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

Veronica Andreo vero@ndreo @end|ng |rom gm@||@com
Sun Jun 28 19:30:29 CEST 2020 

El dom., 28 jun. 2020 a las 19:20, Roger Bivand (<Roger.Bivand using nhh.no>)
escribió:

> On Sun, 28 Jun 2020, Veronica Andreo wrote:
>
> > 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
>
> Please try install.packages("rgdal", repos="http://R-Forge.R-project.org",
>
> configure.args="--disable-loadflags") to be sure to get the current
> version.
>

Yes, this works! rgdal is installed properly now :)
I didn't understand how to properly specify the command before, apologies.
And many thanks!!!

Vero


> Roger
>
> >
> > 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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> >
> > _______________________________________________
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> > 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: 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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