An embedded and charset-unspecified text was scrubbed... Name: not available URL: <https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20111024/bcc37535/attachment.pl>
problem installing geepack package
5 messages · Kathryn Lan, Brian Ripley, Simon Urbanek
This is something you need to take up with the geepack maintainer (who is also the doBy maintainer). I find his misuse of Depends ridiculous: we have Suggests and Enhances for such loose dependencies. You can easily get snow, as a source or a binary package. Did you update your packages? Several packages which came with 2.13.2 have updates available: one is Matrix. lme4 is tied to a specific version of Matrix, and the Mac binary package repository for 2.13.2 has versions of Matrix (0.999375-50) and lme4 (0.999375-40) which do not work together for me. But the current Matrix is 1.0-1 and current lme4 is 0.999375-42. So AFAIK the only option is to install these packages from their sources. Simon: the binary repository on the CRAN master for 2.14.0 has not be updated for 4 weeks and is rather incomplete, and clearly the 2.13.2 area needs some updates. With 2.14.0 less than a week away, this is getting urgent. Brian
On Mon, 24 Oct 2011, Kathryn Lan wrote:
Hello, I am a new R-user. I have a Mac OS.X 10.6.8. I have downloaded R version 2.13.2 (2011-09-30) onto my computer and been able to use basic stats function. Now I want to use the geepack package and when I try to load it using library(geepack), it says I have to load these dependencies. Apparently, some of these packages successfully loaded but some were not (doBy and lme4). The doBy needs the snow package which R says I don't have, and I don't also have lme4 package. I'm wondering why there's so much trouble trying to load this geepack. What is the primary problem behind this? Thank you for your help.
library(geepack)
Loading required package: doBy Loading required package: survival Loading required package: splines Loading required package: R2HTML Loading required package: multcomp Loading required package: mvtnorm Loading required package: lme4 Loading required package: Matrix Loading required package: lattice Attaching package: 'Matrix' The following object(s) are masked from 'package:base': det Error in dyn.load(file, DLLpath = DLLpath, ...) : function 'cholmod_l_start' not provided by package 'Matrix' Error: package 'lme4' could not be loaded [[alternative HTML version deleted]]
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
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
On Oct 25, 2011, at 3:23 AM, Prof Brian Ripley wrote:
This is something you need to take up with the geepack maintainer (who is also the doBy maintainer). I find his misuse of Depends ridiculous: we have Suggests and Enhances for such loose dependencies. You can easily get snow, as a source or a binary package. Did you update your packages? Several packages which came with 2.13.2 have updates available: one is Matrix. lme4 is tied to a specific version of Matrix, and the Mac binary package repository for 2.13.2 has versions of Matrix (0.999375-50) and lme4 (0.999375-40) which do not work together for me. But the current Matrix is 1.0-1 and current lme4 is 0.999375-42. So AFAIK the only option is to install these packages from their sources. Simon: the binary repository on the CRAN master for 2.14.0 has not be updated for 4 weeks and is rather incomplete,
Hmm.. something is wrong, indeed. Those binaries are from the bootstrap manual run, not from the automated builds. I'll have to investigate...
and clearly the 2.13.2 area needs some updates.
Those seem to be up to date, at least on my server: hagal:2.13$ ls -lt|head total 5489384 -rw-r--r-- 1 urbanek admin 22107 Oct 25 05:13 tilting_1.0.tgz -rw-r--r-- 1 urbanek admin 1167011 Oct 25 05:11 sdcTable_0.9.8.tgz -rw-r--r-- 1 urbanek admin 1430008 Oct 25 05:08 rococo_1.0.1.tgz -rw-r--r-- 1 urbanek admin 1923962 Oct 25 05:01 npRmpi_0.40-10.tgz -rw-r--r-- 1 urbanek admin 87766 Oct 25 04:59 neuRosim_0.2-8.tgz -rw-r--r-- 1 urbanek admin 1215339 Oct 25 04:58 mritc_0.3-4.tgz -rw-r--r-- 1 urbanek admin 1914854 Oct 25 04:56 metrumrg_5.3.tgz -rw-r--r-- 1 urbanek admin 1039445 Oct 25 04:50 frailtypack_2.2-19.tgz -rw-r--r-- 1 urbanek admin 1109695 Oct 25 04:46 dti_0.9-6.3.tgz
With 2.14.0 less than a week away, this is getting urgent.
Agreed, my apologies. Simon
Brian On Mon, 24 Oct 2011, Kathryn Lan wrote:
Hello, I am a new R-user. I have a Mac OS.X 10.6.8. I have downloaded R version 2.13.2 (2011-09-30) onto my computer and been able to use basic stats function. Now I want to use the geepack package and when I try to load it using library(geepack), it says I have to load these dependencies. Apparently, some of these packages successfully loaded but some were not (doBy and lme4). The doBy needs the snow package which R says I don't have, and I don't also have lme4 package. I'm wondering why there's so much trouble trying to load this geepack. What is the primary problem behind this? Thank you for your help.
library(geepack)
Loading required package: doBy Loading required package: survival Loading required package: splines Loading required package: R2HTML Loading required package: multcomp Loading required package: mvtnorm Loading required package: lme4 Loading required package: Matrix Loading required package: lattice Attaching package: 'Matrix' The following object(s) are masked from 'package:base': det Error in dyn.load(file, DLLpath = DLLpath, ...) : function 'cholmod_l_start' not provided by package 'Matrix' Error: package 'lme4' could not be loaded [[alternative HTML version deleted]]
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
-- 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
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
On Oct 25, 2011, at 3:23 AM, Prof Brian Ripley wrote:
This is something you need to take up with the geepack maintainer (who is also the doBy maintainer). I find his misuse of Depends ridiculous: we have Suggests and Enhances for such loose dependencies. You can easily get snow, as a source or a binary package. Did you update your packages? Several packages which came with 2.13.2 have updates available: one is Matrix.
Matrix fails check, that's why it's not available: http://www.R-project.org/nosvn/R.check/r-release-macosx-ix86/Matrix-00check.html It seems like a silly reason to fail, but still, it explains .. Cheers, Simon
lme4 is tied to a specific version of Matrix, and the Mac binary package repository for 2.13.2 has versions of Matrix (0.999375-50) and lme4 (0.999375-40) which do not work together for me. But the current Matrix is 1.0-1 and current lme4 is 0.999375-42. So AFAIK the only option is to install these packages from their sources. Simon: the binary repository on the CRAN master for 2.14.0 has not be updated for 4 weeks and is rather incomplete, and clearly the 2.13.2 area needs some updates. With 2.14.0 less than a week away, this is getting urgent. Brian On Mon, 24 Oct 2011, Kathryn Lan wrote:
Hello, I am a new R-user. I have a Mac OS.X 10.6.8. I have downloaded R version 2.13.2 (2011-09-30) onto my computer and been able to use basic stats function. Now I want to use the geepack package and when I try to load it using library(geepack), it says I have to load these dependencies. Apparently, some of these packages successfully loaded but some were not (doBy and lme4). The doBy needs the snow package which R says I don't have, and I don't also have lme4 package. I'm wondering why there's so much trouble trying to load this geepack. What is the primary problem behind this? Thank you for your help.
library(geepack)
Loading required package: doBy Loading required package: survival Loading required package: splines Loading required package: R2HTML Loading required package: multcomp Loading required package: mvtnorm Loading required package: lme4 Loading required package: Matrix Loading required package: lattice Attaching package: 'Matrix' The following object(s) are masked from 'package:base': det Error in dyn.load(file, DLLpath = DLLpath, ...) : function 'cholmod_l_start' not provided by package 'Matrix' Error: package 'lme4' could not be loaded [[alternative HTML version deleted]]
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
-- 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
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
1 day later
An embedded and charset-unspecified text was scrubbed... Name: not available URL: <https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20111026/26ab9485/attachment.pl>