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