CRAN releases of sp, rgdal and rgeos

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Re: CRAN releases of sp, rgdal and rgeos

Roger Bivand
Administrator
On Mon, 18 Jun 2018, MacQueen, Don wrote:

> Success!
>
> This morning I upgraded a Mac to OS 10.13.5 (the so-called High Sierra
> version), then
>
> - Installed R 3.5.0 from CRAN (installed ever 3.3.x)
> - Installed sp 1.3-1, rgdal 1.3-2, rgeos 0.3-28, also sf 0.6-3, from the
>   CRAN binaries that are now available
> - Ran my personal test suite, which exercises the kinds of tasks I
>   perform with those packages
>
> All tests succeeded.
Thanks for reporting - especially on your own test suite. We do what we
can to cover typical use cases, but independent testing in production
settings is reassuring for everybody. We're expecting more PROJ-based
changes later this year and next year, so it is great to have external
test sets to be able to check where any changes in output are coming from.

This is an encouragement to other users whose production depends on R
packages using GDAL, PROJ and/or GEOS to follow this example and keep a
script handy to test your use cases, and a history of output files with
which to compare (diff). We don't worry about changes in the EPSG
versions, but by next year they may be properly anchored too (changes in
PROJ may include reference system definitions with timestamps).

>
> I forgot to control the order of installation, so I don't know if I
> installed sp first, as advised. But I expect that with the binary
> versions it doesn't matter.

Right, the binary builds use the sp version on the build platform.

Best wishes,

Roger

>
> (I don't think it matters for the above, but I also installed the clang
> and gfortran version provided on CRAN's Mac "tools" page, and
> successfully compiled some source packages that require fortran, and
> others that require C).
>
> Thank again for all your work
> -Don
>
> --
> Don MacQueen
> Lawrence Livermore National Laboratory
> 7000 East Ave., L-627
> Livermore, CA 94550
> 925-423-1062
> Lab cell 925-724-7509
>
>
>
> On 6/8/18, 11:15 AM, "R-sig-Geo on behalf of Roger Bivand" <[hidden email] on behalf of [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
>
>    _______________________________________________
>    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
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Re: CRAN releases of sp, rgdal and rgeos

Tomislav Hengl-5
Two weeks ago I installed new GDAL 2.3.* from source, then tried
installing rgdal and got the error about GDAL requires C++11. Then I had
to remove everything and reinstall GDAL 2.2. Would love to be able to
start using the newest GDAL inside R as it seems that many things have
been improved
(https://trac.osgeo.org/gdal/query?group=status&milestone=2.3.0).
Installing GDAL from source takes >20mins so next time I would like to
be sure that I will not have to remove GDAL.

Can somebody point to a step-by-step guide to install GDAL 2.3.* and
rgdal on ubuntu (now that all packages have been updated)?

Much appreciated!

My session info:

 > library(rgdal)
Loading required package: sp
rgdal: version: 1.2-20, (SVN revision 725)
  Geospatial Data Abstraction Library extensions to R successfully loaded
  Loaded GDAL runtime: GDAL 2.2.2, released 2017/09/15
  Path to GDAL shared files: /usr/share/gdal/2.2
  GDAL binary built with GEOS: TRUE
  Loaded PROJ.4 runtime: Rel. 4.9.2, 08 September 2015, [PJ_VERSION: 492]
  Path to PROJ.4 shared files: (autodetected)
  Linking to sp version: 1.2-7
 > sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /opt/microsoft/ropen/3.5.0/lib64/R/lib/libRblas.so
LAPACK: /opt/microsoft/ropen/3.5.0/lib64/R/lib/libRlapack.so



On 19.06.2018 08:47, Roger Bivand wrote:

> On Mon, 18 Jun 2018, MacQueen, Don wrote:
>
>> Success!
>>
>> This morning I upgraded a Mac to OS 10.13.5 (the so-called High
>> Sierra version), then
>>
>> - Installed R 3.5.0 from CRAN (installed ever 3.3.x)
>> - Installed sp 1.3-1, rgdal 1.3-2, rgeos 0.3-28, also sf 0.6-3, from the
>>   CRAN binaries that are now available
>> - Ran my personal test suite, which exercises the kinds of tasks I
>>   perform with those packages
>>
>> All tests succeeded.
>
> Thanks for reporting - especially on your own test suite. We do what
> we can to cover typical use cases, but independent testing in
> production settings is reassuring for everybody. We're expecting more
> PROJ-based changes later this year and next year, so it is great to
> have external test sets to be able to check where any changes in
> output are coming from.
>
> This is an encouragement to other users whose production depends on R
> packages using GDAL, PROJ and/or GEOS to follow this example and keep
> a script handy to test your use cases, and a history of output files
> with which to compare (diff). We don't worry about changes in the EPSG
> versions, but by next year they may be properly anchored too (changes
> in PROJ may include reference system definitions with timestamps).
>
>>
>> I forgot to control the order of installation, so I don't know if I
>> installed sp first, as advised. But I expect that with the binary
>> versions it doesn't matter.
>
> Right, the binary builds use the sp version on the build platform.
>
> Best wishes,
>
> Roger
>
>>
>> (I don't think it matters for the above, but I also installed the
>> clang and gfortran version provided on CRAN's Mac "tools" page, and
>> successfully compiled some source packages that require fortran, and
>> others that require C).
>>
>> Thank again for all your work
>> -Don
>>
>> --
>> Don MacQueen
>> Lawrence Livermore National Laboratory
>> 7000 East Ave., L-627
>> Livermore, CA 94550
>> 925-423-1062
>> Lab cell 925-724-7509
>>
>>
>>
>> On 6/8/18, 11:15 AM, "R-sig-Geo on behalf of Roger Bivand"
>> <[hidden email] on behalf of [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
>>
>>    _______________________________________________
>>    R-sig-Geo mailing list
>>    [hidden email]
>>    https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>>
>>
>
>
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo


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Re: CRAN releases of sp, rgdal and rgeos

Roger Bivand
Administrator
On Tue, 19 Jun 2018, Tomislav Hengl wrote:

> Two weeks ago I installed new GDAL 2.3.* from source, then tried
> installing rgdal and got the error about GDAL requires C++11. Then I had
> to remove everything and reinstall GDAL 2.2. Would love to be able to
> start using the newest GDAL inside R as it seems that many things have
> been improved
> (https://trac.osgeo.org/gdal/query?group=status&milestone=2.3.0).
> Installing GDAL from source takes >20mins so next time I would like to
> be sure that I will not have to remove GDAL.
>
> Can somebody point to a step-by-step guide to install GDAL 2.3.* and
> rgdal on ubuntu (now that all packages have been updated)?
Tom:

There is too little information here: which g++ compiler version, was R
installed from source or not, GDAL was installed from source, but was PROJ
installed from source (and/or GEOS), ... and no verbatim error message.

Please try development rgdal_1.3-3 from R-forge, which has some logic
fixes in configure:

install.packages("rgdal", repos="http://R-Forge.R-project.org")

Did you check whether sf installed with GDAL 2.3.0 and PROJ 5.1.0?

It looks as though CRAN devel debian is using GDAL 2.3.0 (the test saved
output is 2.2.4):

https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/rgdal-00check.html

Hope this helps,

Roger

>
> Much appreciated!
>
> My session info:
>
> > library(rgdal)
> Loading required package: sp
> rgdal: version: 1.2-20, (SVN revision 725)
>  Geospatial Data Abstraction Library extensions to R successfully loaded
>  Loaded GDAL runtime: GDAL 2.2.2, released 2017/09/15
>  Path to GDAL shared files: /usr/share/gdal/2.2
>  GDAL binary built with GEOS: TRUE
>  Loaded PROJ.4 runtime: Rel. 4.9.2, 08 September 2015, [PJ_VERSION: 492]
>  Path to PROJ.4 shared files: (autodetected)
>  Linking to sp version: 1.2-7
> > sessionInfo()
> R version 3.5.0 (2018-04-23)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 16.04.4 LTS
>
> Matrix products: default
> BLAS: /opt/microsoft/ropen/3.5.0/lib64/R/lib/libRblas.so
> LAPACK: /opt/microsoft/ropen/3.5.0/lib64/R/lib/libRlapack.so
>
>
>
> On 19.06.2018 08:47, Roger Bivand wrote:
>> On Mon, 18 Jun 2018, MacQueen, Don wrote:
>>
>>> Success!
>>>
>>> This morning I upgraded a Mac to OS 10.13.5 (the so-called High
>>> Sierra version), then
>>>
>>> - Installed R 3.5.0 from CRAN (installed ever 3.3.x)
>>> - Installed sp 1.3-1, rgdal 1.3-2, rgeos 0.3-28, also sf 0.6-3, from the
>>>   CRAN binaries that are now available
>>> - Ran my personal test suite, which exercises the kinds of tasks I
>>>   perform with those packages
>>>
>>> All tests succeeded.
>>
>> Thanks for reporting - especially on your own test suite. We do what
>> we can to cover typical use cases, but independent testing in
>> production settings is reassuring for everybody. We're expecting more
>> PROJ-based changes later this year and next year, so it is great to
>> have external test sets to be able to check where any changes in
>> output are coming from.
>>
>> This is an encouragement to other users whose production depends on R
>> packages using GDAL, PROJ and/or GEOS to follow this example and keep
>> a script handy to test your use cases, and a history of output files
>> with which to compare (diff). We don't worry about changes in the EPSG
>> versions, but by next year they may be properly anchored too (changes
>> in PROJ may include reference system definitions with timestamps).
>>
>>>
>>> I forgot to control the order of installation, so I don't know if I
>>> installed sp first, as advised. But I expect that with the binary
>>> versions it doesn't matter.
>>
>> Right, the binary builds use the sp version on the build platform.
>>
>> Best wishes,
>>
>> Roger
>>
>>>
>>> (I don't think it matters for the above, but I also installed the
>>> clang and gfortran version provided on CRAN's Mac "tools" page, and
>>> successfully compiled some source packages that require fortran, and
>>> others that require C).
>>>
>>> Thank again for all your work
>>> -Don
>>>
>>> --
>>> Don MacQueen
>>> Lawrence Livermore National Laboratory
>>> 7000 East Ave., L-627
>>> Livermore, CA 94550
>>> 925-423-1062
>>> Lab cell 925-724-7509
>>>
>>>
>>>
>>> On 6/8/18, 11:15 AM, "R-sig-Geo on behalf of Roger Bivand"
>>> <[hidden email] on behalf of [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
>>>
>>>    _______________________________________________
>>>    R-sig-Geo mailing list
>>>    [hidden email]
>>>    https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>>
>>>
>>
>>
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> [hidden email]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
>
> [[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
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Re: CRAN releases of sp, rgdal and rgeos

Tomislav Hengl-5

Hi Roger,

I have now managed to reinstall GDAL 2.3 and the latest versions of
rgdal and sf. These are the steps I have followed:

1. First remove existing installation of GDAL using:

sudo apt-get purge --auto-remove gdal-bin

*this also removes QGIS / anything linked with GDAL.

2. Download GDAL source code
(https://trac.osgeo.org/gdal/wiki/DownloadSource) and follow the
instructions to install from source
(https://trac.osgeo.org/gdal/wiki/BuildingOnUnix)

3. Installation from source code takes quite some time (10-15 minutes).
After that I get:

gdalinfo --version
GDAL 2.3.0, released 2018/05/04

4. Install rgdal from R-forge using e.g.:

R CMD INSTALL rgdal_1.3-3.tar.gz
* installing to library ‘/opt/microsoft/ropen/3.4.3/lib64/R/library’
* installing *source* package ‘rgdal’ ...
checking for g++... g++
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 g++ accepts -g... yes
configure: CC: gcc -std=gnu99
configure: CXX: g++
configure: rgdal: 1.3-3
checking for /usr/bin/svnversion... yes
cat: inst/SVN_VERSION: No such file or directory
configure: svn revision:
checking whether g++ supports C++11 features by default... no
checking whether g++ supports C++11 features with -std=gnu++11... yes
configure: C++11 support available
checking for gdal-config... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.3.0
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: /usr/local/share/gdal/pcs.csv readable... yes
configure: pkg-config proj exists, will use it
configure: PROJ version: 4.9.2
checking proj_api.h presence and usability... yes
checking PROJ version >= 4.8.0... yes
checking projects.h presence and usability... yes
checking PROJ.4: epsg found and readable... yes
checking PROJ.4: conus found and readable... yes
configure: Package CPP flags:  -I/usr/local/include
configure: Package LIBS:  -L/usr/local/lib -lgdal -lproj
configure: creating ./config.status

For sf I had to manually update DBI and units packages as it requires
newest versions.

So now everything works fine. Thank you!

Tom

On 06/19/2018 10:41 AM, Roger Bivand wrote:

> On Tue, 19 Jun 2018, Tomislav Hengl wrote:
>
>> Two weeks ago I installed new GDAL 2.3.* from source, then tried
>> installing rgdal and got the error about GDAL requires C++11. Then I had
>> to remove everything and reinstall GDAL 2.2. Would love to be able to
>> start using the newest GDAL inside R as it seems that many things have
>> been improved
>> (https://trac.osgeo.org/gdal/query?group=status&milestone=2.3.0).
>> Installing GDAL from source takes >20mins so next time I would like to
>> be sure that I will not have to remove GDAL.
>>
>> Can somebody point to a step-by-step guide to install GDAL 2.3.* and
>> rgdal on ubuntu (now that all packages have been updated)?
>
> Tom:
>
> There is too little information here: which g++ compiler version, was R
> installed from source or not, GDAL was installed from source, but was
> PROJ installed from source (and/or GEOS), ... and no verbatim error
> message.
>
> Please try development rgdal_1.3-3 from R-forge, which has some logic
> fixes in configure:
>
> install.packages("rgdal", repos="http://R-Forge.R-project.org")
>
> Did you check whether sf installed with GDAL 2.3.0 and PROJ 5.1.0?
>
> It looks as though CRAN devel debian is using GDAL 2.3.0 (the test saved
> output is 2.2.4):
>
> https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/rgdal-00check.html 
>
>
> Hope this helps,
>
> Roger
>
>>
>> Much appreciated!
>>
>> My session info:
>>
>> > library(rgdal)
>> Loading required package: sp
>> rgdal: version: 1.2-20, (SVN revision 725)
>>  Geospatial Data Abstraction Library extensions to R successfully loaded
>>  Loaded GDAL runtime: GDAL 2.2.2, released 2017/09/15
>>  Path to GDAL shared files: /usr/share/gdal/2.2
>>  GDAL binary built with GEOS: TRUE
>>  Loaded PROJ.4 runtime: Rel. 4.9.2, 08 September 2015, [PJ_VERSION: 492]
>>  Path to PROJ.4 shared files: (autodetected)
>>  Linking to sp version: 1.2-7
>> > sessionInfo()
>> R version 3.5.0 (2018-04-23)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 16.04.4 LTS
>>
>> Matrix products: default
>> BLAS: /opt/microsoft/ropen/3.5.0/lib64/R/lib/libRblas.so
>> LAPACK: /opt/microsoft/ropen/3.5.0/lib64/R/lib/libRlapack.so
>>
>>
>>
>> On 19.06.2018 08:47, Roger Bivand wrote:
>>> On Mon, 18 Jun 2018, MacQueen, Don wrote:
>>>
>>>> Success!
>>>>
>>>> This morning I upgraded a Mac to OS 10.13.5 (the so-called High
>>>> Sierra version), then
>>>>
>>>> - Installed R 3.5.0 from CRAN (installed ever 3.3.x)
>>>> - Installed sp 1.3-1, rgdal 1.3-2, rgeos 0.3-28, also sf 0.6-3, from
>>>> the
>>>>   CRAN binaries that are now available
>>>> - Ran my personal test suite, which exercises the kinds of tasks I
>>>>   perform with those packages
>>>>
>>>> All tests succeeded.
>>>
>>> Thanks for reporting - especially on your own test suite. We do what
>>> we can to cover typical use cases, but independent testing in
>>> production settings is reassuring for everybody. We're expecting more
>>> PROJ-based changes later this year and next year, so it is great to
>>> have external test sets to be able to check where any changes in
>>> output are coming from.
>>>
>>> This is an encouragement to other users whose production depends on R
>>> packages using GDAL, PROJ and/or GEOS to follow this example and keep
>>> a script handy to test your use cases, and a history of output files
>>> with which to compare (diff). We don't worry about changes in the EPSG
>>> versions, but by next year they may be properly anchored too (changes
>>> in PROJ may include reference system definitions with timestamps).
>>>
>>>>
>>>> I forgot to control the order of installation, so I don't know if I
>>>> installed sp first, as advised. But I expect that with the binary
>>>> versions it doesn't matter.
>>>
>>> Right, the binary builds use the sp version on the build platform.
>>>
>>> Best wishes,
>>>
>>> Roger
>>>
>>>>
>>>> (I don't think it matters for the above, but I also installed the
>>>> clang and gfortran version provided on CRAN's Mac "tools" page, and
>>>> successfully compiled some source packages that require fortran, and
>>>> others that require C).
>>>>
>>>> Thank again for all your work
>>>> -Don
>>>>
>>>> --
>>>> Don MacQueen
>>>> Lawrence Livermore National Laboratory
>>>> 7000 East Ave., L-627
>>>> Livermore, CA 94550
>>>> 925-423-1062
>>>> Lab cell 925-724-7509
>>>>
>>>>
>>>>
>>>> On 6/8/18, 11:15 AM, "R-sig-Geo on behalf of Roger Bivand"
>>>> <[hidden email] on behalf of [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
>>>>
>>>>    _______________________________________________
>>>>    R-sig-Geo mailing list
>>>>    [hidden email]
>>>>    https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>> [hidden email]
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>>
>>     [[alternative HTML version deleted]]
>>
>> _______________________________________________
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>> [hidden email]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>

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Re: CRAN releases of sp, rgdal and rgeos

Tomislav Hengl-5
Few more notes on installation of GDAL 2.3.

I was installing GDAL and rgdal on another Ubuntu machine and I
experiences multiple problems with more installations of GDAL and proj4
probably ("unable to load shared object rgdal.so" error). This is what I
realized needs to be done before installing GDAL from source:

1. Install libgdal-dev and libroj-dev (very important otherwise the
installation of rgdal will fail)

|sudo apt-get install libgdal-dev libproj-dev|

2. Download GDAL source code
(https://trac.osgeo.org/gdal/wiki/DownloadSource) and probably best
install it using the checkinstall package:

sudo apt install checkinstall

wget http://download.osgeo.org/gdal/2.3.0/gdal-2.3.0.tar.gz

tar -xvzf gdal-2.3.0.tar.gz

cd gdal-2.3.0

./configure

sudo checkinstall

*checkinstall took 20 minutes on my system, so be ready to take coffee
and relax.

3. This would build a debian package that can then be normally installed
and removed using the gdebi.

4. Install rgdal using install.packages("rgdal")

Thanks Roger for keeping everything up-to-date and stable! GDAL is the
backbone of almost any GIS project I run.

Tom


On 19.06.2018 16:57, Tomislav Hengl wrote:

>
> Hi Roger,
>
> I have now managed to reinstall GDAL 2.3 and the latest versions of
> rgdal and sf. These are the steps I have followed:
>
> 1. First remove existing installation of GDAL using:
>
> sudo apt-get purge --auto-remove gdal-bin
>
> *this also removes QGIS / anything linked with GDAL.
>
> 2. Download GDAL source code
> (https://trac.osgeo.org/gdal/wiki/DownloadSource) and follow the
> instructions to install from source
> (https://trac.osgeo.org/gdal/wiki/BuildingOnUnix)
>
> 3. Installation from source code takes quite some time (10-15
> minutes). After that I get:
>
> gdalinfo --version
> GDAL 2.3.0, released 2018/05/04
>
> 4. Install rgdal from R-forge using e.g.:
>
> R CMD INSTALL rgdal_1.3-3.tar.gz
> * installing to library ‘/opt/microsoft/ropen/3.4.3/lib64/R/library’
> * installing *source* package ‘rgdal’ ...
> checking for g++... g++
> 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 g++ accepts -g... yes
> configure: CC: gcc -std=gnu99
> configure: CXX: g++
> configure: rgdal: 1.3-3
> checking for /usr/bin/svnversion... yes
> cat: inst/SVN_VERSION: No such file or directory
> configure: svn revision:
> checking whether g++ supports C++11 features by default... no
> checking whether g++ supports C++11 features with -std=gnu++11... yes
> configure: C++11 support available
> checking for gdal-config... /usr/local/bin/gdal-config
> checking gdal-config usability... yes
> configure: GDAL: 2.3.0
> 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: /usr/local/share/gdal/pcs.csv readable... yes
> configure: pkg-config proj exists, will use it
> configure: PROJ version: 4.9.2
> checking proj_api.h presence and usability... yes
> checking PROJ version >= 4.8.0... yes
> checking projects.h presence and usability... yes
> checking PROJ.4: epsg found and readable... yes
> checking PROJ.4: conus found and readable... yes
> configure: Package CPP flags:  -I/usr/local/include
> configure: Package LIBS:  -L/usr/local/lib -lgdal -lproj
> configure: creating ./config.status
>
> For sf I had to manually update DBI and units packages as it requires
> newest versions.
>
> So now everything works fine. Thank you!
>
> Tom
>
> On 06/19/2018 10:41 AM, Roger Bivand wrote:
>> On Tue, 19 Jun 2018, Tomislav Hengl wrote:
>>
>>> Two weeks ago I installed new GDAL 2.3.* from source, then tried
>>> installing rgdal and got the error about GDAL requires C++11. Then I
>>> had
>>> to remove everything and reinstall GDAL 2.2. Would love to be able to
>>> start using the newest GDAL inside R as it seems that many things have
>>> been improved
>>> (https://trac.osgeo.org/gdal/query?group=status&milestone=2.3.0).
>>> Installing GDAL from source takes >20mins so next time I would like to
>>> be sure that I will not have to remove GDAL.
>>>
>>> Can somebody point to a step-by-step guide to install GDAL 2.3.* and
>>> rgdal on ubuntu (now that all packages have been updated)?
>>
>> Tom:
>>
>> There is too little information here: which g++ compiler version, was
>> R installed from source or not, GDAL was installed from source, but
>> was PROJ installed from source (and/or GEOS), ... and no verbatim
>> error message.
>>
>> Please try development rgdal_1.3-3 from R-forge, which has some logic
>> fixes in configure:
>>
>> install.packages("rgdal", repos="http://R-Forge.R-project.org")
>>
>> Did you check whether sf installed with GDAL 2.3.0 and PROJ 5.1.0?
>>
>> It looks as though CRAN devel debian is using GDAL 2.3.0 (the test
>> saved output is 2.2.4):
>>
>> https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/rgdal-00check.html 
>>
>>
>> Hope this helps,
>>
>> Roger
>>
>>>
>>> Much appreciated!
>>>
>>> My session info:
>>>
>>> > library(rgdal)
>>> Loading required package: sp
>>> rgdal: version: 1.2-20, (SVN revision 725)
>>>  Geospatial Data Abstraction Library extensions to R successfully
>>> loaded
>>>  Loaded GDAL runtime: GDAL 2.2.2, released 2017/09/15
>>>  Path to GDAL shared files: /usr/share/gdal/2.2
>>>  GDAL binary built with GEOS: TRUE
>>>  Loaded PROJ.4 runtime: Rel. 4.9.2, 08 September 2015, [PJ_VERSION:
>>> 492]
>>>  Path to PROJ.4 shared files: (autodetected)
>>>  Linking to sp version: 1.2-7
>>> > sessionInfo()
>>> R version 3.5.0 (2018-04-23)
>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>> Running under: Ubuntu 16.04.4 LTS
>>>
>>> Matrix products: default
>>> BLAS: /opt/microsoft/ropen/3.5.0/lib64/R/lib/libRblas.so
>>> LAPACK: /opt/microsoft/ropen/3.5.0/lib64/R/lib/libRlapack.so
>>>
>>>
>>>
>>> On 19.06.2018 08:47, Roger Bivand wrote:
>>>> On Mon, 18 Jun 2018, MacQueen, Don wrote:
>>>>
>>>>> Success!
>>>>>
>>>>> This morning I upgraded a Mac to OS 10.13.5 (the so-called High
>>>>> Sierra version), then
>>>>>
>>>>> - Installed R 3.5.0 from CRAN (installed ever 3.3.x)
>>>>> - Installed sp 1.3-1, rgdal 1.3-2, rgeos 0.3-28, also sf 0.6-3,
>>>>> from the
>>>>>   CRAN binaries that are now available
>>>>> - Ran my personal test suite, which exercises the kinds of tasks I
>>>>>   perform with those packages
>>>>>
>>>>> All tests succeeded.
>>>>
>>>> Thanks for reporting - especially on your own test suite. We do what
>>>> we can to cover typical use cases, but independent testing in
>>>> production settings is reassuring for everybody. We're expecting more
>>>> PROJ-based changes later this year and next year, so it is great to
>>>> have external test sets to be able to check where any changes in
>>>> output are coming from.
>>>>
>>>> This is an encouragement to other users whose production depends on R
>>>> packages using GDAL, PROJ and/or GEOS to follow this example and keep
>>>> a script handy to test your use cases, and a history of output files
>>>> with which to compare (diff). We don't worry about changes in the EPSG
>>>> versions, but by next year they may be properly anchored too (changes
>>>> in PROJ may include reference system definitions with timestamps).
>>>>
>>>>>
>>>>> I forgot to control the order of installation, so I don't know if I
>>>>> installed sp first, as advised. But I expect that with the binary
>>>>> versions it doesn't matter.
>>>>
>>>> Right, the binary builds use the sp version on the build platform.
>>>>
>>>> Best wishes,
>>>>
>>>> Roger
>>>>
>>>>>
>>>>> (I don't think it matters for the above, but I also installed the
>>>>> clang and gfortran version provided on CRAN's Mac "tools" page, and
>>>>> successfully compiled some source packages that require fortran, and
>>>>> others that require C).
>>>>>
>>>>> Thank again for all your work
>>>>> -Don
>>>>>
>>>>> --
>>>>> Don MacQueen
>>>>> Lawrence Livermore National Laboratory
>>>>> 7000 East Ave., L-627
>>>>> Livermore, CA 94550
>>>>> 925-423-1062
>>>>> Lab cell 925-724-7509
>>>>>
>>>>>
>>>>>
>>>>> On 6/8/18, 11:15 AM, "R-sig-Geo on behalf of Roger Bivand"
>>>>> <[hidden email] on behalf of [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
>>>>>
>>>>>    _______________________________________________
>>>>>    R-sig-Geo mailing list
>>>>>    [hidden email]
>>>>>    https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> R-sig-Geo mailing list
>>>> [hidden email]
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>>
>>>     [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>> [hidden email]
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>

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