[R-sig-Geo] cannot install rgdal after updating to fedora32

Veronica Andreo vero@ndreo @end|ng |rom gm@||@com
Sun Jun 28 15:41:39 CEST 2020 

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://stat.ethz.ch/pipermail/r-sig-geo/attachments/20200628/d2e3eca7/attachment.html>

-------------- next part --------------
A non-text attachment was scrubbed...
Name: config.log
Type: text/x-log
Size: 8624 bytes
Desc: not available
URL: <https://stat.ethz.ch/pipermail/r-sig-geo/attachments/20200628/d2e3eca7/attachment.bin>

More information about the R-sig-Geo mailing list