[R-sig-Geo] cannot install rgdal after updating to fedora32
Bennet Fauber
bennet @end|ng |rom um|ch@edu
Sun Jun 28 20:35:33 CEST 2020
Vero, Ista, and Roger,
I used Ista's help to get a Docker container in which I could try this.
Yes, there does seem to be something wrong with the R packages for
Fedora 32, as I am also getting this when installing packages (not
just rgdal)
Warning in file.create(f.tg) :
cannot create file '/usr/share/doc/R/html/packages.html', reason 'No
such file or directory'
Warning in utils::make.packages.html(.Library, docdir = R.home("doc")) :
cannot update HTML package index
I believe that they (Fedora) also did not include building the HTML
documentation for R.
The particular LDFLAG that is causing the issue seems to be this one,
LDFLAGS='-specs=/usr/lib/rpm/redhat/redhat-hardened-ld'
as that fails with the same message, but using all the others (the
following line used the additional printing of LDFLAGS, thank you
Roger!), as in the following,
install.packages('rgdal', repos="https://R-Forge.R-project.org",
configure.vars=c("LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now'"))
does work. I don't know if that helps you any, Roger, but I thought
that might help if someone reports this to Fedora. I agree with you
that they probably should be dropped.
I am confused by them having the compiler syntax `-Wl,<linker options,
comma separated>`. I think if those were CFLAGS, that would result in
a line like
ld -z relro --as-needed -z now
where these are the explanations from the `ld` man page.
-z relro Create RELRO program header (default)
-z now Mark object non-lazy runtime binding
--as-needed Only set DT_NEEDED for following
dynamic libs if used
I am not working on Fedora, so my ability to pursue further is limited.
Thanks, Roger, for providing a solution so quickly!
-- bennet
On Sun, Jun 28, 2020 at 1:30 PM Veronica Andreo <veroandreo using gmail.com> wrote:
>
>
>
> 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
>> >>
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
>> > R-sig-Geo mailing list
>> > R-sig-Geo using r-project.org
>> > 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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