Hello, I am using a dual processor Power Mac G5: System Version: Mac OS X 10.3.9 (7W98) Kernel Version: Darwin 7.9.0 I work with a series of custom cDNA microarray platforms (~10). I annotated them using ABPkgBuilder from the AnnBuilder package. This has worked nicely. The packages built under bioconductor 1.8 (for R 2.2 ) can be installed on the the newer bioconductor 1.9 (for R 2.4) with the shell command, to install, e.g., the package "foo": $ sudo R CMD INSTALL foo Password: * Installing *source* package 'foo' ... ** R ** data ** moving datasets to lazyload DB ** help >>> Building/Updating help pages for package 'foo' Formats: text html latex example ** building package indices ... * DONE (foo) However when I try to use it, lookUp returns an error (and exerpt of the traceback): Error in `parent.env<-`(`*tmp*`, value = NULL) : use of NULL environment is defunct > traceback() 13: `parent.env<-`(`*tmp*`, value = NULL) 12: function (n) { if (existsInFrame(n, envenv)) getFromFrame(n, envenv) else { e <- mkenv() set(n, e, envenv) key <- getFromFrame(n, env) data <- lazyLoadDBfetch(key, datafile, compressed, envhook) parent.env(e) <- data$enclos vars <- names(data$bindings) for (i in along(vars)) set(vars[i], data$bindings[[i]], e) e } }("env::1") 11: .Call("R_lazyLoadDBfetch", key, file, compressed, hook, PACKAGE = "base") 10: lazyLoadDBfetch(key, datafile, compressed, envhook) 9: get(paste(data, what, sep = "")) 8: mget(x, env = get(paste(data, what, sep = "")), ifnotfound = NA) 7: lookUp(keys, "foo", x) ... I am thus rebuilding the packages anew. The problem is that downloading the public databases (UniGene, etc...) takes a substantial amount of time. In addition, in my system, the temporarty folders are automatically and periodically removed along with the downloaded files, which disrupts the process when it takes very long. The downloaded files are named automatically [with tempfile()] and put in the per-session temporary directory: $ ls -l /private/tmp/RtmptH8Ikl/ total 1168204 -rw-r--r-- 1 David wheel 684448428 Oct 24 12:31 file1c06dac8Hs.data -rw-r--r-- 1 David wheel 500952812 Oct 24 12:50 file6058ed8gene2accession -rw-r--r-- 1 David wheel 2151508 Oct 24 11:57 tempFile10d63af1 -rw-r--r-- 1 David wheel 2151508 Oct 24 11:59 tempFile3ab50c2a -rw-r--r-- 1 David wheel 2234013 Oct 24 15:44 tempFile427c3c55 -rw-r--r-- 1 David wheel 2151508 Oct 24 12:01 tempFile4431b782 -rw-r--r-- 1 David wheel 2151508 Oct 24 11:58 tempFile60b7acd9 So I can't easily keep track of them. I am looking for a way to download the files only once to a local, non-temporary directory, and to retrieve or choose their names. Then, I want to build the first package and reuse the downloaded files for the remaining packages. Once I have achieved this, I can use the procedure to update my annotation packages, for example, monthly. I know that ABPkgBuilder has a "fromWeb" argument to allow for local source files but I can't figure out how to pass the location or names of these files to the function. If I knew I'd still have to figure out how to retrieve the file names and locations in the first place. If somebody has already solved this problem it would save me a lot of time to know about it. Else, I will post the solution when/if I get to it. Thanks a lot, David Weiss Solis --------------------------------------------------------- p.s: session information : > sessionInfo() R version 2.4.0 (2006-10-03) powerpc-apple-darwin7.9.0 locale: C attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: AnnBuilder RSQLite DBI annotate XML Biobase marray "1.12.0" "0.4-4" "0.1-10" "1.12.0" "0.97-8" "1.12.1" "1.12.0" limma foo "2.9.1" "1.1.0" ----------------------------------------------------------- Ir. David Weiss Solis IRIBHM Bldg C, room C.4.116? ULB, Campus Erasme, CP602? 808 route de Lennik? B-1070 Brussels? Belgium Phone: +32-2-555 4220? Fax: +32-2-555 4655 E-mail: dweiss at ulb.ac.be URL: http://homepages.ulb.ac.be/~dweiss/