Re: [R] Cannot update some packages after upgrade to 2.1.1

From: Kevin E. Thorpe <kevin.thorpe_at_utoronto.ca>
Date: Wed 20 Jul 2005 - 23:57:17 EST

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?

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@utoronto.ca  Tel: 416.946.8081  Fax: 416.971.2462

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Received on Thu Jul 21 00:06:37 2005

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