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cannot install rgdal after updating to fedora32

Veronica Andreo

Sun, Jun 28, 2020 10:08 AM

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

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 '

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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Thread (4 messages)

Veronica Andreo cannot install rgdal after updating to fedora32 Jun 28 Roger Bivand cannot install rgdal after updating to fedora32 Jun 28 Veronica Andreo cannot install rgdal after updating to fedora32 Jun 28 Bennet Fauber cannot install rgdal after updating to fedora32 Jun 28