Re: [R] [R-pkgs] New versions of Matrix and lme4 packages for R-2.4.0
On Tue, 03-Oct-2006 at 09:56AM -0500, Douglas Bates wrote:
| Versions 0.9975-1 of the Matrix and lme4 packages will soon be available on
| CRAN for use with R version 2.4.0 or later.
How quickly things change!! When I got to look at CRAN, the latest
versions were 0.9975-1 of lme4 and 0.9975-2 of Matrix which I tried.
platform x86_64-unknown-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 2
minor 4.0
year 2006
month 10
day03
svn rev39566
language R
version.string R version 2.4.0 (2006-10-03)
Matrix installs, but with a number of warnings like these:
Warning in matchSignature(signature, fdef, where) :
in the method signature for function coerce no definition for class:
matrix.csr
Warning in matchSignature(signature, fdef, where) :
in the method signature for function coerce no definition for class:
matrix.csr
When I try to install lme4, it fails with messages like these:
*Installing *source* package 'lme4' ...
** libs
gcc -I/usr/local/R-2.4.0/include -I/usr/local/R-2.4.0/include
-I/usr/local/include-fpic -g -O2 -std=gnu99 -c init.c -o init.o
In file included from init.c:1:
lme4_utils.h:4:20: error: Matrix.h: No such file or directory
In file included from init.c:1:
lme4_utils.h:14: error: syntax error before ��c��
My guess is that the warnings from the Matrix installation were not
irrelevant, and that the type of error would indicate to the
cognoscenti[1] what could be missing in my installation. If the
second part of my guess is not correct, I'll gladly supply more of the
messages if the above is insufficient. Of course, I'm open to
correction on the first part also.
TIA
1. cognoscenti:- persons who have superior knowledge and understanding
of a particular field, (http://dictionary.reference.com/search?q=cognoscenti)
--
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_( Y )_Middle minds discuss events
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[R] [R-pkgs] New versions of Matrix and lme4 packages for R-2.4.0
Versions 0.9975-1 of the Matrix and lme4 packages will soon be available on CRAN for use with R version 2.4.0 or later. Purpose of the packages: The Matrix package provides S4 classes and methods for sparse and dense matrices. The lme4 package provides functions for fitting and assessing linear or generalized linear mixed effects models (also called multilevel models). Like the Matrix package, the lme4 package uses S4 classes and methods. Features of this release: - These package versions are designed for use with release 2.4.0 or later of R. Because of enhancements in S4 classes and methods in R-2.4.0 the packages load much faster than before and the functions can be organized differently. In particular, the lmer function for fitting linear or generalized linear models is again in the lme4 package. The C code of lme4 now calls C code that is exported from Matrix Matrix package improvements: - The Matrix() constructor function has become more versatile and you are advised to read the help page and try its examples. - Reorganization and simplification of source code (source package is about 1/3 the previous size). Much greater use of virtual classes in method definitions. - LU and QR decompositions for sparse matrices using the CSparse library of C functions written by Tim Davis and documented in his 2006 SIAM book Direct Methods for Sparse Linear Systems. New function Cholesky (in addition to function chol) that allows the full range of CHOLMOD library options for sparse Cholesky decompositions. - New classes to distinguish between sparse logical matrices and sparse pattern matrices. - NAs are now properly dealt with in sparse and dense matrices. - Printing of sparse matrices now distinguishes structural zeros and values that can be nonzero but happen to be equal to zero. - New functions triu, tril and band patterned after those in Octave and Matlab. lme4 package improvements: - Allow specification of nested random effects using terms of the form (1|block/field) - Model specifications without fixed effects, such as travel ~ (1|Rail), are allowed. Previously the implicit intercept term needed to be explicitly specified as travel ~ 1 + (1 | Rail). - Error declared when the number of levels of a grouping factor is not less than the number of observations. - Default estimation method for GLMMs is now optimization of the Laplace approximation to the log-likelihood - Reorganization and simplification of source code. Allow for models, such as multilevel item response theory models or models with carry-over of teacher effects, that extend the linear or generalized linear mixed model. - Fixed bug, reported by Goran Brostrom, in calculation of standard errors of coefficients in a binomial GLMM where the response is given as a matrix. On behalf of the authors Martin Maechler and Douglas Bates ___ R-packages mailing list R-packages@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-packages __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] [R-pkgs] New versions of Matrix and lme4 packages for R-2.4.0
Thanks, Douglas. It works. Only one gripe. Every time I want to try a new version of your software, I have to get, compile, patch the latest bleeding edge version of R as well: ERROR: This R is version 2.3.1 package 'Matrix' needs R = 2.4.0 Douglas Bates wrote: Versions 0.9975-1 of the Matrix and lme4 packages will soon be available on CRAN for use with R version 2.4.0 or later. Purpose of the packages: The Matrix package provides S4 classes and methods for sparse and dense matrices. The lme4 package provides functions for fitting and assessing linear or generalized linear mixed effects models (also called multilevel models). Like the Matrix package, the lme4 package uses S4 classes and methods. ... __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] New versions of Matrix and lme4 packages
I have uploaded version 0.96-1 of both Matrix and lme4 to CRAN. The source package should migrate to CRAN over the weekend and binary packages should be available some time next week. As for previous releases, the versions of these two packages are interdependent. The lme4 package requires Matrix_0.96-1 or later but we cannot enforce the other dependency. Please remember that if you upgrade the Matrix package you should also upgrade the lme4 package. The method for fitting generalized linear mixed models using the Laplacian approximation is considerably faster in this version. Also, the packages have been reorganized so the interdependence will not be as strong in the future. ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ 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
