[R-sig-Geo] cannot install rgdal after updating to fedora32
Roger Bivand
Roger@B|v@nd @end|ng |rom nhh@no
Sun Jun 28 19:20:18 CEST 2020
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.
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
>>>
>>> _______________________________________________
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>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
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--
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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