Hi Marc, Diego, Thank you both for your help. It turns out you're both right, it was a permissions issue. Apparently R was trying to write something into a directory outside my home directory and/or temporary directories (strictly speaking, I don't think it should have to do this). It turns out I didn't have to run R as root, but I did have to run it as the user I originally used to install R and Bioconductor. Is there perhaps a temporary file which is being written to somewhere in the R installation directories, rather than tempdir()? I've had a quick look through the code, but I can't see anything obvious. Many thanks, Tim Rayner 2008/7/14 Marc Carlson <mcarlson at="" fhcrc.org="">: > Hi Tim, > > I have had someone tell me that they had this problem once before, but it > was ultimately a permissions problem. Are you able to run this as root? > > Marc ------------------------------------------------------------------- 2008/7/15 Diego Diez <diez at="" kuicr.kyoto-u.ac.jp="">: > Hi, > > you have to run this in a root session, i.e. making "sudo R". > > Diego. > > > On Tue, Jul 15, 2008 at 1:11 AM, Tim Rayner <tfrayner at="" gmail.com=""> wrote: >> Hi, >> >> I'm having a problem building a custom AnnotationDbi-style package >> using the SQLForge functions. It appears that something from the >> RSQLite package is disagreeing with the makeHUMANCHIP_DB function, >> such that there's an "attempt to write a readonly database". See below >> for a full transcript: >> >>> library('AnnotationDbi') >> Loading required package: Biobase >> Loading required package: tools >> >> Welcome to Bioconductor >> >> Vignettes contain introductory material. To view, type >> 'openVignette()'. To cite Bioconductor, see >> 'citation("Biobase")' and for packages 'citation(pkgname)'. >> >> Loading required package: DBI >> Loading required package: RSQLite >>> makeHUMANCHIP_DB( >> affy=FALSE, >> prefix='Human25kOligoSet.db', >> fileName='refseq.txt', >> baseMapType='refseq', >> outputDir='.', >> version='0.1', >> manufacturer='MRC', >> chipName='Human 25k Oligo Set', >> manufacturerUrl='http://www.geneservice.co.uk') >> baseMapType is refseq >> Prepending Metadata >> Creating Genes table >> Error in sqliteExecStatement(con, statement, bind.data) : >> RS-DBI driver: (RS_SQLite_exec: could not execute1: attempt to write >> a readonly database) >>> sessionInfo() >> R version 2.7.1 (2008-06-23) >> i386-apple-darwin8.10.1 >> >> locale: >> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 >> >> attached base packages: >> [1] tools stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4 >> [4] Biobase_2.0.1 >> >> >> All the packages were installed with biocLite(..., type='source'). The >> "refseq.txt" file is a two-column file with arbitrary probe >> identifiers linked to Refseq accessions, as described in the SQLForge >> vignette. Has anyone else seen this problem? Can anyone point me to >> where my error might be? >> >> Many thanks in advance, >> >> Tim Rayner >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > > -- > Diego Diez, Ph > Bioinformatics center, > Institute for Chemical Research, > Kyoto University. > Gokasho, Uji, Kyoto 611-0011 JAPAN > diez at kuicr.kyoto-u.ac.jp >