search for: cholmod

Hi R usrs, I want to build R-2.10.0 on HP-UX, but I got following error message: ld: Unsatisfied symbol "zgemm" in file CHOLMOD.a[cholmod_l_super_numeric.o] ld: Unsatisfied symbol "zgemv" in file CHOLMOD.a[cholmod_l_super_solve.o] ld: Unsatisfied symbol "zherk" in file CHOLMOD.a[cholmod_l_super_numeric.o] ld: Unsatisfied symbol "ztrsm" in file CHOLMOD.a[cholmod_l_super_numeric.o] ld: Unsatisfie...

Hi All, I want to build R-2.10.0 on HP-UX, but I got following error message: ld: Unsatisfied symbol "zgemm" in file CHOLMOD.a[cholmod_l_super_numeric.o] ld: Unsatisfied symbol "zgemv" in file CHOLMOD.a[cholmod_l_super_solve.o] ld: Unsatisfied symbol "zherk" in file CHOLMOD.a[cholmod_l_super_numeric.o] ld: Unsatisfied symbol "ztrsm" in file CHOLMOD.a[cholmod_l_super_numeric.o] ld: Unsatisfie...

Hello, I have been attempting to run a poisson glmm using lme4 for some time now and have had a lot of trouble. I would say 9 times out of 10 I receive the following warning: CHOLMOD warning: %h Error in mer_finalize(ans) : Cholmod error `not positive definite' at file:../Cholesky/t_cholmod_rowfac.c, line 432 My data are counts of microbe colony forming units (CFUs) collected from termite cuticles and the surrounding environment over a 3 year period. I am attempting to...

I have a pretty large sparse matrix of integers: > dim(tasa) [1] 91650 37651 I need to add one to it in order to take logs, but I'm getting the following error: > tasa = log(tasa + 1) CHOLMOD error: problem too large Error in asMethod(object) : Cholmod error `problem too large' I have 2 Gb of RAM, and the current workspace is barely 300mb. Is there any workaround to this? Anyone has any experience with this error? Thanks, -Jose -- Jose Quesada, PhD. http://www.andrew.cmu.edu/~jq...

I have a pretty large sparse matrix of integers: > dim(tasa) [1] 91650 37651 I need to add one to it in order to take logs, but I'm getting the following error: > tasa = log(tasa + 1) CHOLMOD error: problem too large Error in asMethod(object) : Cholmod error `problem too large' I have 2 Gb of RAM, and the current workspace is barely 300mb. Is there any workaround to this? Anyone has any experience with this error? Thanks, -Jose -- Jose Quesada, PhD. http://www.andrew.cmu.edu/~jq...

Hi, I am getting a warning message when I am fitting a generalized linear mixed model (m1.2 below). CHOLMOD warning: matrix not positive definite Error in objective(.par, ...) : Cholmod error `matrix not positive definite' at file:../Supernodal/t_cholmod_super_numeric.c, line 614 Any idea? Thanks for your help, Reza > sessionInfo() R version 2.4.1 (2006-12-18) i386-pc-mingw32 locale: LC...

..., family=quasipoisson) But if I try the exact same model with a different variable, totmas, the model looks as follows: model<-lmer(aphids~totmas+zone+(1|zone/site), family=quasipoisson) Totmas is also a continuous variable just like densroot, but in this case I receive the following message: CHOLMOD warning: &߆e Error in objective(.par, ...) : Cholmod error `matrix not positive definite' at file:../Supernodal/t_cholmod_super_numeric.c, line 613 Moreover, if I test yet another continuous variable "vitality", to my surprise R just crashes completely. This is a mystery to...

...NES -fPIC -g -O2 -c Csparse.c -o Csparse.o ... numerous lines deleted ... gcc -I/usr/local/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -fPIC -g -O2 -c triplet_to_col.c -o triplet_to_col.o f77 -fPIC -g -O2 -c zpotf2.f -o zpotf2.o f77 -fPIC -g -O2 -c zpotrf.f -o zpotrf.o touch CHOLMOD.stamp UMFPACK.stamp COLAMD.stamp CCOLAMD.stamp AMD.stamp Metis.stamp LDL.stamp gmake[1]: Entering directory `/tmp/R.INSTALL.WMODs1/Matrix/src/CHOLMOD' ( cd Lib ; make ) make: don't know how to make w. Stop gmake[1]: *** [library] Error 2 I am running: > version _...

...e -I/usr/include -I/usr/sfw/include -KPIC -O -I/opt/SUNWspro/prod/include -c sparseQR.c -o sparseQR.o ( cd Lib ; make clean ) ( cd Lib ; make clean ) ( cd Source ; make clean ) ( cd Source ; make clean ) ( cd Lib ; make lib ) CC -m64 -I/home/choid/bin/R281/lib/R/include -I../../UFconfig -I../../CHOLMOD/Include -I../Include -DNPARTITION -I/usr/local/include -I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O -I/opt/SUNWspro/prod/include -c ../Source/spqr_rmap.cpp CC -m64 -I/home/choid/bin/R281/lib/R/include -I../../UFconfig -I../../CHOLMOD/Include -I../Include -DNPARTITION...

...3699 0.851474 -3.66912 0.0283103 -0.118455 0.193071 -1.35997 0.103926 -0.0112525 -0.262753 -0.414740 -27.2429  10:           nan: -0.174440 0.823699 0.851474 -3.66912 0.0283103 -0.118455 0.193071 -1.35997 0.103926 -0.0112525 -0.262753 -0.414740 -27.2429 Message d'avis : In mer_finalize(ans) :   Cholmod warning 'not positive definite' at file:../Cholesky/t_cholmod_rowfac.c, line 432 >  sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252    LC_MONETARY=French_France.1252 LC_NUMERIC=C                  [5] L...

Hi: I was trying to use apply on a sparse matrix from package Matrix, and I get the error: Error in asMethod(object) : Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 106 Is there a way to apply a function to all the rows without bumping into this problem? Here is a simplified example: > dim(sm) [1] 72913 43052 > class(sm) [1] "dgCMatrix" attr(,"package") [1] &q...

All: Attached is the output file from building R 2.10.0 on RedHat Linux. I have never previously experienced any problems when building R from source with new releases. But, now I get a compile error with the Matrix package: CHOLMOD/Include/cholmod.h:87:22: error: UFconfig.h: No such file or directory make[3]: *** [CHMfactor.o] Error 1 make[3]: Leaving directory `/tmp/RtmppKsKKl/R.INSTALL327b23c6/Matrix/src' ERROR: compilation failed for package 'Matrix' Any help or suggestions would be appreciated. I am simply...

...the goal is to factor the new matrix A +- C %*% t(C) where C is (n, r). For instance, C is 1-column when adding/removing an observation in a linear regression. Of special interest is the case where A is sparse. Looking at the 'Matrix' package (help and source code), it seems that the CHOLMOD library shipped with 'Matrix' allows this, but is not (yet?) interfaced in 'Matrix', where the 'update' method for Cholesky decomposition objects seems limited to a new matrix A + m*I with a scalar (diagonal) modification. If this is true: are there plans to implement suc...

...n BLAS. The errors occur in the first example in lme4 in a call to lmer. It looks like they would occur in any call to lmer. Running under the debugger shows that the segfault occurs in a call to dtrsm (a level-3 BLAS routine to solve a triangular system of equations) that is called from within a cholmod (sparse matrix library) routine. Has anyone succeeded in running R CMD check on the lme4 package with accelerated BLAS? I'm trying to pin down is this occurs only with ACML or also with Atlas and/or Goto's BLAS.

...ow that we also have "pattern" matrices (purely binary: TRUE/FALSE, no NA) notably sparse ones, those "ngCMatrix" etc, all starting with "n" (from ``patter[n]``) which do play a prominent role in the internal sparse matrix algorithms, notably of the (underlying C code) CHOLMOD library in the so-called "symbolic" cholesky decomposition and other such operations. Another reason you may use them because they are equivalent to incidence matrices of unweighted (directed or undirected) graphs. Now, as the subject says, I'm bringing up the topic of what should ha...

...-installed as well ? [Technical !] This is because lme4 has a 'LinkingTo: Matrix' in its DESCRIPTION and indeed, lme4's C code is using part of Matrix' C code. The change in Matrix: Part of the C-level interface in Matrix is now (again, after several years) using the standard CHOLMOD typedef of UFlong. This means that the C API of Matrix should behave conformly with what other instances of CHOLMOD export. (*) For some, it may be amusing to read https://stat.ethz.ch/pipermail/r-packages/2008/000911.html which was the last announcement of Matrix on R-packages. ____...

...Any help would be very appreciated. Many thanks by advance. PS: I tested fm2<-lmer(data=NGud,family=poisson, seed~hab*seedtray +(1|site)+(1|site/hab)) which also made R crashing. And, fm2<-lmer(data=NGud,family=poisson, seed~hab*seedtray +(1|site/hab)) and for this, I obtained : CHOLMOD warning: matrix not positive definite Error in devLaplace(PQLpars) : Cholmod error `matrix not positive definite' at file:../Supernodal/t_cholmod_super_numeric.c, line 614 J?r?me Lema?tre ?tudiant au doctorat Chaire de recherche industrielle CRSNG - Universit? Laval en sylviculture et fau...

...+ res=eval(parse(text=model)) + res=AIC(logLik(x)) + res=as.vector(res) + totres=rbind(totres,res)} The output would then be just a list of all the AIC of each model. For 1 of the models (the one in the [] above) I'm getting the following error message, which I don't know what it means: CHOLMOD warning: matrix not positive definite Error in objective(.par, ...) : Cholmod error `matrix not positive definite' at file:../Supernodal/t_cholmod_super_numeric.c, line 614 Could anybody give me some advice on using Tweedie distributions and does anybody have an idea what this error message...

...-installed as well ? [Technical !] This is because lme4 has a 'LinkingTo: Matrix' in its DESCRIPTION and indeed, lme4's C code is using part of Matrix' C code. The change in Matrix: Part of the C-level interface in Matrix is now (again, after several years) using the standard CHOLMOD typedef of UFlong. This means that the C API of Matrix should behave conformly with what other instances of CHOLMOD export. (*) For some, it may be amusing to read https://stat.ethz.ch/pipermail/r-packages/2008/000911.html which was the last announcement of Matrix on R-packages. ____...

...nopy+Veg_cm+Treatment+(1|Site/Block/Plot)+(1|Year), family=poisson, REML=FALSE), where richness = integer Y & Treatment = factor Canopy & Veg_cm = numerical, continous Site/Block/Plot= factor Year = integer I get the following warning message: Warning messages: 1: In mer_finalize(ans) : Cholmod warning 'not positive definite' at file:../Cholesky/t_cholmod_rowfac.c, line 432 2: In mer_finalize(ans) : singular convergence (7) Is this due to the nature of my fixed/random factors or the way I put up the random factors? In lme I could include a component for autocorrelation, ex:cor=c...