[R] Cannot update some packages after upgrade to 2.1.1

[Uwe Ligges]

Prof Brian Ripley wrote:

> On Wed, 20 Jul 2005, Kevin E. Thorpe wrote:
> 
> 
>>Thank you for the information. I have contacted the RPM maintainer and am 
>>awaiting a response.
>>
>>It occurs to me that my "problem" could also be fixed by putting ATLAS on my 
>>system. Are there advantages to doing that or any reasons not to?
> 
> 
> It is a good idea unless you share R systems between different 
> architectures (even down to the vintage of P4 or Xeon chips). We do and so 
> tend to avoid ATLAS (which gets statically compiled in by default).


We are using you ATLAS-optimized Rblas.dll files for our facutly wide 
Windows installation.

Additional to the regular .../bin directory, we have copies called 
.../bin-At, .../bin-P3, .../bin-P4 but the regular Rblas.dll replaced by 
those optimized Rblas.dll files.
Hence one can simply call .../bin-P4/RGui.exe on any P4/Xeon machine and 
do not need a seperate installation for another Athlon machine using the 
.../bin-At/RGui.exe, for example.


Uwe


> 
>>Prof Brian Ripley wrote:
>>
>>
>>>-lf77blas is part of ATLAS, so I do suspect the RPM builder had ATLAS 
>>>installed.
>>>
>>>lme4 needs a compatible Matrix installed.
>>>
>>>I do think installing from the sources would solve this, but probably you 
>>>need to discuss this with the RPM maintainer as a dependency appears to be 
>>>missing.
>>>
>>>On Fri, 15 Jul 2005, Kevin E. Thorpe wrote:
>>>
>>>
>>>>I just upgraded to version 2.1.1 (from 2.0.1) today.
>>>>
>>>>
>>>>>R.version
>>>>
>>>>_
>>>>platform i686-pc-linux-gnu
>>>>arch i686
>>>>os linux-gnu
>>>>system i686, linux-gnu
>>>>status
>>>>major 2
>>>>minor 1.1
>>>>year 2005
>>>>month 06
>>>>day 20
>>>>language R
>>>>
>>>>I am using SuSE 9.2 and did the upgrade using rpm -U with the RPM
>>>>available on CRAN. After upgrading r-base, I ran update.packages().
>>>>Four previously installed packages failed to update:
>>>>
>>>>Matrix (0.95-5 to 0.97-4)
>>>>gam (0.93 to 0.94)
>>>>lme4 (0.95-3 to 0.96-1)
>>>>mgcv (1.3-1 to 1.3-4)
>>>>
>>>>In the case of Matrix, gam and mgcv I get the message:
>>>>
>>>>[long path]/ld: cannot find -lf77blas
>>>>
>>>>In the case of lme4 the messages are:
>>>>
>>>>** preparing package for lazy loading
>>>>Error in setMethod("coef", signature(object = "lmList"), function(object, 
>>>>:
>>>>no existing definition for function 'coef'
>>>>Error: unable to load R code in package 'lme4'
>>>>Execution halted
>>>>ERROR: lazy loading failed for package 'lme4'
>>>>
>>>>I have searched the SuSE repository for any package that provides
>>>>f77blas but came up empty.
>>>>
>>>>I also could not identify any relevant messages in the mailing list
>>>>archives.
>>>>
>>>>Is R looking for that library because it was present on the machine
>>>>the RPM was built on? Would building R myself solve the missing library
>>>>problem or did I do something wrong?
>>>>
>>
>>
>>-- 
>>Kevin E. Thorpe
>>Biostatistician/Trialist, Knowledge Translation Program
>>Assistant Professor, Department of Public Health Sciences
>>Faculty of Medicine, University of Toronto
>>email: kevin.thorpe at utoronto.ca  Tel: 416.946.8081  Fax: 416.971.2462
>>
>>
> 
>