R SIG Fedora - Jun 2020 - -specs=/usr/lib/rpm/redhat/redhat-hardened-ld woes

In the rgdal package, configure.ac has had : ${LDFLAGS=`"${RBIN}" CMD 
config LDFLAGS`} at least since 2012, so picking up LDFLAGS known to the R 
version installed. Very recently, users installing rgdal from source with 
R installed from RPM are seeing problems, such as those reported in this 
thread: https://stat.ethz.ch/pipermail/r-sig-geo/2020-June/028251.html

The diagnosis by Bennet Fauber, that

LDFLAGS='-specs=/usr/lib/rpm/redhat/redhat-hardened-ld'

is the problem, that LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now' 
works OK, and that the -specs= conflict with autoconf has not been 
resolved seems accurate to me (see also 
https://developers.redhat.com/blog/2018/03/21/compiler-and-linker-flags-gcc/, 
https://bugzilla.redhat.com/show_bug.cgi?id=1343892).

I realise that the R RPM needs to follow RH/F standards, but has something 
happened in the RPM ecosystem recently to poison the -spec/autoconf 
relationship?

Reprex:  install.packages("rgdal",
repos="http://R-Forge.R-project.org")
and  install.packages("rgdal",
repos="http://R-Forge.R-project.org",
configure.args="--disable-loadflags") on a system with R RPM, plus
GDAL
and PROJ (gdal-devel proj-devel proj-epsg proj-nad sqlite-devel I think).

Are there any known work-arounds that might apply to other packages using 
autoconf?

Roger

-- 
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

On Mon, 29 Jun 2020 at 10:21, Roger Bivand <Roger.Bivand at nhh.no>
wrote:
>
> In the rgdal package, configure.ac has had : ${LDFLAGS=`"${RBIN}"
CMD
> config LDFLAGS`} at least since 2012, so picking up LDFLAGS known to the R
> version installed. Very recently, users installing rgdal from source with
> R installed from RPM are seeing problems, such as those reported in this
> thread: https://stat.ethz.ch/pipermail/r-sig-geo/2020-June/028251.html
>
> The diagnosis by Bennet Fauber, that
>
> LDFLAGS='-specs=/usr/lib/rpm/redhat/redhat-hardened-ld'
>
> is the problem, that LDFLAGS='-Wl,-z,relro -Wl,--as-needed
-Wl,-z,now'
> works OK, and that the -specs= conflict with autoconf has not been
> resolved seems accurate to me (see also
>
https://developers.redhat.com/blog/2018/03/21/compiler-and-linker-flags-gcc/,
> https://bugzilla.redhat.com/show_bug.cgi?id=1343892).
>
> I realise that the R RPM needs to follow RH/F standards, but has something
> happened in the RPM ecosystem recently to poison the -spec/autoconf
> relationship?
Did something change in rgdal's flags from 1.5-10 to 1.5-12? Because
the former installs fine. You can see in [1] that it fails since the
last update.

[1] https://copr.fedorainfracloud.org/coprs/iucar/cran/package/R-CRAN-rgdal/

-- 
I?aki ?car

On Mon, 29 Jun 2020 at 11:24, I?aki Ucar <iucar at fedoraproject.org>
wrote:
>
> On Mon, 29 Jun 2020 at 10:21, Roger Bivand <Roger.Bivand at nhh.no>
wrote:
> >
> > In the rgdal package, configure.ac has had :
${LDFLAGS=`"${RBIN}" CMD
> > config LDFLAGS`} at least since 2012, so picking up LDFLAGS known to
the R
> > version installed. Very recently, users installing rgdal from source
with
> > R installed from RPM are seeing problems, such as those reported in
this
> > thread: https://stat.ethz.ch/pipermail/r-sig-geo/2020-June/028251.html
> >
> > The diagnosis by Bennet Fauber, that
> >
> > LDFLAGS='-specs=/usr/lib/rpm/redhat/redhat-hardened-ld'
> >
> > is the problem, that LDFLAGS='-Wl,-z,relro -Wl,--as-needed
-Wl,-z,now'
> > works OK, and that the -specs= conflict with autoconf has not been
> > resolved seems accurate to me (see also
> >
https://developers.redhat.com/blog/2018/03/21/compiler-and-linker-flags-gcc/,
> > https://bugzilla.redhat.com/show_bug.cgi?id=1343892).
> >
> > I realise that the R RPM needs to follow RH/F standards, but has
something
> > happened in the RPM ecosystem recently to poison the -spec/autoconf
> > relationship?
>
> Did something change in rgdal's flags from 1.5-10 to 1.5-12? Because
> the former installs fine. You can see in [1] that it fails since the
> last update.
I see that rgdal changed to C++ recently. The issue is in rgdal,
because the configure script is missing:

CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXXFLAGS`

as indicated in Writing R Extensions (note that CPPFLAGS are *not*
CXXFLAGS; I say this because it's a common mistake).

-- 
I?aki ?car