[BioC] Problem installing hexbin?

[Sander Oom]

Seth Falcon wrote:
> David Henderson <dnadave at insightful.com> writes:
> 
>> Hi Robert:
>>
>>
>> Here's what I see on my SuSE 10.0 laptop:
>>
>> minime{david}103: gfortran --version
>> GNU Fortran 95 (GCC 4.0.2 20050901 (prerelease) (SUSE Linux))
>> Copyright (C) 2005 Free Software Foundation, Inc.
>>
>> GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
>> You may redistribute copies of GNU Fortran
>> under the terms of the GNU General Public License.
>> For more information about these matters, see the file named COPYING
>> minime{david}104: R CMD INSTALL hexbin_1.4.0.tar.gz
>> * 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
> 
> Dave, I think you have an old version of the hexbin code.  
> 
>     hexbin> svn log -v -r 14557
>     ------------------------------------------------------------------------
>     r14557 | nikko at hailmail.net | 2005-10-24 09:11:18 -0700 (Mon, 24 Oct 2005) | 3 lines
>     Changed paths:
>        M /trunk/madman/Rpacks/hexbin/R/hexplom.R
>        M /trunk/madman/Rpacks/hexbin/src/hbin.f
>     
>     debugging, fixed hbin.f to comply with gfortran error messages. Now it 
>     compiles
>                                                                                      
> 
>     ~/hexbin/src> svn diff -r 14556:HEAD
>     Index: hbin.f
>     ===================================================================
>     --- hbin.f      (.../trunk/madman/Rpacks/hexbin/src)    (revision 14556)
>     +++ hbin.f      (.../branches/RELEASE_1_8/madman/Rpacks/hexbin/src)     (revision 17729)
>     @@ -15,7 +15,8 @@
>      
>             integer n, nc, cell(*), cnt(*), bnd(2), cellid(*)
>      c       cellid(*): length 1 or n
>     -       double precision x(n), y(n), xcm(*),ycm(*), rx(2),ry(2), size,shape
>     +       double precision x(n), y(n), xcm(*),ycm(*), rx(2),ry(2), size
>     +        double precision shape
>             integer i, i1, i2, iinc
>             integer j1, j2, jinc
>             integer L, lmax, lat           
> 
> Can you try with the latest:
> http://bioconductor.org/packages/1.8/bioc/html/hexbin.html
> 
> + seth
> 
> _______________________________________________
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Hi Seth,

Thanks for your help! A little progress was achieved, but still no
correct result:

> srcHexbin <- "http://bioconductor.org/packages/1.8/bioc/src/contrib/"
> install.packages("hexbin", contriburl=srcHexbin)
trying URL
'http://bioconductor.org/packages/1.8/bioc/src/contrib//hexbin_1.6.0.tar.gz'
Content type 'application/x-gzip' length 512021 bytes
opened URL
==================================================
downloaded 500Kb

* Installing *source* package 'hexbin' ...
** libs
gfortran   -fPIC   -c hbin.f -o hbin.o
gfortran   -fPIC   -c hcell.f -o hcell.o
gfortran   -fPIC   -c herode.f -o herode.o
gfortran   -fPIC   -c hsm.f -o hsm.o
gcc -shared -L/usr/local/lib -o hexbin.so hbin.o hcell.o herode.o hsm.o
 -lgfortran -lm -lgcc_s -L/usr/lib/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Error in setMethod("plot", signature(x = "hexbin", y = "missing"),
gplot.hexbin) :
        no existing definition for function 'plot'
Error: unable to load R code in package 'hexbin'
Execution halted
ERROR: lazy loading failed for package 'hexbin'
** Removing '/usr/lib/R/library/hexbin'

The downloaded packages are in
        /tmp/RtmpeM8437/downloaded_packages
Warning message:
installation of package 'hexbin' had non-zero exit status in:
install.packages("hexbin", contriburl = srcHexbin)
>

I regularly run this code to keep up tot date:

options(repos = "http://cran.r-project.org/")
( theNew <- new.packages(ask=FALSE) )
install.packages(theNew)
update.packages(ask=FALSE, checkBuilt=T)

Thanks,

Sander.





> version
         _
platform i686-pc-linux-gnu
arch     i686
os       linux-gnu
system   i686, linux-gnu
status
major    2
minor    2.1
year     2005
month    12
day      20
svn rev  36812
language R
>