[R] Cannot update some packages after upgrade to 2.1.1
Prof Brian Ripley
ripley at stats.ox.ac.uk
Wed Jul 20 16:04:35 CEST 2005
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).
> Prof Brian Ripley wrote:
>> -lf77blas is part of ATLAS, so I do suspect the RPM builder had ATLAS
>> 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
>> 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
>>> 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
>>> 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
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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