[R-sig-Debian] Trouble building R 3.5.0 under Ubuntu 18.04 (Bionic Beaver)

[Steve Gutreuter]

All of my attempts to build R 3.5.0 from sources under Ubuntu 18.04
have failed, and I cannot figure out what I am doing wrong. I have
tried may things, including :

export LDFLAGS="$LDFLAGS -fPIC"
export CXXFLAGS="$CXXFLAGS -fPIC"
export CFLAGS="$CFLAGS -fPIC"
./configure --enable-R-shlib --prefix=/usr/lib/R/3.5.0

#### Configure completes normally without errors or warnings

make

#### make fails, always with lines like:

gcc -Wl,--export-dynamic -fopenmp -fPIC -o R.bin Rmain.o
CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o altrep.o apply.o
arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o
colors.o complex.o connections.o context.o cum.o dcf.o datetime.o
debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o
edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-
ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o
iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o
match.o memory.o names.o objects.o options.o paste.o platform.o plot.o
plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o
qsort.o radixsort.o random.o raw.o registration.o relop.o rlocale.o
saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o
startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o
unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o
g_her_glyph.o xxxpr.o `ls ../unix/*.o ../appl/*.o ../nmath/*.o`
../extra/tre/libtre.a -L"../../lib" -lRblas -lgfortran -lm
-lquadmath -lreadline -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc
-licui18n
/usr/bin/x86_64-linux-gnu-ld: ../appl/dchdc.o: relocation R_X86_64_32
against `.rodata' can not be used when making a PIE object; recompile
with -fPIC
/usr/bin/x86_64-linux-gnu-ld: ../appl/dpbfa.o: relocation R_X86_64_32
against `.rodata' can not be used when making a PIE object; recompile
with -fPIC
/usr/bin/x86_64-linux-gnu-ld: ../appl/dpbsl.o: relocation R_X86_64_32
against `.rodata' can not be used when making a PIE object; recompile
with -fPIC
/usr/bin/x86_64-linux-gnu-ld: ../appl/dpoco.o: relocation R_X86_64_32
against `.rodata' can not be used when making a PIE object; recompile
with -fPIC
/usr/bin/x86_64-linux-gnu-ld: ../appl/dpodi.o: relocation R_X86_64_32
against `.rodata' can not be used when making a PIE object; recompile
with -fPIC
/usr/bin/x86_64-linux-gnu-ld: ../appl/dpofa.o: relocation R_X86_64_32
against `.rodata' can not be used when making a PIE object; recompile
with -fPIC
/usr/bin/x86_64-linux-gnu-ld: ../appl/dposl.o: relocation R_X86_64_32
against `.rodata' can not be used when making a PIE object; recompile
with -fPIC
/usr/bin/x86_64-linux-gnu-ld: ../appl/dqrdc2.o: relocation R_X86_64_32
against `.rodata' can not be used when making a PIE object; recompile
with -fPIC
/usr/bin/x86_64-linux-gnu-ld: ../appl/dqrdc.o: relocation R_X86_64_32
against `.rodata' can not be used when making a PIE object; recompile
with -fPIC
/usr/bin/x86_64-linux-gnu-ld: ../appl/dqrls.o: relocation R_X86_64_32S
against `.rodata' can not be used when making a PIE object; recompile
with -fPIC
/usr/bin/x86_64-linux-gnu-ld: ../appl/dqrsl.o: relocation R_X86_64_32
against `.rodata' can not be used when making a PIE object; recompile
with -fPIC
/usr/bin/x86_64-linux-gnu-ld: ../appl/dqrutl.o: relocation R_X86_64_32S
against `.rodata' can not be used when making a PIE object; recompile
with -fPIC
/usr/bin/x86_64-linux-gnu-ld: ../appl/dsvdc.o: relocation R_X86_64_32
against `.rodata' can not be used when making a PIE object; recompile
with -fPIC
/usr/bin/x86_64-linux-gnu-ld: ../appl/dtrco.o: relocation R_X86_64_32
against `.rodata' can not be used when making a PIE object; recompile
with -fPIC
/usr/bin/x86_64-linux-gnu-ld: ../appl/dtrsl.o: relocation R_X86_64_32
against `.rodata' can not be used when making a PIE object; recompile
with -fPIC
/usr/bin/x86_64-linux-gnu-ld: final link failed: Nonrepresentable
section on output
collect2: error: ld returned 1 exit status
Makefile:145: recipe for target 'R.bin' failed
make[3]: *** [R.bin] Error 1
make[3]: Leaving directory '/home/steve/src/R/R-3.5.0/src/main'
Makefile:137: recipe for target 'R' failed
make[2]: *** [R] Error 2
make[2]: Leaving directory '/home/steve/src/R/R-3.5.0/src/main'
Makefile:28: recipe for target 'R' failed
make[1]: *** [R] Error 1
make[1]: Leaving directory '/home/steve/src/R/R-3.5.0/src'
Makefile:60: recipe for target 'R' failed

The same occurs with or without --enable-R-shlib

My interpretation is that -fPIC is not being seen by the compilers, but
the call to gcc clearly includes it.

I would greatly appreciate any advice on how to get this build to
succeed.

Best,
Steve

[Dirk Eddelbuettel]

On 24 May 2018 at 09:15, Steve Gutreuter wrote:
| All of my attempts to build R 3.5.0 from sources under Ubuntu 18.04
| have failed, and I cannot figure out what I am doing wrong. I have

Ubuntu builds
https://launchpad.net/~marutter/+archive/ubuntu/rrutter3.5
with sources if you want to know more.

Based on my Debian builds which you can peruse at
https://salsa.debian.org/edd/r-base

That said, R 3.5.0 is _not_ compatible with R 3.4.* and before so if you
install these binaries expect _all_ old R packages, whether from r-cran-* or
locally installed, to croak. Which is why R 3.5.0 is not yet mirrored at
CRAN -- we're just not there yet.

| tried may things, including :
|
| export LDFLAGS="$LDFLAGS -fPIC"
| export CXXFLAGS="$CXXFLAGS -fPIC"
| export CFLAGS="$CFLAGS -fPIC"
| ./configure --enable-R-shlib --prefix=/usr/lib/R/3.5.0

I am not sure where you got those settings from. That is (AICR) not what it
is in the R Installation + Administration manual which you should consult if
you insist on doing it locally.

I have a fairly strongly held conviction that the available binaries are
actually better for you (we make many informed choices for you and add
several bells as well as a few whistles) but you are free to ignore it.

Dirk