[R-sig-Debian] Problems compiling packages from source: can't find -lquadmath.

[Simon Blomberg]

Hi Dirk,

I downgraded r-base-core, r-base-dev back to squeeze, and then upgraded 
them again to testing. It seems to have fixed the problem! Most packages 
are compiling happily now.

Thanks for your advice!

Simon.

On 12/01/12 13:46, Dirk Eddelbuettel wrote:
> On 12 January 2012 at 12:51, Simon Blomberg wrote:
> | Hi all,
> |
> | I have recently installed Debian squeeze on a Dell T7500, but I have
> | pinned R and friends to come from the unstable distribution. Currently I
> | have these Debian packages installed (with dependencies):
> |
> | r-base-core 2.14.1-1
> | r-base-dev 2.14.1-1
> |
> | The problem comes when installing new source packages from CRAN using
> | install.packages(). Below is a typical installation output:
> |
> | * installing *source* package ‘gee’ ...
> | ** libs
> | gfortran -fpic -O3 -pipe -g -c dgedi.f -o dgedi.o
> | gfortran -fpic -O3 -pipe -g -c dgefa.f -o dgefa.o
> | gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c ugee.c -o ugee.o
> | gcc -std=gnu99 -shared -o gee.so dgedi.o dgefa.o ugee.o -lblas
> | -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib64/R/lib -lR
> | /usr/bin/ld: cannot find -lquadmath
> | collect2: ld returned 1 exit status
> | make: *** [gee.so] Error 1
> | ERROR: compilation failed for package ‘gee’
> | * removing ‘/usr/local/lib/R/site-library/gee’
> |
> | The downloaded packages are in
> | ‘/tmp/Rtmp7Cgdu4/downloaded_packages’
> | Warning message:
> | In install.packages("gee") :
> | installation of package ‘gee’ had non-zero exit status
> |
> | The problem seems to be with the location of libquadmath. I tried
> | putting a symbolic link to libquadmath.so.0.0.0 (which is in
> | /usr/lib/x86_64-linux-gnu) in /usr/lib64/R/lib , after reading the
> | following thread (with the help of an internet translator!):
> |
> | http://r-br.2285057.n4.nabble.com/R-br-lquadmath-td4124090.html
> |
> | However, this has not solved the problem at all.
> |
> | Can anyone help me with this?
>
> Funny you bring that up because I saw the -lquadmath in a link line the other
> day and wondered "where on earth did that come from" :)
>
> So now, on this (Ubuntu 11.10) box, we can start the chase:
>
> edd at max:~$ locate libquadmath|wc -l
> 64                                              # a lot, some are older .deb packages
> edd at max:~$ locate libquadmath.so|wc -l
> 6                                               # still a lot
> edd at max:~$ locate libquadmath.so|head -2        # so let's look at the first two
> /usr/lib/gcc/x86_64-linux-gnu/4.6/libquadmath.so
> /usr/lib/gcc/x86_64-linux-gnu/4.6/32/libquadmath.so
> edd at max:~$ dpkg -S /usr/lib/gcc/x86_64-linux-gnu/4.6/libquadmath.so
> gcc-4.6: /usr/lib/gcc/x86_64-linux-gnu/4.6/libquadmath.so
> edd at max:~$
>
> So gcc brings this along.  I suspect you are (for once) bitten by the
> unstable/testing split.  The /new/ R packages (r-base-core etc) were probably
> built against a different compiler than the one you use.  You need to bring
> that back in sync, either by also letting the new compiler in (risque as it
> will bring a new libc) or (safer, boring) getting maybe the squeeze build of
> R onto your system, or (more work) reb-building the Debian R package on your
> system to match you compiler.
>
> Let me assure you that "the system" as a whole works, I would have heard by
> now if r-base-core broke builds of r-cran-* packages. The Debian archive
> rebuilds those way too frequently for anything substantial to slip through.
>
> So looks like this is yours.  Sorry that are bitten by a compiler transition,
> but "he who lives at the edge of unstable ... "  ;-)
>
> Cheers,  Dirk
>
> | Thanks in advance,
> |
> | Simon.
> |
> | --
> | Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat.
> | Lecturer and Consultant Statistician
> | School of Biological Sciences
> | The University of Queensland
> | St. Lucia Queensland 4072
> | Australia
> | T: +61 7 3365 2506
> | email: S.Blomberg1_at_uq.edu.au
> | http://www.uq.edu.au/~uqsblomb/
> |
> | Policies:
> | 1.  I will NOT analyse your data for you.
> | 2.  Your deadline is your problem.
> |
> | Statistics is the grammar of science - Karl Pearson.
> |
> | _______________________________________________
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> | R-SIG-Debian at r-project.org
> | https://stat.ethz.ch/mailman/listinfo/r-sig-debian
>


-- 
Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat.
Lecturer and Consultant Statistician
School of Biological Sciences
The University of Queensland
St. Lucia Queensland 4072
Australia
T: +61 7 3365 2506
email: S.Blomberg1_at_uq.edu.au
http://www.uq.edu.au/~uqsblomb/

Policies:
1.  I will NOT analyse your data for you.
2.  Your deadline is your problem.

Statistics is the grammar of science - Karl Pearson.