cannot install rgdal after updating to fedora32
On Sun, 28 Jun 2020, Ista Zahn wrote:
I can reproduce this error using the official Fedora 32 docker image:
The error is in the RPM propagating its LDFLAGS which are not needed (or cause no havoc) in simple tests for C compiler functionality in ./configure. For the arguably broken R rpm, use either LDFLAGS="" or the svn rev. 1020 configure argument --disable-loadflags. The load flags are far more than is sensibly needed to check whether the compile train works. I have used RH, RHEL and Fedora since the last century, and have always installed R from source. Recently, the TexLive packaging system drew in (totally unecessarily) a dependency on the R rpm, which I now have to avoid using. My rpm: $ /usr/bin/R CMD config LDFLAGS -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld and compiled from source: $ R CMD config LDFLAGS -L/usr/local/lib64 Why the rpm LDFLAGS demolish a simple AC_LANG(C++) (guesswork, now line 504 in configure.ac) is unknown for me, hence the need for the workaround. I advise strongly against binary packaging of rgdal for Linux, and was not aware that any such packaging had been attempted. Changes in GDAL and PROJ happen fast, and Fedora/Centos etc. have been really slow to update. If anyone understands why the R Fedora rpm imposes such vicious LDFLAGS and can explain why they are needed and how to run a cross platform configure script without having to special-case platforms, I'd be mildly interested to know. sf has also been through similar trouble as mentioned earlier in this thread. Roger
docker run -it library/fedora:32
dnf install 'dnf-command(builddep)'
dnf builddep R-rgdal
R
install.packages("rgdal")
* 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... no
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
`/tmp/Rtmp2o3TMz/R.INSTALLf5d2a7cbb3e/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 ?/usr/lib64/R/library/rgdal?
The downloaded source packages are in
?/tmp/RtmpooFgiH/downloaded_packages?
Updating HTML index of packages in '.Library'
Warning messages:
1: In install.packages("rgdal") :
installation of package ?rgdal? had non-zero exit status
2: In file.create(f.tg) :
cannot create file '/usr/share/doc/R/html/packages.html', reason 'No
such file or directory'
3: In make.packages.html(.Library) : cannot update HTML package index
I don't have any insight into what happens here, but it is reproducible. Best, Ista 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 '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 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