Question

Segmentation fault

0

Entering edit mode

Mayte Suarez-Farinas ▴ 300

@mayte-suarez-farinas-694

Last seen 10.2 years ago

Hi all! I installed version 1.9 of R and also devel version of Bioconductor libraries. But I found the following problems. I will be grateful if somebody else can give me some hint.... 1. I couldn't install all BioC package througth getBioC(relLevel="devel",libName="all") Loading required package: reposTools Warning messages: 1: 'package.description' is deprecated. Use 'packageDescription' instead. See help("Deprecated") 2: 'package.description' is deprecated. Use 'packageDescription' instead. See help("Deprecated") 3: cannot open: HTTP status was `404 Not Found' Note: http://www.bioconductor.org/repository/release1.2/package/Source does not seem to have a valid repository, skipping Error in repPkgInfos(reposEntry, pkg, type) : No direct or inherited method for function "repPkgInfos" for this call 2. Then I just install the default packages (getBioC(relLevel="devel")) But I got the following Segmentation fault error while I run mva.pairs function. See output: library(affy) Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Warning message: 'package.description' is deprecated. Use 'packageDescription' instead. See help("Deprecated") > library(affydata) > data(Dilution) > mva.pairs(Dilution) Error in log(x, base) : Non-numeric argument to mathematical function > mva.pairs(exprs(Dilution)) Segmentation fault Here the system information: platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status beta major 1 minor 9.0 year 2004 month 03 day 22 language R -- Mayte Suarez Farinas The Rockefeller University 1230 York Avenue, Box 212 New York, NY 10021 phone: 1-212-327-8186 fax: 1-212-327-7422

• 1.2k views

ADD COMMENT • link updated 20.7 years ago by Jeff Gentry ★ 3.9k • written 20.7 years ago by Mayte Suarez-Farinas ▴ 300

score 0 · Answer 1 · 2004-03-25

0

Entering edit mode

Jeff Gentry ★ 3.9k

@jeff-gentry-12

Last seen 10.2 years ago

> 1. I couldn't install all BioC package througth > getBioC(relLevel="devel",libName="all") How did you get getBioC.R? Did you have an older version saved on disk and used that? Or did you source it directly from bioconductor.org?

ADD COMMENT • link 20.7 years ago Jeff Gentry ★ 3.9k

0

Entering edit mode

On Thu, 25 Mar 2004, Jeff Gentry wrote: Directly from Bioconductor througth "source("http://www.bioconductor.org/getBioC.R") > > 1. I couldn't install all BioC package througth > > getBioC(relLevel="devel",libName="all") > > How did you get getBioC.R? Did you have an older version saved on disk > and used that? Or did you source it directly from bioconductor.org? > -- Mayte Suarez Farinas The Rockefeller University 1230 York Avenue, Box 212 New York, NY 10021 phone: 1-212-327-8186 fax: 1-212-327-7422

ADD REPLY • link 20.7 years ago Mayte Suarez-Farinas ▴ 300

0

Entering edit mode

> Directly from Bioconductor througth > "source("http://www.bioconductor.org/getBioC.R") It would appear that perhaps the prevRepos code (where it tries to update from the repository that you originally downloaded things from) is being too aggressive - that's the only reason I can think of that it would be tryign to download from the 1.2 repository. I will look into this. In the meantime, can you try deleting the file <pathtor>/library/liblisting.rda and see if that helps?

ADD REPLY • link 20.7 years ago Jeff Gentry ★ 3.9k

0

Entering edit mode

On Fri, 26 Mar 2004, Jeff Gentry wrote: > It would appear that perhaps the prevRepos code (where it tries to update > from the repository that you originally downloaded things from) is being > too aggressive - that's the only reason I can think of that it would be > tryign to download from the 1.2 repository. I will look into this. > In the meantime, can you try deleting the file > <pathtor>/library/liblisting.rda and see if that helps? No, Jeff, It doesn't work. In fact I deleted liblisting.rda, and when I load affy (library(affy)) it appears inmediately in R/library. Kind regards.. -- Mayte Suarez Farinas The Rockefeller University 1230 York Avenue, Box 212 New York, NY 10021 phone: 1-212-327-8186 fax: 1-212-327-7422

ADD REPLY • link 20.7 years ago Mayte Suarez-Farinas ▴ 300

0

Entering edit mode

Hello All, May I ask those of you that have used CV cut offs for eliminating non variable genes on Affy chips, what is the cut off you tend to use? I thank you for your attention, Lawrence _______________________________ Lawrence-Paul Petalidis Ph.D Candidate Department of Pathology Division of Molecular Histopathology University of Cambridge

ADD REPLY • link 20.7 years ago Lawrence Paul Petalidis ▴ 130