From tcallawa at redhat.com  Tue Nov  2 17:53:32 2010
From: tcallawa at redhat.com (Tom "spot" Callaway)
Date: Tue, 02 Nov 2010 12:53:32 -0400
Subject: [Rd] make error for R 2.13.0 (and 2.12.0)
In-Reply-To: <4CBBF15E.6040104@gmail.com>
References: <20101018003908.GA990@cs.toronto.edu> <4CBBF15E.6040104@gmail.com>
Message-ID: <4CD0420C.40604@redhat.com>

On 10/18/2010 03:03 AM, Peter Dalgaard wrote:
> On 10/18/2010 02:39 AM, Radford Neal wrote:
>> Regarding Tengfei Yin's post about an error trying to install
>> "cluster" in 2.13.0, I have gotten an error with this package when
>> trying to install the released version of 2.12.0.  Here is the output
>> on an Ubuntu Linux system:
> 
> Hmm, g77 along with a recent gcc? It is usually gfortran on current
> linux systems. It's strange that it got past the configure step though.
> What did the configure output look like? A look at "nm cluster.so" could
> also be informative.

RHEL 4 throws the same error (RHEL 5, RHEL 6, and all current Fedora
targets (F12-F15) are fine):

* installing *source* package 'cluster' ...
** libs
make[3]: Entering directory `/tmp/RtmpbbtMdO/R.INSTALL5ad6c5f4/cluster/src'
gcc -m64 -std=gnu99 -I/builddir/build/BUILD/R-2.12.0/include
-I/usr/local/include    -fpic  -O2 -g -pipe -m64 -c clara.c -o clara.o
g77 -m64   -fpic  -O2 -g -pipe -m64 -c daisy.f -o daisy.o
g77 -m64   -fpic  -O2 -g -pipe -m64 -c dysta.f -o dysta.o
gcc -m64 -std=gnu99 -I/builddir/build/BUILD/R-2.12.0/include
-I/usr/local/include    -fpic  -O2 -g -pipe -m64 -c fanny.c -o fanny.o
gcc -m64 -std=gnu99 -I/builddir/build/BUILD/R-2.12.0/include
-I/usr/local/include    -fpic  -O2 -g -pipe -m64 -c init.c -o init.o
g77 -m64   -fpic  -O2 -g -pipe -m64 -c meet.f -o meet.o
g77 -m64   -fpic  -O2 -g -pipe -m64 -c mona.f -o mona.o
gcc -m64 -std=gnu99 -I/builddir/build/BUILD/R-2.12.0/include
-I/usr/local/include    -fpic  -O2 -g -pipe -m64 -c pam.c -o pam.o
gcc -m64 -std=gnu99 -I/builddir/build/BUILD/R-2.12.0/include
-I/usr/local/include    -fpic  -O2 -g -pipe -m64 -c sildist.c -o sildist.o
gcc -m64 -std=gnu99 -I/builddir/build/BUILD/R-2.12.0/include
-I/usr/local/include    -fpic  -O2 -g -pipe -m64 -c spannel.c -o spannel.o
g77 -m64   -fpic  -O2 -g -pipe -m64 -c twins.f -o twins.o
gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o cluster.so clara.o
daisy.o dysta.o fanny.o init.o meet.o mona.o pam.o sildist.o spannel.o
twins.o -lg2c -lm -L/builddir/build/BUILD/R-2.12.0/lib -lR
make[3]: Leaving directory `/tmp/RtmpbbtMdO/R.INSTALL5ad6c5f4/cluster/src'
installing to /builddir/build/BUILD/R-2.12.0/library/cluster/libs
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'cluster'
    finding HTML links ... done
    agnes                                   html
    agnes.object                            html
    agriculture                             html
    animals                                 html
    bannerplot                              html
    chorSub                                 html
    clara                                   html
    clara.object                            html
    clusplot                                html
    clusplot.default                        html
Rd warning:
/tmp/RtmpbbtMdO/R.INSTALL5ad6c5f4/cluster/man/clusplot.default.Rd:198:
missing file link 'cov.mve'
    clusplot.partition                      html
    cluster-internal                        html
    coef.hclust                             html
    daisy                                   html
    diana                                   html
    dissimilarity.object                    html
    ellipsoidhull                           html
Rd warning:
/tmp/RtmpbbtMdO/R.INSTALL5ad6c5f4/cluster/man/ellipsoidhull.Rd:36:
missing file link 'cov.mve'
Rd warning:
/tmp/RtmpbbtMdO/R.INSTALL5ad6c5f4/cluster/man/ellipsoidhull.Rd:86:
missing file link 'cov.mve'
    fanny                                   html
    fanny.object                            html
    flower                                  html
    lower.to.upper.tri.inds                 html
    mona                                    html
    mona.object                             html
    pam                                     html
    pam.object                              html
    partition.object                        html
    plantTraits                             html
    plot.agnes                              html
Rd warning:
/tmp/RtmpbbtMdO/R.INSTALL5ad6c5f4/cluster/man/plot.agnes.Rd:73: missing
file link 'plot.dendrogram'
    plot.diana                              html
    plot.mona                               html
    plot.partition                          html
    pltree                                  html
    pltree.twins                            html
    pluton                                  html
    predict.ellipsoid                       html
    print.agnes                             html
    print.clara                             html
    print.diana                             html
    print.dissimilarity                     html
Rd warning:
/tmp/RtmpbbtMdO/R.INSTALL5ad6c5f4/cluster/man/print.dissimilarity.Rd:27:
missing file link 'print.dist'
    print.fanny                             html
    print.mona                              html
    print.pam                               html
    ruspini                                 html
    silhouette                              html
    sizeDiss                                html
    summary.agnes                           html
    summary.clara                           html
    summary.diana                           html
    summary.mona                            html
    summary.pam                             html
    twins.object                            html
    volume.ellipsoid                        html
    votes.repub                             html
    xclara                                  html
** building package indices ...
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object
'/builddir/build/BUILD/R-2.12.0/library/cluster/libs/cluster.so':
  /builddir/build/BUILD/R-2.12.0/library/cluster/libs/cluster.so:
undefined symbol: cl_daisy_
ERROR: loading failed
* removing '/builddir/build/BUILD/R-2.12.0/library/cluster'
make[2]: Leaving directory
`/builddir/build/BUILD/R-2.12.0/src/library/Recommended'
make[1]: Leaving directory
`/builddir/build/BUILD/R-2.12.0/src/library/Recommended'

******
Full build log is here:
http://koji.fedoraproject.org/koji/getfile?taskID=2571563&name=build.log

Default gcc in RHEL 4 is 3.4.6-10, which has g77 rather than gfortran.
It looks like this code no longer compiles properly with g77.

Thankfully, RHEL 4 also includes a copy of gcc 4.1, so I should be able
to work around this by using that instead.

~spot



[Rd] make error for R 2.13.0 (and 2.12.0)
Tom "spot" Callaway