[R-sig-Geo] cannot install rgdal after updating to fedora32
Erwan LE PENNEC
|epennec @end|ng |rom gm@||@com
Sun Jun 28 15:46:00 CEST 2020
Using the new --disable-loadflags in install.packages:
install.packages("rgdal_1.5-13.tar.gz", repos = NULL, type = "source",
configure.args = "--disable-loadflags")
should solve the issue.
Erwan
On Sun, Jun 28, 2020 at 3:42 PM Veronica Andreo <veroandreo using gmail.com>
wrote:
> Dear Roger,
>
> Thanks for the answer.
>
> R is installed from Fedora repos and no, I do not have any issues with sf.
> It installs and loads just fine.
>
> I downloaded the new rgdal tar.gz from R-forge, but I get the same error
> that was reported yesterday; config.log file attached. The first error I
> see there is in line 98-99 about a -V not recognized and then another one
> for -qversion. Are those relevant?
>
> Vero
> ---
> install.packages("~/Downloads/rgdal_1.5-13.tar.gz", repos = NULL, type =
> "source")
> Installing package into
> ‘/home/veroandreo/R/x86_64-redhat-linux-gnu-library/3.6’
> (as ‘lib’ is unspecified)
> * installing *source* package ‘rgdal’ ...
> ** using staged installation
> configure: R_HOME: /usr/lib64/R
> configure: CC: gcc -m64
> configure: CXX: g++ -m64 -std=gnu++11
> configure: CFLAGS: -O2 -g -pipe -Wall -Werror=format-security
> -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions
> -fstack-protector-strong -grecord-gcc-switches
> -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1
> -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic
> -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection
> configure: CPPFLAGS: -I/usr/local/include
> configure: LDFLAGS: -Wl,-z,relro -Wl,--as-needed -Wl,-z,now
> -specs=/usr/lib/rpm/redhat/redhat-hardened-ld
> loadflags: yes
> configure: LDFLAGS: -Wl,-z,relro -Wl,--as-needed -Wl,-z,now
> -specs=/usr/lib/rpm/redhat/redhat-hardened-ld
> configure: CXX11 is: g++ -m64, CXX11STD is: -std=gnu++11
> configure: CXX is: g++ -m64 -std=gnu++11
> configure: C++11 support available
> configure: rgdal: 1.5-13
> checking for /usr/bin/svnversion... yes
> cat: inst/SVN_VERSION: No such file or directory
> configure: svn revision:
> checking for gdal-config... /usr/bin/gdal-config
> checking gdal-config usability... yes
> configure: GDAL: 3.0.4
> checking GDAL version >= 1.11.4... yes
> checking GDAL version <= 2.5 or >= 3.0... yes
> checking GDAL: linking with --libs only... yes
> checking GDAL: gdal-config data directory readable... yes
> checking GDAL: /usr/share/gdal/stateplane.csv readable... yes
> configure: pkg-config proj exists, will use it
> configure: PROJ version: 6.3.2
> configure: PROJ CPP flags: -DPROJ_H_API
> configure: PROJ LIBS: -lproj
> checking PROJ header API:... yes
> 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... configure: error: in
> `/home/veroandreo/tmp/Rtmp9DsGuk/R.INSTALL16352f5a74a/rgdal':
> configure: error: cannot run C++ compiled programs.
> If you meant to cross compile, use `--host'.
> See `config.log' for more details
> ERROR: configuration failed for package ‘rgdal’
> * removing ‘/home/veroandreo/R/x86_64-redhat-linux-gnu-library/3.6/rgdal’
> Warning in install.packages :
> installation of package ‘/home/veroandreo/Downloads/rgdal_1.5-13.tar.gz’
> had non-zero exit status
>
>
>
> El dom., 28 jun. 2020 a las 14:44, Roger Bivand (<Roger.Bivand using nhh.no>)
> escribió:
>
>> On Sun, 28 Jun 2020, Roger Bivand wrote:
>>
>> > Vero,
>> >
>> > On Sat, 27 Jun 2020, Veronica Andreo wrote:
>> >
>> >> See the attached config.log file
>> >>
>> >
>> > How did you install R itself? If an rpm, then
>> >
>> > https://github.com/r-spatial/sf/issues/1369
>> >
>> > may be relevant, also if you see errors installing sf. You would need
>> to
>> > unset LDFLAGS before installing:
>> >
>> > https://github.com/r-spatial/sf/issues/1369#issuecomment-614096865
>> >
>> > Please report back on this.
>>
>> LDFLAGS needs unsetting. Revision 1020 on R-Forge
>>
>> https://r-forge.r-project.org/R/?group_id=884
>>
>> includes a new configure argument --disable-loadflags to assist in
>> unsetting the very specific R rpm LDFLAGS. Please report if this fixes
>> the
>> problem.
>>
>> Roger
>>
>>
>> >
>> > Roger
>> >
>> >> El sáb., 27 jun. 2020 a las 21:29, Veronica Andreo
>> >> (<veroandreo using gmail.com>)
>> >> escribió:
>> >>
>> >>> Hello everyone
>> >>>
>> >>> I have just updated my system to fedora 32 (which fetched GDAL 3 and
>> PROJ
>> >>> 6) and when updating my R packages, I get the following error for
>> rgdal.
>> >>> Can someone help me out here? What does it mean that it cannot run
>> C++
>> >>> compiled programs? And do I want to crosscompile?
>> >>>
>> >>> Thanks much in advance
>> >>>
>> >>> Vero
>> >>>
>> >>> ---
>> >>>
>> >>> install.packages("rgdal")
>> >>> Installing package into
>> >>> ‘/home/veroandreo/R/x86_64-redhat-linux-gnu-library/3.6’
>> >>> (as ‘lib’ is unspecified)
>> >>> trying URL 'http://cran.rstudio.com/src/contrib/rgdal_1.5-12.tar.gz'
>> >>> Content type 'application/x-gzip' length 2302403 bytes (2.2 MB)
>> >>> ==================================================
>> >>> downloaded 2.2 MB
>> >>>
>> >>> * installing *source* package ‘rgdal’ ...
>> >>> ** package ‘rgdal’ successfully unpacked and MD5 sums checked
>> >>> ** using staged installation
>> >>> configure: R_HOME: /usr/lib64/R
>> >>> configure: CC: gcc -m64
>> >>> configure: CXX: g++ -m64 -std=gnu++11
>> >>> configure: CXX11 is: g++ -m64, CXX11STD is: -std=gnu++11
>> >>> configure: CXX is: g++ -m64 -std=gnu++11
>> >>> configure: C++11 support available
>> >>> configure: rgdal: 1.5-12
>> >>> checking for /usr/bin/svnversion... yes
>> >>> configure: svn revision: 1018
>> >>> checking for gdal-config... /usr/bin/gdal-config
>> >>> checking gdal-config usability... yes
>> >>> configure: GDAL: 3.0.4
>> >>> checking GDAL version >= 1.11.4... yes
>> >>> checking GDAL version <= 2.5 or >= 3.0... yes
>> >>> checking GDAL: linking with --libs only... yes
>> >>> checking GDAL: gdal-config data directory readable... yes
>> >>> checking GDAL: /usr/share/gdal/stateplane.csv readable... yes
>> >>> configure: pkg-config proj exists, will use it
>> >>> configure: PROJ version: 6.3.2
>> >>> configure: PROJ CPP flags: -DPROJ_H_API
>> >>> configure: PROJ LIBS: -lproj
>> >>> checking PROJ header API:... yes
>> >>> 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... configure: error: in
>> >>> `/home/veroandreo/tmp/Rtmpo7AtPr/R.INSTALL12cc66f8f895/rgdal':
>> >>> configure: error: cannot run C++ compiled programs. <<<<--- here
>> >>> If you meant to cross compile, use `--host'.
>> >>> See `config.log' for more details
>> >>> ERROR: configuration failed for package ‘rgdal’
>> >>> * removing
>> ‘/home/veroandreo/R/x86_64-redhat-linux-gnu-library/3.6/rgdal’
>> >>> * restoring previous
>> >>> ‘/home/veroandreo/R/x86_64-redhat-linux-gnu-library/3.6/rgdal’
>> >>> Warning in install.packages :
>> >>> installation of package ‘rgdal’ had non-zero exit status
>> >>>
>> >>> ---
>> >>>
>> >>> sessionInfo()
>> >>> R version 3.6.3 (2020-02-29)
>> >>> Platform: x86_64-redhat-linux-gnu (64-bit)
>> >>> Running under: Fedora 32 (Thirty Two)
>> >>>
>> >>> Matrix products: default
>> >>> BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.9.so
>> >>>
>> >>> Random number generation:
>> >>> RNG: Mersenne-Twister
>> >>> Normal: Inversion
>> >>> Sample: Rounding
>> >>>
>> >>> locale:
>> >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>> >>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>> >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> >>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>> >>>
>> >>> attached base packages:
>> >>> [1] stats graphics grDevices utils datasets methods base
>> >>>
>> >>> loaded via a namespace (and not attached):
>> >>> [1] compiler_3.6.3 tools_3.6.3
>> >>>
>> >>
>> >
>> >
>>
>> --
>> Roger Bivand
>> Department of Economics, Norwegian School of Economics,
>> Helleveien 30, N-5045 Bergen, Norway.
>> voice: +47 55 95 93 55; e-mail: Roger.Bivand using nhh.no
>> https://orcid.org/0000-0003-2392-6140
>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>
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