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
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