Roger Bivand
2020-Jun-29 08:20 UTC
[R-sig-Fedora] -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
Iñaki Ucar
2020-Jun-29 09:24 UTC
[R-sig-Fedora] -specs=/usr/lib/rpm/redhat/redhat-hardened-ld woes
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
Iñaki Ucar
2020-Jun-29 10:27 UTC
[R-sig-Fedora] -specs=/usr/lib/rpm/redhat/redhat-hardened-ld woes
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