Re: [R] Cannot update some packages after upgrade to 2.1.1
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). After following the discussion between you and Uwe, and thinking a bit, I've decided to give it a try. My system is basically stand-alone so different architectures are not an issue. Now my question (recognising this may be the wrong list). I successfully compiled ATLAS, but it isn't clear to me from the install instructions that came with it how to make the libraries seen by gcc and g77 and therefore, presumably by the configure script with the R source. How do I make the libraries available? I've looked at the ATLAS project page and done a couple RSiteSearch's but have not yet recognised the answer to my question. 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: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.971.2462 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Cannot update some packages after upgrade to 2.1.1
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: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.971.2462 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Cannot update some packages after upgrade to 2.1.1
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 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: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.971.2462 -- Brian D. Ripley, [EMAIL PROTECTED] 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, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Cannot update some packages after upgrade to 2.1.1
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: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.971.2462 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Cannot update some packages after upgrade to 2.1.1
On Wed, 20 Jul 2005, Uwe Ligges wrote: 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. That is fine on Windows, which has a separate Rblas.dll exactly to enable this to be done. You can also do it on Debian Linux, which has a dynamic libatlas (as I understand it). On other systems with a static ATLAS library, the BLAS is compiled into the R installation in many (up to hundreds) of places, including each package that uses a BLAS. It's all too easy to build R on, say, an Athlon and discover it segfaults on a Xeon because an Athlon-optimized ATLAS has been compiled in. (I've done it more than once, and it needs the whole setup to be reinstalled, including many of the packages without it being obvious which ones). 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: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.971.2462 -- Brian D. Ripley, [EMAIL PROTECTED] 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, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Cannot update some packages after upgrade to 2.1.1
-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 major2 minor1.1 year 2005 month06 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: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.971.2462 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED] 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, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Cannot update some packages after upgrade to 2.1.1
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 major2 minor1.1 year 2005 month06 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: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.971.2462 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
