Hi all, Following some updates to R that I received via Synaptic Package Manager on Ubuntu 16.04 (looks like I now have R 3.4.4-1xenial0), I have been unable to reinstall rgdal, and I need help. Initially I was getting error messages about dependencies on GDAL 1.11.4, but after following instructions to install GDAL from source (into my /usr/local directory) I'm now getting a different set of error messages (see the output error messages posted below my signature). I can't tell if this means that I've made a mistake installing GDAL or if there's some other problem with my setup/configuration. I really need rgdal for the analyses I do in R and could use some help figuring this out. Thanks, Alex> install.packages("rgdal")Installing package into ?/home/athorn/R/x86_64-pc-linux-gnu-library/3.4? (as ?lib? is unspecified) trying URL 'https://cloud.r-project.org/src/contrib/rgdal_1.3-4.tar.gz' Content type 'application/x-gzip' length 1664774 bytes (1.6 MB) =================================================downloaded 1.6 MB * installing *source* package ?rgdal? ... ** package ?rgdal? successfully unpacked and MD5 sums checked configure: R_HOME: /usr/lib/R configure: CC: gcc -std=gnu99 configure: CXX: g++ configure: C++11 support available configure: rgdal: 1.3-4 checking for /usr/bin/svnversion... no configure: svn revision: 766 checking for gdal-config... /usr/local/bin/gdal-config checking gdal-config usability... yes configure: GDAL: 2.3.1 checking C++11 support for GDAL >= 2.3.0... yes checking GDAL version >= 1.11.4... yes checking gdal: linking with --libs only... no checking gdal: linking with --libs and --dep-libs... no In file included from /usr/local/include/gdal.h:45:0, from gdal_test.cc:1: /usr/local/include/cpl_port.h:187:6: error: #error Must have C++11 or newer. # error Must have C++11 or newer. ^ In file included from /usr/local/include/gdal.h:49:0, from gdal_test.cc:1: /usr/local/include/cpl_minixml.h:202:47: error: expected template-name before '<' token class CPLXMLTreeCloser: public std::unique_ptr<CPLXMLNode, CPLXMLTreeCloserDeleter> ^ /usr/local/include/cpl_minixml.h:202:47: error: expected '{' before '<' token /usr/local/include/cpl_minixml.h:202:47: error: expected unqualified-id before '<' token In file included from /usr/local/include/ogr_api.h:45:0, from /usr/local/include/gdal.h:50, from gdal_test.cc:1: /usr/local/include/ogr_core.h:79:28: error: expected '}' before end of line /usr/local/include/ogr_core.h:79:28: error: expected declaration before end of line In file included from /usr/local/include/gdal.h:45:0, from gdal_test.cc:1: /usr/local/include/cpl_port.h:187:6: error: #error Must have C++11 or newer. # error Must have C++11 or newer. ^ In file included from /usr/local/include/gdal.h:49:0, from gdal_test.cc:1: /usr/local/include/cpl_minixml.h:202:47: error: expected template-name before '<' token class CPLXMLTreeCloser: public std::unique_ptr<CPLXMLNode, CPLXMLTreeCloserDeleter> ^ /usr/local/include/cpl_minixml.h:202:47: error: expected '{' before '<' token /usr/local/include/cpl_minixml.h:202:47: error: expected unqualified-id before '<' token In file included from /usr/local/include/ogr_api.h:45:0, from /usr/local/include/gdal.h:50, from gdal_test.cc:1: /usr/local/include/ogr_core.h:79:28: error: expected '}' before end of line /usr/local/include/ogr_core.h:79:28: error: expected declaration before end of line configure: Install failure: compilation and/or linkage problems. configure: error: GDALAllRegister not found in libgdal. ERROR: configuration failed for package ?rgdal? * removing ?/home/athorn/R/x86_64-pc-linux-gnu-library/3.4/rgdal? The downloaded source packages are in ?/tmp/RtmpeuSDnj/downloaded_packages? Warning message: In install.packages("rgdal") : installation of package ?rgdal? had non-zero exit status>
Hi Alex, I don't use Ubuntu, but if I saw that error message I would upgrade my C++ compiler and try again. With luck, this is what caused the cascade of errors beneath it. Jim On Fri, Aug 10, 2018 at 1:36 AM, Alexandra Thorn <mail at alexandrathorn.com> wrote:> Hi all, > > Following some updates to R that I received via Synaptic Package > Manager on Ubuntu 16.04 (looks like I now have R 3.4.4-1xenial0), I > have been unable to reinstall rgdal, and I need help. > > Initially I was getting error messages about dependencies on GDAL > 1.11.4, but after following instructions to install GDAL from source > (into my /usr/local directory) I'm now getting a different set of error > messages (see the output error messages posted below my signature). > > I can't tell if this means that I've made a mistake installing GDAL or > if there's some other problem with my setup/configuration. I really > need rgdal for the analyses I do in R and could use some help figuring > this out. > > Thanks, > Alex > >> install.packages("rgdal") > Installing package into ?/home/athorn/R/x86_64-pc-linux-gnu-library/3.4? > (as ?lib? is unspecified) > trying URL 'https://cloud.r-project.org/src/contrib/rgdal_1.3-4.tar.gz' > Content type 'application/x-gzip' length 1664774 bytes (1.6 MB) > =================================================> downloaded 1.6 MB > > * installing *source* package ?rgdal? ... > ** package ?rgdal? successfully unpacked and MD5 sums checked > configure: R_HOME: /usr/lib/R > configure: CC: gcc -std=gnu99 > configure: CXX: g++ > configure: C++11 support available > configure: rgdal: 1.3-4 > checking for /usr/bin/svnversion... no > configure: svn revision: 766 > checking for gdal-config... /usr/local/bin/gdal-config > checking gdal-config usability... yes > configure: GDAL: 2.3.1 > checking C++11 support for GDAL >= 2.3.0... yes > checking GDAL version >= 1.11.4... yes > checking gdal: linking with --libs only... no > checking gdal: linking with --libs and --dep-libs... no > In file included from /usr/local/include/gdal.h:45:0, > from gdal_test.cc:1: > /usr/local/include/cpl_port.h:187:6: error: #error Must have C++11 or > newer. # error Must have C++11 or newer. > ^ > In file included from /usr/local/include/gdal.h:49:0, > from gdal_test.cc:1: > /usr/local/include/cpl_minixml.h:202:47: error: expected template-name > before '<' token class CPLXMLTreeCloser: public > std::unique_ptr<CPLXMLNode, CPLXMLTreeCloserDeleter> ^ > /usr/local/include/cpl_minixml.h:202:47: error: expected '{' before '<' > token /usr/local/include/cpl_minixml.h:202:47: error: expected > unqualified-id before '<' token In file included > from /usr/local/include/ogr_api.h:45:0, > from /usr/local/include/gdal.h:50, from gdal_test.cc:1: > /usr/local/include/ogr_core.h:79:28: error: expected '}' before end of > line /usr/local/include/ogr_core.h:79:28: error: expected declaration > before end of line In file included > from /usr/local/include/gdal.h:45:0, from gdal_test.cc:1: > /usr/local/include/cpl_port.h:187:6: error: #error Must have C++11 or > newer. # error Must have C++11 or newer. > ^ > In file included from /usr/local/include/gdal.h:49:0, > from gdal_test.cc:1: > /usr/local/include/cpl_minixml.h:202:47: error: expected template-name > before '<' token class CPLXMLTreeCloser: public > std::unique_ptr<CPLXMLNode, CPLXMLTreeCloserDeleter> ^ > /usr/local/include/cpl_minixml.h:202:47: error: expected '{' before '<' > token /usr/local/include/cpl_minixml.h:202:47: error: expected > unqualified-id before '<' token In file included > from /usr/local/include/ogr_api.h:45:0, > from /usr/local/include/gdal.h:50, from gdal_test.cc:1: > /usr/local/include/ogr_core.h:79:28: error: expected '}' before end of > line /usr/local/include/ogr_core.h:79:28: error: expected declaration > before end of line configure: Install failure: compilation and/or > linkage problems. configure: error: GDALAllRegister not found in > libgdal. ERROR: configuration failed for package ?rgdal? > * removing ?/home/athorn/R/x86_64-pc-linux-gnu-library/3.4/rgdal? > > The downloaded source packages are in > ?/tmp/RtmpeuSDnj/downloaded_packages? > Warning message: > In install.packages("rgdal") : > installation of package ?rgdal? had non-zero exit status >> > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
There are quite a few messages on R-sig-geo about installing rgdal on Ubuntu.
Maybe one of them contains your solution?
(I use Mac, so can't help directly)
-Don
--
Don MacQueen
Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062
Lab cell 925-724-7509
?On 8/9/18, 8:36 AM, "R-help on behalf of Alexandra Thorn"
<r-help-bounces at r-project.org on behalf of mail at alexandrathorn.com>
wrote:
Hi all,
Following some updates to R that I received via Synaptic Package
Manager on Ubuntu 16.04 (looks like I now have R 3.4.4-1xenial0), I
have been unable to reinstall rgdal, and I need help.
Initially I was getting error messages about dependencies on GDAL
1.11.4, but after following instructions to install GDAL from source
(into my /usr/local directory) I'm now getting a different set of error
messages (see the output error messages posted below my signature).
I can't tell if this means that I've made a mistake installing GDAL
or
if there's some other problem with my setup/configuration. I really
need rgdal for the analyses I do in R and could use some help figuring
this out.
Thanks,
Alex
> install.packages("rgdal")
Installing package into ?/home/athorn/R/x86_64-pc-linux-gnu-library/3.4?
(as ?lib? is unspecified)
trying URL
'https://cloud.r-project.org/src/contrib/rgdal_1.3-4.tar.gz'
Content type 'application/x-gzip' length 1664774 bytes (1.6 MB)
================================================= downloaded 1.6 MB
* installing *source* package ?rgdal? ...
** package ?rgdal? successfully unpacked and MD5 sums checked
configure: R_HOME: /usr/lib/R
configure: CC: gcc -std=gnu99
configure: CXX: g++
configure: C++11 support available
configure: rgdal: 1.3-4
checking for /usr/bin/svnversion... no
configure: svn revision: 766
checking for gdal-config... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.3.1
checking C++11 support for GDAL >= 2.3.0... yes
checking GDAL version >= 1.11.4... yes
checking gdal: linking with --libs only... no
checking gdal: linking with --libs and --dep-libs... no
In file included from /usr/local/include/gdal.h:45:0,
from gdal_test.cc:1:
/usr/local/include/cpl_port.h:187:6: error: #error Must have C++11 or
newer. # error Must have C++11 or newer.
^
In file included from /usr/local/include/gdal.h:49:0,
from gdal_test.cc:1:
/usr/local/include/cpl_minixml.h:202:47: error: expected template-name
before '<' token class CPLXMLTreeCloser: public
std::unique_ptr<CPLXMLNode, CPLXMLTreeCloserDeleter> ^
/usr/local/include/cpl_minixml.h:202:47: error: expected '{' before
'<'
token /usr/local/include/cpl_minixml.h:202:47: error: expected
unqualified-id before '<' token In file included
from /usr/local/include/ogr_api.h:45:0,
from /usr/local/include/gdal.h:50, from gdal_test.cc:1:
/usr/local/include/ogr_core.h:79:28: error: expected '}' before end
of
line /usr/local/include/ogr_core.h:79:28: error: expected declaration
before end of line In file included
from /usr/local/include/gdal.h:45:0, from gdal_test.cc:1:
/usr/local/include/cpl_port.h:187:6: error: #error Must have C++11 or
newer. # error Must have C++11 or newer.
^
In file included from /usr/local/include/gdal.h:49:0,
from gdal_test.cc:1:
/usr/local/include/cpl_minixml.h:202:47: error: expected template-name
before '<' token class CPLXMLTreeCloser: public
std::unique_ptr<CPLXMLNode, CPLXMLTreeCloserDeleter> ^
/usr/local/include/cpl_minixml.h:202:47: error: expected '{' before
'<'
token /usr/local/include/cpl_minixml.h:202:47: error: expected
unqualified-id before '<' token In file included
from /usr/local/include/ogr_api.h:45:0,
from /usr/local/include/gdal.h:50, from gdal_test.cc:1:
/usr/local/include/ogr_core.h:79:28: error: expected '}' before end
of
line /usr/local/include/ogr_core.h:79:28: error: expected declaration
before end of line configure: Install failure: compilation and/or
linkage problems. configure: error: GDALAllRegister not found in
libgdal. ERROR: configuration failed for package ?rgdal?
* removing ?/home/athorn/R/x86_64-pc-linux-gnu-library/3.4/rgdal?
The downloaded source packages are in
?/tmp/RtmpeuSDnj/downloaded_packages?
Warning message:
In install.packages("rgdal") :
installation of package ?rgdal? had non-zero exit status
>
______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Or ask on R-sig-debian... On August 9, 2018 3:13:38 PM PDT, "MacQueen, Don via R-help" <r-help at r-project.org> wrote:>There are quite a few messages on R-sig-geo about installing rgdal on >Ubuntu. Maybe one of them contains your solution? >(I use Mac, so can't help directly) > >-Don > >-- >Don MacQueen >Lawrence Livermore National Laboratory >7000 East Ave., L-627 >Livermore, CA 94550 >925-423-1062 >Lab cell 925-724-7509 > > > >?On 8/9/18, 8:36 AM, "R-help on behalf of Alexandra Thorn" ><r-help-bounces at r-project.org on behalf of mail at alexandrathorn.com> >wrote: > > Hi all, > > Following some updates to R that I received via Synaptic Package > Manager on Ubuntu 16.04 (looks like I now have R 3.4.4-1xenial0), I > have been unable to reinstall rgdal, and I need help. > > Initially I was getting error messages about dependencies on GDAL > 1.11.4, but after following instructions to install GDAL from source >(into my /usr/local directory) I'm now getting a different set of error > messages (see the output error messages posted below my signature). > > I can't tell if this means that I've made a mistake installing GDAL or > if there's some other problem with my setup/configuration. I really > need rgdal for the analyses I do in R and could use some help figuring > this out. > > Thanks, > Alex > > > install.packages("rgdal") >Installing package into >?/home/athorn/R/x86_64-pc-linux-gnu-library/3.4? > (as ?lib? is unspecified) >trying URL 'https://cloud.r-project.org/src/contrib/rgdal_1.3-4.tar.gz' > Content type 'application/x-gzip' length 1664774 bytes (1.6 MB) > =================================================> downloaded 1.6 MB > > * installing *source* package ?rgdal? ... > ** package ?rgdal? successfully unpacked and MD5 sums checked > configure: R_HOME: /usr/lib/R > configure: CC: gcc -std=gnu99 > configure: CXX: g++ > configure: C++11 support available > configure: rgdal: 1.3-4 > checking for /usr/bin/svnversion... no > configure: svn revision: 766 > checking for gdal-config... /usr/local/bin/gdal-config > checking gdal-config usability... yes > configure: GDAL: 2.3.1 > checking C++11 support for GDAL >= 2.3.0... yes > checking GDAL version >= 1.11.4... yes > checking gdal: linking with --libs only... no > checking gdal: linking with --libs and --dep-libs... no > In file included from /usr/local/include/gdal.h:45:0, > from gdal_test.cc:1: > /usr/local/include/cpl_port.h:187:6: error: #error Must have C++11 or > newer. # error Must have C++11 or newer. > ^ > In file included from /usr/local/include/gdal.h:49:0, > from gdal_test.cc:1: > /usr/local/include/cpl_minixml.h:202:47: error: expected template-name > before '<' token class CPLXMLTreeCloser: public > std::unique_ptr<CPLXMLNode, CPLXMLTreeCloserDeleter> ^ >/usr/local/include/cpl_minixml.h:202:47: error: expected '{' before '<' > token /usr/local/include/cpl_minixml.h:202:47: error: expected > unqualified-id before '<' token In file included > from /usr/local/include/ogr_api.h:45:0, > from /usr/local/include/gdal.h:50, from gdal_test.cc:1: > /usr/local/include/ogr_core.h:79:28: error: expected '}' before end of > line /usr/local/include/ogr_core.h:79:28: error: expected declaration > before end of line In file included > from /usr/local/include/gdal.h:45:0, from gdal_test.cc:1: > /usr/local/include/cpl_port.h:187:6: error: #error Must have C++11 or > newer. # error Must have C++11 or newer. > ^ > In file included from /usr/local/include/gdal.h:49:0, > from gdal_test.cc:1: > /usr/local/include/cpl_minixml.h:202:47: error: expected template-name > before '<' token class CPLXMLTreeCloser: public > std::unique_ptr<CPLXMLNode, CPLXMLTreeCloserDeleter> ^ >/usr/local/include/cpl_minixml.h:202:47: error: expected '{' before '<' > token /usr/local/include/cpl_minixml.h:202:47: error: expected > unqualified-id before '<' token In file included > from /usr/local/include/ogr_api.h:45:0, > from /usr/local/include/gdal.h:50, from gdal_test.cc:1: > /usr/local/include/ogr_core.h:79:28: error: expected '}' before end of > line /usr/local/include/ogr_core.h:79:28: error: expected declaration > before end of line configure: Install failure: compilation and/or > linkage problems. configure: error: GDALAllRegister not found in > libgdal. ERROR: configuration failed for package ?rgdal? > * removing ?/home/athorn/R/x86_64-pc-linux-gnu-library/3.4/rgdal? > > The downloaded source packages are in > ?/tmp/RtmpeuSDnj/downloaded_packages? > Warning message: > In install.packages("rgdal") : > installation of package ?rgdal? had non-zero exit status > > > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide >http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > >______________________________________________ >R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide >http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code.-- Sent from my phone. Please excuse my brevity.