When using gfortran associated with gcc 4.0.2, I get the following
error
when trying to install the hexbin package:
> biocLite("hexbin")
Running bioCLite version 0.1 with R version 2.2.0
Running biocinstall version 1.1 with R version 2.2.0
trying URL
'http://www.bioconductor.org/packages/bioc/1.7/src/contrib/hexbin_1.4.
0.tar.gz'
Content type 'application/x-gzip' length 491520 bytes
opened URL
==================================================
downloaded 480Kb
* Installing *source* package 'hexbin' ...
** libs
gfortran -fPIC -O2 -c hbin.f -o hbin.o
In file hbin.f:1
subroutine hbin(x,y,cell,cnt,xcm,ycm, size, shape,
1
Error: Symbol 'shape' at (1) has no IMPLICIT type
make: *** [hbin.o] Error 1
ERROR: compilation failed for package 'hexbin'
** Removing '/usr/local/lib/R/library/hexbin'
The downloaded packages are in
/tmp/Rtmpz13994/downloaded_packages
Warning message:
installation of package 'hexbin' had non-zero exit status in:
install.packages(pkgs = "hexbin", repos =
c("http://www.bioconductor.org/packages/bioc/1.7",
Thanks!!
Dave H
--
David A. Henderson, Ph.D.
Insightful Corporation
1700 Westlake Avenue North, Suite 500
Seattle, WA 98109-3044
Tel: 206-802-2307
Fax: 206-283-8691
DNADave at Insightful.Com
http://www.insightful.com
Is this on a mac? At least on a mac there are issues with gcc4 and
the fortran compiler and that might still be the case for other
systems as well. It is possible (I think) to get it working, but it is
not really recommended unless you have a specific need for gcc4. I
assume that the rest of R and BioC have been compiled using gcc4?
Hmm, that was not much of a help.
Kasper
On Nov 9, 2005, at 5:53 PM, David Henderson wrote:
> When using gfortran associated with gcc 4.0.2, I get the following
> error
> when trying to install the hexbin package:
>
>> biocLite("hexbin")
>
> Running bioCLite version 0.1 with R version 2.2.0
>
> Running biocinstall version 1.1 with R version 2.2.0
> trying URL
> 'http://www.bioconductor.org/packages/bioc/1.7/src/contrib/
> hexbin_1.4.0.tar.gz'
> Content type 'application/x-gzip' length 491520 bytes
> opened URL
> ==================================================
> downloaded 480Kb
>
> * Installing *source* package 'hexbin' ...
> ** libs
> gfortran -fPIC -O2 -c hbin.f -o hbin.o
> In file hbin.f:1
>
> subroutine hbin(x,y,cell,cnt,xcm,ycm, size, shape,
> 1
> Error: Symbol 'shape' at (1) has no IMPLICIT type
> make: *** [hbin.o] Error 1
> ERROR: compilation failed for package 'hexbin'
> ** Removing '/usr/local/lib/R/library/hexbin'
>
> The downloaded packages are in
> /tmp/Rtmpz13994/downloaded_packages
> Warning message:
> installation of package 'hexbin' had non-zero exit status in:
> install.packages(pkgs = "hexbin", repos =
> c("http://www.bioconductor.org/packages/bioc/1.7",
>
> Thanks!!
>
> Dave H
> --
> David A. Henderson, Ph.D.
> Insightful Corporation
> 1700 Westlake Avenue North, Suite 500
> Seattle, WA 98109-3044
> Tel: 206-802-2307
> Fax: 206-283-8691
> DNADave at Insightful.Com
> http://www.insightful.com
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
Hi Kasper:
I hope all is well in the Bay area!
-----Original Message-----
> Is this on a mac? At least on a mac there are issues with gcc4 and
> the fortran compiler and that might still be the case for other
> systems as well. It is possible (I think) to get it working, but it
is
> not really recommended unless you have a specific need for gcc4. I
> assume that the rest of R and BioC have been compiled using gcc4?
No mac, yet. I'm still on x86 architecture. The cpu is actually an
AMD
Athlon-XP-M. I did compile the rest of R, CRAN, and Bioconductor
(yes, all
of it) using gcc 4.0.2. There were numerous warnings on many fortran
files,
mainly due to typecasting, but so far the packages I've used that
included
the warnings haven't behaved badly...
I take it you haven't upgraded to SuSE 10, yet?
> Hmm, that was not much of a help.
It's the thought that counts!! ;^)
Thanks!!
Dave H
Hi Dave,
On 9 Nov 2005, dnadave at insightful.com wrote:
> No mac, yet. I'm still on x86 architecture. The cpu is actually an
> AMD Athlon-XP-M. I did compile the rest of R, CRAN, and
> Bioconductor (yes, all of it) using gcc 4.0.2. There were numerous
> warnings on many fortran files, mainly due to typecasting, but so
> far the packages I've used that included the warnings haven't
> behaved badly...
>
> I take it you haven't upgraded to SuSE 10, yet?
We are not testing with gcc 4.x at this time. Our impression is that,
for our purposes, it isn't ready for prime time yet (you're example is
further evidence).
On OS X it is possible to switch between gcc 4.x and 3.x using a
command called gcc_select. Perhaps there is something similar w/ SuSE
that would allow you to use gcc 3.x without confusing your entire
system?
So basically, I would recommend not using gcc 4.x (yet). We certainly
don't want to spend time trying to fix something that in the end is a
compiler bug.
Best,
+ seth
Hi Seth:
> We are not testing with gcc 4.x at this time. Our impression is
that,
> for our purposes, it isn't ready for prime time yet (you're example
is
> further evidence).
I was concerned about this when I tried the 10beta earlier this
Summer. I
thought then that SuSE was a bit premature in moing from 3.9.x to
4.0.2.
> On OS X it is possible to switch between gcc 4.x and 3.x using a
> command called gcc_select. Perhaps there is something similar w/
SuSE
> that would allow you to use gcc 3.x without confusing your entire
> system?
A quick check shows that SuSE lacks this neat feature. It sounds
quite
useful.
> So basically, I would recommend not using gcc 4.x (yet). We
certainly
> don't want to spend time trying to fix something that in the end is
a
> compiler bug.
I'm inclined to agree that it is a compiler bug. I just installed the
package after a quick edit of hbin.f (the offending file). The
problem was
twofold. First, some of the variable names where up against a
preceeding
comma when declared. Once that was rectified (why it had to be, I do
not
know), the variable names extended beyond the right margin. Second, I
had to
move the last two variables on that line to a new line. Once both
tasks were
completed it compiled without complaint.
I'll send an e-mail to the maintainer with the fix required to compile
with
gcc 4.0.2.
Now to see if it behaves correctly.
Thanks!!
Dave H