search for: affycoretool

Hi again, I have been playing around with the order of loading packages, and as far as I can tell, there's nothing specific with affycoretools that's causing my Rgui to crash (i.e., shuts down and the Microsoft 'please send error report' box pops up). Instead, it has something to do with the order & type of packages that are loaded that add items to the menu bar by themselves, or adding more options under 'Vignett...

I am having problem installing the affycoretools package. When I do it through biocLite, I get error messages saying the package XML cannot be installed and that I need a more recent version of libxml2. When I try to install the tar.gz file, I get the message /usr/local/R/2.4.0/lib/R/bin/exec/R: error while loading shared libraries: libg2c.so....

...-8;LC_IDENTIFICATION=C attached base packages: [1] "splines" "stats" "graphics" "grDevices" "datasets" "utils" [7] "tools" "methods" "base" other attached packages: multtest rat2302cdf affycoretools annaffy xtable "1.13.1" "1.15.0" "1.7.8" "1.7.3" "1.4-3" gcrma matchprobes biomaRt RCurl XML "2.7.3" "1.7.4" "1.9.21"...

...-8;LC_IDENTIFICATION=C attached base packages: [1] "splines" "stats" "graphics" "grDevices" "datasets" "utils" [7] "tools" "methods" "base" other attached packages: multtest rat2302cdf affycoretools annaffy xtable "1.13.1" "1.15.0" "1.7.8" "1.7.3" "1.4-3" gcrma matchprobes biomaRt RCurl XML "2.7.3" "1.7.4" "1.9.21"...

...-8;LC_IDENTIFICATION=C attached base packages: [1] "splines" "stats" "graphics" "grDevices" "datasets" "utils" [7] "tools" "methods" "base" other attached packages: multtest rat2302cdf affycoretools annaffy xtable "1.13.1" "1.15.0" "1.7.8" "1.7.3" "1.4-3" gcrma matchprobes biomaRt RCurl XML "2.7.3" "1.7.4" "1.9.21"...

Hi, I have a microarray dataset of dimension 25000x30 and try to clustering using hclust(). But the clustering on the rows failed due to the size: > y<-hclust(dist(data),method='average') Error: cannot allocate vector of size 1.9 Gb I tried to increase the memory using memory.limit(size=3000), still got the same error. I also tried agnes() from cluster package and pvclust() from

I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is

...attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: made4 scatterplot3d ade4 affycoretools annaffy "1.8.0" "0.3-24" "1.4-2" "1.7.5" "1.6.1" xtable gcrma matchprobes biomaRt RCurl "1.4-3" "2.6.0" "1.6.0" "1.8.1&q...

...tin > > "Mark Kimpel" <mwkimpel@gmail.com> writes: > > > I'm having same problem on Ubuntu 64-bit Hardy Heron. A bunch of > security > > patches from Ubuntu came out and I installed them today. After that was > when > > I first noted the problem (affycoretools, which I use all the time, > won't > > load). Below is my initial output, what follows is my reinstallation > output > > followed by the same error messages as obtained intially. I wonder if a > > security patch has changed Curl? Or did RCurl just change? I have been &g...

...tin > > "Mark Kimpel" <mwkimpel@gmail.com> writes: > > > I'm having same problem on Ubuntu 64-bit Hardy Heron. A bunch of > security > > patches from Ubuntu came out and I installed them today. After that was > when > > I first noted the problem (affycoretools, which I use all the time, > won't > > load). Below is my initial output, what follows is my reinstallation > output > > followed by the same error messages as obtained intially. I wonder if a > > security patch has changed Curl? Or did RCurl just change? I have been &g...