  TRUE     TRUE
113        Terragen                                     Terragen heightfield   TRUE FALSE     TRUE
114             TIL                                          EarthWatch .TIL  FALSE FALSE     TRUE
115             TSX                                       TerraSAR-X Product  FALSE FALSE     TRUE
116         USGSDEM                       USGS Optional ASCII DEM (and CDED)  FALSE  TRUE     TRUE
117           VICAR                                          MIPL VICAR file  FALSE FALSE     TRUE
118             VRT                                           Virtual Raster   TRUE  TRUE     TRUE
119             WCS                                 OGC Web Coverage Service  FALSE FALSE     TRUE
120             WMS                                      OGC Web Map Service  FALSE  TRUE     TRUE
121            WMTS                                 OGC Web Mab Tile Service  FALSE  TRUE     TRUE
122             XPM                                        X11 PixMap Format  FALSE  TRUE     TRUE
123             XYZ                                        ASCII Gridded XYZ  FALSE  TRUE     TRUE
124            ZMap                                           ZMap Plus Grid  FALSE  TRUE     TRUE

> On Jun 11, 2018, at 3:54 PM, Roger Bivand <[hidden email]> wrote:
>
> On Mon, 11 Jun 2018, Ben Tupper wrote:
>
>> Hi,
>>
>> I used CRAN binary ala ...
>>
>>> install.packages("rgdal")
>>
>> I used that same for sp and rgeos.
>
> Good, thanks. They probably do not have the very latest versions of the external dependencies, but do work and provide a reasonable selection of GDAL drivers.
>
> Roger
>
>>
>> Ben
>>
>>
>>> On Jun 11, 2018, at 3:45 PM, Roger Bivand <[hidden email]> wrote:
>>>
>>> On Mon, 11 Jun 2018, Ben Tupper wrote:
>>>
>>>> Hi,
>>>>
>>>> I have been able to install all three without issue.  I have encountered no issues with usage.
>>>
>>> Ben,
>>>
>>> Thanks for this report. How did you install rgdal - CRAN binary (now at 1.3.2 for R 3.5.0) or source install using GDAL and PROJ installed in what way? It's useful to record ways in which installation on OSX has been accomplished.
>>>
>>> Roger
>>>
>>>
>>>
>>>>
>>>>> sessionInfo()
>>>> R version 3.5.0 (2018-04-23)
>>>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>>> Running under: macOS Sierra 10.12.6
>>>>
>>>> Matrix products: default
>>>> BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
>>>> LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
>>>>
>>>> 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] rgeos_0.3-28 rgdal_1.3-2  sp_1.3-1
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] compiler_3.5.0  tools_3.5.0     grid_3.5.0      lattice_0.20-35
>>>>
>>>> Thanks for all you do!
>>>>
>>>> Cheers,
>>>> Ben
>>>>
>>>>
>>>>> On Jun 11, 2018, at 3:53 AM, Roger Bivand <[hidden email]> wrote:
>>>>>
>>>>> On Mon, 11 Jun 2018, Gilles Benjamin Leduc wrote:
>>>>>
>>>>>> Good monday!
>>>>>>
>>>>>> I tried to update rgdal, I get a warning telling me the installation had a non-null exit status. I haven't cheak if it was working…
>>>>>
>>>>> Thanks for responding - every user data point helps!
>>>>>
>>>>> Could you please provide the output of sessionInfo(), and any error messages you see on trying to update?
>>>>>
>>>>> Roger
>>>>>
>>>>>>
>>>>>> Benjamin
>>>>>>
>>>>>>
>>>>>> Le Vendredi 8 Juin 2018 18:15 GMT, Roger Bivand <[hidden email]> a écrit:
>>>>>>
>>>>>>> There are new releases of sp, rgdal and rgeos on CRAN. Please install sp
>>>>>>> first, then the other two, which link to the installed sp. They all
>>>>>>
>>>>>>> address so-called rchk issues, which have not so far been a problem, but
>>>>>>> might have become more fragile as R's internal memory management is made
>>>>>>> even more efficient. This involves compiled code using memory allocated by
>>>>>>> R to be freed by R's garbage collector, which has to know if an object is
>>>>>>> still being used. Tomas Kalibera, the author of rchk, helped resolve and
>>>>>>> explain the issues encountered - what was good coding practice fifteen
>>>>>>> years ago isn't always still good practice.
>>>>>>>
>>>>>>> In addition, the earliest versions of GDAL and PROJ with which rgdal will
>>>>>>> work have been updated, and set to PROJ 4.8.0 and GDAL 1.11.4. The current
>>>>>>> released versions of PROJ and GDAL are to be prefered, as bugs have been
>>>>>>> fixed and new features and drivers introduced. A check has been put
>>>>>>
>>>>>>> in place to trap attempts to install rgdal without a C++11-capable
>>>>>>> compiler when the GDAL version is >=2.3.0 - which requires C++11. rgeos is
>>>>>>> ready for the forthcoming version of GEOS.
>>>>>>>
>>>>>>> The CRAN team has also been very supportive of our efforts to bring
>>>>>>
>>>>>>> compiled code in these packages into rchk compliance.
>>>>>>>
>>>>>>> Please get in touch if you see any loose ends in these releases.
>>>>>>>
>>>>>>> Roger
>>>>>>>
>>>>>>> --
>>>>>>> Roger Bivand
>>>>>>> Department of Economics, Norwegian School of Economics,
>>>>>>> Helleveien 30, N-5045 Bergen, Norway.
>>>>>>> voice: +47 55 95 93 55; e-mail: [hidden email]
>>>>>>> http://orcid.org/0000-0003-2392-6140
>>>>>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> R-sig-Geo mailing list
>>>>>>> [hidden email]
>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> Roger Bivand
>>>>> Department of Economics, Norwegian School of Economics,
>>>>> Helleveien 30, N-5045 Bergen, Norway.
>>>>> voice: +47 55 95 93 55; e-mail: [hidden email] <mailto:[hidden email]>
>>>>> http://orcid.org/0000-0003-2392-6140 <http://orcid.org/0000-0003-2392-6140>
>>>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en_______________________________________________ <https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en_______________________________________________>
>>>>> R-sig-Geo mailing list
>>>>> [hidden email] <mailto:[hidden email]>
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo <https://stat.ethz.ch/mailman/listinfo/r-sig-geo>
>>>> Ben Tupper
>>>> Bigelow Laboratory for Ocean Sciences
>>>> 60 Bigelow Drive, P.O. Box 380
>>>> East Boothbay, Maine 04544
>>>> http://www.bigelow.org
>>>>
>>>> Ecological Forecasting: https://eco.bigelow.org/
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>> --
>>> Roger Bivand
>>> Department of Economics, Norwegian School of Economics,
>>> Helleveien 30, N-5045 Bergen, Norway.
>>> voice: +47 55 95 93 55; e-mail: [hidden email]
>>> http://orcid.org/0000-0003-2392-6140
>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>
>> Ben Tupper
>> Bigelow Laboratory for Ocean Sciences
>> 60 Bigelow Drive, P.O. Box 380
>> East Boothbay, Maine 04544
>> http://www.bigelow.org
>>
>> Ecological Forecasting: https://eco.bigelow.org/
>>
>>
>>
>>
>>
>>
>
> --
> Roger Bivand
> Department of Economics, Norwegian School of Economics,
> Helleveien 30, N-5045 Bergen, Norway.
> voice: +47 55 95 93 55; e-mail: [hidden email] <mailto:[hidden email]>
> http://orcid.org/0000-0003-2392-6140 <http://orcid.org/0000-0003-2392-6140>
> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en <https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en> Ben Tupper
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive, P.O. Box 380
East Boothbay, Maine 04544
http://www.bigelow.org

Ecological Forecasting: https://eco.bigelow.org/






        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo

Re: CRAN releases of sp, rgdal and rgeos

Mon, 06/11/2018 - 14:54
On Mon, 11 Jun 2018, Ben Tupper wrote:

> Hi,
>
> I used CRAN binary ala ...
>
>> install.packages("rgdal")
>
> I used that same for sp and rgeos.

Good, thanks. They probably do not have the very latest versions of the
external dependencies, but do work and provide a reasonable selection of
GDAL drivers.

Roger

>
> Ben
>
>
>> On Jun 11, 2018, at 3:45 PM, Roger Bivand <[hidden email]> wrote:
>>
>> On Mon, 11 Jun 2018, Ben Tupper wrote:
>>
>>> Hi,
>>>
>>> I have been able to install all three without issue.  I have encountered no issues with usage.
>>
>> Ben,
>>
>> Thanks for this report. How did you install rgdal - CRAN binary (now at 1.3.2 for R 3.5.0) or source install using GDAL and PROJ installed in what way? It's useful to record ways in which installation on OSX has been accomplished.
>>
>> Roger
>>
>>
>>
>>>
>>>> sessionInfo()
>>> R version 3.5.0 (2018-04-23)
>>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>> Running under: macOS Sierra 10.12.6
>>>
>>> Matrix products: default
>>> BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
>>> LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
>>>
>>> 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] rgeos_0.3-28 rgdal_1.3-2  sp_1.3-1
>>>
>>> loaded via a namespace (and not attached):
>>> [1] compiler_3.5.0  tools_3.5.0     grid_3.5.0      lattice_0.20-35
>>>
>>> Thanks for all you do!
>>>
>>> Cheers,
>>> Ben
>>>
>>>
>>>> On Jun 11, 2018, at 3:53 AM, Roger Bivand <[hidden email]> wrote:
>>>>
>>>> On Mon, 11 Jun 2018, Gilles Benjamin Leduc wrote:
>>>>
>>>>> Good monday!
>>>>>
>>>>> I tried to update rgdal, I get a warning telling me the installation had a non-null exit status. I haven't cheak if it was working…
>>>>
>>>> Thanks for responding - every user data point helps!
>>>>
>>>> Could you please provide the output of sessionInfo(), and any error messages you see on trying to update?
>>>>
>>>> Roger
>>>>
>>>>>
>>>>> Benjamin
>>>>>
>>>>>
>>>>> Le Vendredi 8 Juin 2018 18:15 GMT, Roger Bivand <[hidden email]> a écrit:
>>>>>
>>>>>> There are new releases of sp, rgdal and rgeos on CRAN. Please install sp
>>>>>> first, then the other two, which link to the installed sp. They all
>>>>>
>>>>>> address so-called rchk issues, which have not so far been a problem, but
>>>>>> might have become more fragile as R's internal memory management is made
>>>>>> even more efficient. This involves compiled code using memory allocated by
>>>>>> R to be freed by R's garbage collector, which has to know if an object is
>>>>>> still being used. Tomas Kalibera, the author of rchk, helped resolve and
>>>>>> explain the issues encountered - what was good coding practice fifteen
>>>>>> years ago isn't always still good practice.
>>>>>>
>>>>>> In addition, the earliest versions of GDAL and PROJ with which rgdal will
>>>>>> work have been updated, and set to PROJ 4.8.0 and GDAL 1.11.4. The current
>>>>>> released versions of PROJ and GDAL are to be prefered, as bugs have been
>>>>>> fixed and new features and drivers introduced. A check has been put
>>>>>
>>>>>> in place to trap attempts to install rgdal without a C++11-capable
>>>>>> compiler when the GDAL version is >=2.3.0 - which requires C++11. rgeos is
>>>>>> ready for the forthcoming version of GEOS.
>>>>>>
>>>>>> The CRAN team has also been very supportive of our efforts to bring
>>>>>
>>>>>> compiled code in these packages into rchk compliance.
>>>>>>
>>>>>> Please get in touch if you see any loose ends in these releases.
>>>>>>
>>>>>> Roger
>>>>>>
>>>>>> --
>>>>>> Roger Bivand
>>>>>> Department of Economics, Norwegian School of Economics,
>>>>>> Helleveien 30, N-5045 Bergen, Norway.
>>>>>> voice: +47 55 95 93 55; e-mail: [hidden email]
>>>>>> http://orcid.org/0000-0003-2392-6140
>>>>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>>>>>
>>>>>> _______________________________________________
>>>>>> R-sig-Geo mailing list
>>>>>> [hidden email]
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>> --
>>>> Roger Bivand
>>>> Department of Economics, Norwegian School of Economics,
>>>> Helleveien 30, N-5045 Bergen, Norway.
>>>> voice: +47 55 95 93 55; e-mail: [hidden email] <mailto:[hidden email]>
>>>> http://orcid.org/0000-0003-2392-6140 <http://orcid.org/0000-0003-2392-6140>
>>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en_______________________________________________ <https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en_______________________________________________>
>>>> R-sig-Geo mailing list
>>>> [hidden email] <mailto:[hidden email]>
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo <https://stat.ethz.ch/mailman/listinfo/r-sig-geo>
>>> Ben Tupper
>>> Bigelow Laboratory for Ocean Sciences
>>> 60 Bigelow Drive, P.O. Box 380
>>> East Boothbay, Maine 04544
>>> http://www.bigelow.org
>>>
>>> Ecological Forecasting: https://eco.bigelow.org/
>>>
>>>
>>>
>>>
>>>
>>>
>>
>> --
>> Roger Bivand
>> Department of Economics, Norwegian School of Economics,
>> Helleveien 30, N-5045 Bergen, Norway.
>> voice: +47 55 95 93 55; e-mail: [hidden email]
>> http://orcid.org/0000-0003-2392-6140
>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>
> Ben Tupper
> Bigelow Laboratory for Ocean Sciences
> 60 Bigelow Drive, P.O. Box 380
> East Boothbay, Maine 04544
> http://www.bigelow.org
>
> Ecological Forecasting: https://eco.bigelow.org/
>
>
>
>
>
> --
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: [hidden email]
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Roger Bivand
Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway

Re: CRAN releases of sp, rgdal and rgeos

Mon, 06/11/2018 - 14:51
Hi,

I used CRAN binary ala ...

> install.packages("rgdal")

I used that same for sp and rgeos.  

Ben


> On Jun 11, 2018, at 3:45 PM, Roger Bivand <[hidden email]> wrote:
>
> On Mon, 11 Jun 2018, Ben Tupper wrote:
>
>> Hi,
>>
>> I have been able to install all three without issue.  I have encountered no issues with usage.
>
> Ben,
>
> Thanks for this report. How did you install rgdal - CRAN binary (now at 1.3.2 for R 3.5.0) or source install using GDAL and PROJ installed in what way? It's useful to record ways in which installation on OSX has been accomplished.
>
> Roger
>
>
>
>>
>>> sessionInfo()
>> R version 3.5.0 (2018-04-23)
>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>> Running under: macOS Sierra 10.12.6
>>
>> Matrix products: default
>> BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
>> LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
>>
>> 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] rgeos_0.3-28 rgdal_1.3-2  sp_1.3-1
>>
>> loaded via a namespace (and not attached):
>> [1] compiler_3.5.0  tools_3.5.0     grid_3.5.0      lattice_0.20-35
>>
>> Thanks for all you do!
>>
>> Cheers,
>> Ben
>>
>>
>>> On Jun 11, 2018, at 3:53 AM, Roger Bivand <[hidden email]> wrote:
>>>
>>> On Mon, 11 Jun 2018, Gilles Benjamin Leduc wrote:
>>>
>>>> Good monday!
>>>>
>>>> I tried to update rgdal, I get a warning telling me the installation had a non-null exit status. I haven't cheak if it was working…
>>>
>>> Thanks for responding - every user data point helps!
>>>
>>> Could you please provide the output of sessionInfo(), and any error messages you see on trying to update?
>>>
>>> Roger
>>>
>>>>
>>>> Benjamin
>>>>
>>>>
>>>> Le Vendredi 8 Juin 2018 18:15 GMT, Roger Bivand <[hidden email]> a écrit:
>>>>
>>>>> There are new releases of sp, rgdal and rgeos on CRAN. Please install sp
>>>>> first, then the other two, which link to the installed sp. They all
>>>>
>>>>> address so-called rchk issues, which have not so far been a problem, but
>>>>> might have become more fragile as R's internal memory management is made
>>>>> even more efficient. This involves compiled code using memory allocated by
>>>>> R to be freed by R's garbage collector, which has to know if an object is
>>>>> still being used. Tomas Kalibera, the author of rchk, helped resolve and
>>>>> explain the issues encountered - what was good coding practice fifteen
>>>>> years ago isn't always still good practice.
>>>>>
>>>>> In addition, the earliest versions of GDAL and PROJ with which rgdal will
>>>>> work have been updated, and set to PROJ 4.8.0 and GDAL 1.11.4. The current
>>>>> released versions of PROJ and GDAL are to be prefered, as bugs have been
>>>>> fixed and new features and drivers introduced. A check has been put
>>>>
>>>>> in place to trap attempts to install rgdal without a C++11-capable
>>>>> compiler when the GDAL version is >=2.3.0 - which requires C++11. rgeos is
>>>>> ready for the forthcoming version of GEOS.
>>>>>
>>>>> The CRAN team has also been very supportive of our efforts to bring
>>>>
>>>>> compiled code in these packages into rchk compliance.
>>>>>
>>>>> Please get in touch if you see any loose ends in these releases.
>>>>>
>>>>> Roger
>>>>>
>>>>> --
>>>>> Roger Bivand
>>>>> Department of Economics, Norwegian School of Economics,
>>>>> Helleveien 30, N-5045 Bergen, Norway.
>>>>> voice: +47 55 95 93 55; e-mail: [hidden email]
>>>>> http://orcid.org/0000-0003-2392-6140
>>>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>>>>
>>>>> _______________________________________________
>>>>> R-sig-Geo mailing list
>>>>> [hidden email]
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>> --
>>> Roger Bivand
>>> Department of Economics, Norwegian School of Economics,
>>> Helleveien 30, N-5045 Bergen, Norway.
>>> voice: +47 55 95 93 55; e-mail: [hidden email] <mailto:[hidden email]>
>>> http://orcid.org/0000-0003-2392-6140 <http://orcid.org/0000-0003-2392-6140>
>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en_______________________________________________ <https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en_______________________________________________>
>>> R-sig-Geo mailing list
>>> [hidden email] <mailto:[hidden email]>
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo <https://stat.ethz.ch/mailman/listinfo/r-sig-geo>
>> Ben Tupper
>> Bigelow Laboratory for Ocean Sciences
>> 60 Bigelow Drive, P.O. Box 380
>> East Boothbay, Maine 04544
>> http://www.bigelow.org
>>
>> Ecological Forecasting: https://eco.bigelow.org/
>>
>>
>>
>>
>>
>>
>
> --
> Roger Bivand
> Department of Economics, Norwegian School of Economics,
> Helleveien 30, N-5045 Bergen, Norway.
> voice: +47 55 95 93 55; e-mail: [hidden email]
> http://orcid.org/0000-0003-2392-6140
> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
Ben Tupper
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive, P.O. Box 380
East Boothbay, Maine 04544
http://www.bigelow.org

Ecological Forecasting: https://eco.bigelow.org/






        [[alternative HTML version deleted]]

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R-sig-Geo mailing list
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Re: CRAN releases of sp, rgdal and rgeos

Mon, 06/11/2018 - 14:45
On Mon, 11 Jun 2018, Ben Tupper wrote:

> Hi,
>
> I have been able to install all three without issue.  I have encountered
> no issues with usage.

Ben,

Thanks for this report. How did you install rgdal - CRAN binary (now at
1.3.2 for R 3.5.0) or source install using GDAL and PROJ installed in what
way? It's useful to record ways in which installation on OSX has been
accomplished.

Roger



>
>> sessionInfo()
> R version 3.5.0 (2018-04-23)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS Sierra 10.12.6
>
> Matrix products: default
> BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
> LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
>
> 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] rgeos_0.3-28 rgdal_1.3-2  sp_1.3-1
>
> loaded via a namespace (and not attached):
> [1] compiler_3.5.0  tools_3.5.0     grid_3.5.0      lattice_0.20-35
>
> Thanks for all you do!
>
> Cheers,
> Ben
>
>
>> On Jun 11, 2018, at 3:53 AM, Roger Bivand <[hidden email]> wrote:
>>
>> On Mon, 11 Jun 2018, Gilles Benjamin Leduc wrote:
>>
>>> Good monday!
>>>
>>> I tried to update rgdal, I get a warning telling me the installation had a non-null exit status. I haven't cheak if it was working…
>>
>> Thanks for responding - every user data point helps!
>>
>> Could you please provide the output of sessionInfo(), and any error messages you see on trying to update?
>>
>> Roger
>>
>>>
>>> Benjamin
>>>
>>>
>>> Le Vendredi 8 Juin 2018 18:15 GMT, Roger Bivand <[hidden email]> a écrit:
>>>
>>>> There are new releases of sp, rgdal and rgeos on CRAN. Please install sp
>>>> first, then the other two, which link to the installed sp. They all
>>>
>>>> address so-called rchk issues, which have not so far been a problem, but
>>>> might have become more fragile as R's internal memory management is made
>>>> even more efficient. This involves compiled code using memory allocated by
>>>> R to be freed by R's garbage collector, which has to know if an object is
>>>> still being used. Tomas Kalibera, the author of rchk, helped resolve and
>>>> explain the issues encountered - what was good coding practice fifteen
>>>> years ago isn't always still good practice.
>>>>
>>>> In addition, the earliest versions of GDAL and PROJ with which rgdal will
>>>> work have been updated, and set to PROJ 4.8.0 and GDAL 1.11.4. The current
>>>> released versions of PROJ and GDAL are to be prefered, as bugs have been
>>>> fixed and new features and drivers introduced. A check has been put
>>>
>>>> in place to trap attempts to install rgdal without a C++11-capable
>>>> compiler when the GDAL version is >=2.3.0 - which requires C++11. rgeos is
>>>> ready for the forthcoming version of GEOS.
>>>>
>>>> The CRAN team has also been very supportive of our efforts to bring
>>>
>>>> compiled code in these packages into rchk compliance.
>>>>
>>>> Please get in touch if you see any loose ends in these releases.
>>>>
>>>> Roger
>>>>
>>>> --
>>>> Roger Bivand
>>>> Department of Economics, Norwegian School of Economics,
>>>> Helleveien 30, N-5045 Bergen, Norway.
>>>> voice: +47 55 95 93 55; e-mail: [hidden email]
>>>> http://orcid.org/0000-0003-2392-6140
>>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>>>
>>>> _______________________________________________
>>>> R-sig-Geo mailing list
>>>> [hidden email]
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>>
>>>
>>>
>>>
>>
>> --
>> Roger Bivand
>> Department of Economics, Norwegian School of Economics,
>> Helleveien 30, N-5045 Bergen, Norway.
>> voice: +47 55 95 93 55; e-mail: [hidden email] <mailto:[hidden email]>
>> http://orcid.org/0000-0003-2392-6140 <http://orcid.org/0000-0003-2392-6140>
>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en_______________________________________________ <https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en_______________________________________________>
>> R-sig-Geo mailing list
>> [hidden email] <mailto:[hidden email]>
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo <https://stat.ethz.ch/mailman/listinfo/r-sig-geo>
> Ben Tupper
> Bigelow Laboratory for Ocean Sciences
> 60 Bigelow Drive, P.O. Box 380
> East Boothbay, Maine 04544
> http://www.bigelow.org
>
> Ecological Forecasting: https://eco.bigelow.org/
>
>
>
>
>
> --
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: [hidden email]
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Roger Bivand
Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway

Re: CRAN releases of sp, rgdal and rgeos

Mon, 06/11/2018 - 12:56
Hi,

I have been able to install all three without issue.  I have encountered no issues with usage.  

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

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] rgeos_0.3-28 rgdal_1.3-2  sp_1.3-1    

loaded via a namespace (and not attached):
[1] compiler_3.5.0  tools_3.5.0     grid_3.5.0      lattice_0.20-35

Thanks for all you do!

Cheers,
Ben


> On Jun 11, 2018, at 3:53 AM, Roger Bivand <[hidden email]> wrote:
>
> On Mon, 11 Jun 2018, Gilles Benjamin Leduc wrote:
>
>> Good monday!
>>
>> I tried to update rgdal, I get a warning telling me the installation had a non-null exit status. I haven't cheak if it was working…
>
> Thanks for responding - every user data point helps!
>
> Could you please provide the output of sessionInfo(), and any error messages you see on trying to update?
>
> Roger
>
>>
>> Benjamin
>>
>>
>> Le Vendredi 8 Juin 2018 18:15 GMT, Roger Bivand <[hidden email]> a écrit:
>>
>>> There are new releases of sp, rgdal and rgeos on CRAN. Please install sp
>>> first, then the other two, which link to the installed sp. They all
>>
>>> address so-called rchk issues, which have not so far been a problem, but
>>> might have become more fragile as R's internal memory management is made
>>> even more efficient. This involves compiled code using memory allocated by
>>> R to be freed by R's garbage collector, which has to know if an object is
>>> still being used. Tomas Kalibera, the author of rchk, helped resolve and
>>> explain the issues encountered - what was good coding practice fifteen
>>> years ago isn't always still good practice.
>>>
>>> In addition, the earliest versions of GDAL and PROJ with which rgdal will
>>> work have been updated, and set to PROJ 4.8.0 and GDAL 1.11.4. The current
>>> released versions of PROJ and GDAL are to be prefered, as bugs have been
>>> fixed and new features and drivers introduced. A check has been put
>>
>>> in place to trap attempts to install rgdal without a C++11-capable
>>> compiler when the GDAL version is >=2.3.0 - which requires C++11. rgeos is
>>> ready for the forthcoming version of GEOS.
>>>
>>> The CRAN team has also been very supportive of our efforts to bring
>>
>>> compiled code in these packages into rchk compliance.
>>>
>>> Please get in touch if you see any loose ends in these releases.
>>>
>>> Roger
>>>
>>> --
>>> Roger Bivand
>>> Department of Economics, Norwegian School of Economics,
>>> Helleveien 30, N-5045 Bergen, Norway.
>>> voice: +47 55 95 93 55; e-mail: [hidden email]
>>> http://orcid.org/0000-0003-2392-6140
>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>> [hidden email]
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>>
>>
>>
>>
>
> --
> Roger Bivand
> Department of Economics, Norwegian School of Economics,
> Helleveien 30, N-5045 Bergen, Norway.
> voice: +47 55 95 93 55; e-mail: [hidden email] <mailto:[hidden email]>
> http://orcid.org/0000-0003-2392-6140 <http://orcid.org/0000-0003-2392-6140>
> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en_______________________________________________ <https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en_______________________________________________>
> R-sig-Geo mailing list
> [hidden email] <mailto:[hidden email]>
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo <https://stat.ethz.ch/mailman/listinfo/r-sig-geo> Ben Tupper
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive, P.O. Box 380
East Boothbay, Maine 04544
http://www.bigelow.org

Ecological Forecasting: https://eco.bigelow.org/






        [[alternative HTML version deleted]]

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Re: CRAN releases of sp, rgdal and rgeos

Mon, 06/11/2018 - 04:15
 
 

-------- Message original --------
Sujet: Re: [R-sig-Geo] CRAN releases of   sp, rgdal and rgeos
Date: Lundi 11 Juin 2018 08:24 GMT
De: "Gilles Benjamin Leduc" <[hidden email]>
Pour: [hidden email]
 
 
Here it is:

> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.5

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
[1] RColorBrewer_1.1-2 seqinr_3.4-5      

loaded via a namespace (and not attached):
[1] MASS_7.3-50    compiler_3.4.2 tools_3.4.2    ade4_1.7-11




installing to /Library/Frameworks/R.framework/Versions/3.4/Resources/library/utf8/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (utf8)
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2018c.1.0/zoneinfo/Europe/Helsinki'
* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ correctement décompressé et sommes MD5 vérifiées
configure: CC: clang
configure: CXX: clang++
configure: rgdal: 1.3-2
checking for /usr/bin/svnversion... yes
configure: svn revision: 755
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ accepts -g... yes
checking whether clang++ supports C++11 features by default... no
checking whether clang++ supports C++11 features with -std=gnu++11... yes
configure: C++11 support available
checking for gdal-config... no
no
configure: error: gdal-config not found or not executable.
ERROR: configuration failed for package ‘rgdal’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rgdal’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rgdal’

Les packages source téléchargés sont dans
        ‘/private/var/folders/j0/gxxcvrr13rgg1xwfmf01yb240000gn/T/RtmpUleCF6/downloaded_packages’
Warning message:
In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  l'installation du package ‘rgdal’ a eu un statut de sortie non nul


Have a nice Monday

Benjamin  
 
 
Le Lundi 11 Juin 2018 07:53 GMT, Roger Bivand <[hidden email]> a écrit:
 
> On Mon, 11 Jun 2018, Gilles Benjamin Leduc wrote:
>
> > Good monday!
> >
> > I tried to update rgdal, I get a warning telling me the installation had
> > a non-null exit status. I haven't cheak if it was working…>
> Thanks for responding - every user data point helps!
>
> Could you please provide the output of sessionInfo(), and any error > messages you see on trying to update?
>
> Roger
>
> >
> > Benjamin
> >
> >
> > Le Vendredi 8 Juin 2018 18:15 GMT, Roger Bivand <[hidden email]> a écrit:
> >
> >> There are new releases of sp, rgdal and rgeos on CRAN. Please install sp
> >> first, then the other two, which link to the installed sp. They all
> >
> >> address so-called rchk issues, which have not so far been a problem, but
> >> might have become more fragile as R's internal memory management is made
> >> even more efficient. This involves compiled code using memory allocated by
> >> R to be freed by R's garbage collector, which has to know if an object is
> >> still being used. Tomas Kalibera, the author of rchk, helped resolve and
> >> explain the issues encountered - what was good coding practice fifteen
> >> years ago isn't always still good practice.
> >>
> >> In addition, the earliest versions of GDAL and PROJ with which rgdal will
> >> work have been updated, and set to PROJ 4.8.0 and GDAL 1.11.4. The current
> >> released versions of PROJ and GDAL are to be prefered, as bugs have been
> >> fixed and new features and drivers introduced. A check has been put
> >
> >> in place to trap attempts to install rgdal without a C++11-capable> >> compiler when the GDAL version is >=2.3.0 - which requires C++11. rgeos is
> >> ready for the forthcoming version of GEOS.
> >>
> >> The CRAN team has also been very supportive of our efforts to bring
> >
> >> compiled code in these packages into rchk compliance.
> >>
> >> Please get in touch if you see any loose ends in these releases.
> >>
> >> Roger
> >>
> >> --
> >> Roger Bivand
> >> Department of Economics, Norwegian School of Economics,
> >> Helleveien 30, N-5045 Bergen, Norway.
> >> voice: +47 55 95 93 55; e-mail: [hidden email]
> >> http://orcid.org/0000-0003-2392-6140
> >> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
> >>
> >> _______________________________________________
> >> R-sig-Geo mailing list
> >> [hidden email]
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >
> >
> >
> >
> >
>
> --
> Roger Bivand
> Department of Economics, Norwegian School of Economics,
> Helleveien 30, N-5045 Bergen, Norway.
> voice: +47 55 95 93 55; e-mail: [hidden email]
> http://orcid.org/0000-0003-2392-6140
> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo

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