[R-sig-Geo] cannot install rgdal after updating to fedora32
Veronica Andreo
vero@ndreo @end|ng |rom gm@||@com
Sun Jun 28 19:08:02 CEST 2020
Hi Bennet,
[cc-ing the list too]
Thanks for the explanations about the config.log file
I tried with your suggestion, but the error still appears as originally
reported
Best,
Vero
El dom., 28 jun. 2020 a las 17:00, Bennet Fauber (<bennet using umich.edu>)
escribió:
> Hi, Vero,
>
> Your Fedora is using GCC version 10, which is newer and may have
> changed options. Just to help you with reading the config.log, this
> is the part that matters here.
>
> #--- The following line is the command that configure is actually running
> configure:3006: g++ -m64 -std=gnu++11 -o conftest
> -I/usr/local/include -DPROJ_H_API -Wl,-z,relro -Wl,--as-needed
> -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld conftest.cpp
> -lproj -L/usr/lib64 -lgdal >&5/usr/bin/ld: /home/veroandreo
>
> #--- This is the error that it generated
> /tmp/ccNranTE.o: relocation R_X86_64_32 against `.rodata' can not be
> used when making a PIE object; recompile with -fPIE
>
> #--- This is configure telling you that an error occured, but not what it
> is
> collect2: error: ld returned 1 exit status
>
> #--- If the g++ command had succeeded, there would be a program file
> called 'conftest' that it could run
> configure:3017: ./conftest
> configure: line 3019: ./conftest: No such file or directory
>
> I will take a wild stab in the dark and suggest you try
>
> > install.packages('rgdal', configure.vars=c("CXXFLAGS=-no-pie"))
>
>
>
> On Sun, Jun 28, 2020 at 9:42 AM 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
> >
> > _______________________________________________
> > R-sig-Geo mailing list
> > R-sig-Geo using r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
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