cannot install rgdal after updating to fedora32
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 at gmail.com> wrote:
El dom., 28 jun. 2020 a las 19:20, Roger Bivand (<Roger.Bivand at nhh.no>) escribi?:
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 at umich.edu>) escribi?:
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 at 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 at nhh.no>)
escribi?:
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 s?b., 27 jun. 2020 a las 21:29, Veronica Andreo (<veroandreo at gmail.com>) escribi?:
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 '
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 at nhh.no https://orcid.org/0000-0003-2392-6140 https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
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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 at nhh.no https://orcid.org/0000-0003-2392-6140 https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en