[BioC] hexbin package 1.1-4

[Byron Ellis]

Wrong version of g77---you probably have the fink version (which does  
not work properly). The version you need is at hpc.sourceforge.net,  
please check the R Mac OS X FAQ for further information.


On Nov 5, 2004, at 7:31 PM, Nicholas Lewin-Koh wrote:

> Hi,
> It looks like the fortran libraries are not being found or there is a
> problem with your
> gcc install. The error message is telling you when the shared library  
> is
> being built
> the linker can't find the necessary libraries. I don't work on a mac
> so I won't be too much help, But it does not look like the problem is
> hexbin.
>
> Nicholas
>
>
> On Fri, 5 Nov 2004 10:35:35 -0500, "ulas karaoz" <ulask at bu.edu> said:
>> Hi,
>> The problem seems to be specific to MAC OS 10.
>> I tried to install it on command line in Unix, no problem.
>> In MACOS 10.3.5, trying to install it on command line gave me the
>> following error:
>>
>> :~/Desktop ul$ R CMD INSTALL hexbin_1.1-4.tar.gz
>> * Installing *source* package 'hexbin' ...
>> ** libs
>> g77   -fno-common  -g -O2 -c hbin.f -o hbin.o
>> g77   -fno-common  -g -O2 -c hcell.f -o hcell.o
>> g77   -fno-common  -g -O2 -c herode.f -o herode.o
>> g77   -fno-common  -g -O2 -c hsm.f -o hsm.o
>> gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
>> hexbin.so hbin.o hcell.o herode.o hsm.o  -L/usr/local/lib
>> -L/usr/local/lib/gcc/powerpc-apple-darwin6.6/3.4
>> -L/usr/local/lib/gcc/powerpc-apple-darwin6.6/3.4/../../.. -lfrtbegin
>> -lg2c -lSystem -lcc_dynamic -framework R
>> ld: warning -L: directory name
>> (/usr/local/lib/gcc/powerpc-apple-darwin6.6/3.4) does not exist
>> ld: warning -L: directory name
>> (/usr/local/lib/gcc/powerpc-apple-darwin6.6/3.4/../../..) does not
>> exist
>> ld: can't locate file for: -lfrtbegin
>> make: *** [hexbin.so] Error 1
>> ERROR: compilation failed for package 'hexbin'
>> ** Removing
>> '/Library/Frameworks/R.framework/Versions/1.9.1/Resources/library/
>> hexbin'
>>
>>
>>
>> On Nov 5, 2004, at 9:06 AM, Nicholas Lewin-Koh wrote:
>>
>>> Hi
>>> Can you try on the command line in your unix shell
>>> % R CMD INSTALL hexbin_1.1-4.tar.gz
>>>
>>> And let us know what the error messages are? I need to know if it is  
>>> a
>>> fortran problem, R code , examples documentation, .....
>>> There are a gizillion reasons why it could fail without more to go on
>>> it
>>> is hard to help.
>>>
>>> Nicholas
>>>
>>>
>>>> ulas wrote:
>>> I run R on MACOSX, and i have tried to install it from source local
>>> package file (tarball) that i have downloaded from
>>>
>>> The only error message i am getting is:
>>>> install.from.file()
>>> npackage installation failed
>>>
>>> I am sure that the tarball i have downloaded was complete.
>>> I have tried to unzip/untar it and have tried to do it from a local
>>> source directory, it failed as well.
>>> thanks.
>>>
>>> On Nov 4, 2004, at 12:56 PM, Robert Gentleman wrote:
>>>
>>>> On Thu, Nov 04, 2004 at 12:51:20PM -0500, ulas karaoz wrote:
>>>>> Hi,
>>>>> Did anyone successfully installed the hexbin 1.1-4 at
>>>>>
>>>>>
>>> http://www.bioconductor.org/repository/devel/package/Source/ 
>>> hexbin_1.1
>>>>> -4.tar.gz
>>>>>
>>>>> for some reason, it fails for me.
>>>>
>>>>  In which of the several million different possible ways? It would
>>>>  help if you 1) read the posting guide and 2) provided a proper bug
>>>>  report.
>>>>
>>>>
>>>>> What is the problem with  the old version, 1.0.10?
>>>>> thanks.
>>>>>
>>>>> --------------------------------------------
>>>>> Ulas Karaoz
>>>>> Boston University
>>>>> Ph.D.Student in Bioinformatics
>>>>> zlab.bu.edu
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>
>>>> --  
>>>>
>>> +-------------------------------------------------------------------- 
>>> --
>>>> -----+
>>>> | Robert Gentleman                 phone : (617)
>>> 632-5250
>>>>      |
>>>> | Associate Professor              fax:   (617)
>>> 632-2444
>>>>      |
>>>> | Department of Biostatistics      office:
>>> M1B20
>>>>      |
>>>> | Harvard School of Public Health  email:
>>> rgentlem at jimmy.harvard.edu
>>>>      |
>>>>
>>> +-------------------------------------------------------------------- 
>>> --
>>>> -----+
>>>>
>>> --------------------------------------------
>>> Ulas Karaoz
>>> Boston University
>>> Ph.D.Student in Bioinformatics
>>> zlab.bu.edu
>>>
>>>
>>>
>> --------------------------------------------
>> Ulas Karaoz
>> Boston University
>> Ph.D.Student in Bioinformatics
>> zlab.bu.edu
>>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
---
Byron Ellis (ellis at stat.harvard.edu)
"Oook" -- The Librarian