Hi Mark, I think you might have missed some updates, as the current AnnotationDbi that I get is version 0.99.1 (which _is_ a higher version). > sessionInfo() R version 2.6.0 alpha (2007-09-12 r42830) i386-apple-darwin8.10.1 locale: C attached base packages: [1] splines tools stats graphics grDevices datasets utils [8] methods base other attached packages: [1] affycoretools_1.9.5 annaffy_1.9.5 KEGG_1.99.10 [4] GO_1.99.1 gcrma_2.9.1 matchprobes_1.9.10 [7] biomaRt_1.11.14 RCurl_0.8-1 GOstats_2.3.17 [10] Category_2.3.39 genefilter_1.15.11 survival_2.32 [13] RBGL_1.13.6 annotate_1.15.12 xtable_1.5-1 [16] GO.db_1.99.3 AnnotationDbi_0.99.1 RSQLite_0.6-0 [19] DBI_0.2-3 graph_1.15.20 limma_2.11.13 [22] affy_1.15.9 preprocessCore_0.99.19 affyio_1.5.11 [25] Biobase_1.15.34 loaded via a namespace (and not attached): [1] XML_1.92-1 cluster_1.11.8 Best, Jim
Mark W Kimpel wrote:
I just updated my packages and now cannot load affycoretools. I
downloaded today's R-beta build and re-updated packages but the problem
persists. I do have 3 packages (below) that do not update properly, but
I don't think any of them should be contributing to this problem.
I almost think it could be something as silly as GO.db not recognizing
that 0.1.15 is the latest ver. of AnnotationDbi, i.e. is 0.1.15 > 0.99.
Anyway, thought I should report this so we can get the devel release
tidied up before release. Oh, yeah, also so I can get my beloved
affycoretools working again ;)
Mark
The downloaded packages are in
/tmp/Rtmp9aX8RX/downloaded_packages
[1] "packages updated"
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, contriburl =
contriburl, :
installation of package 'MANOR' had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, contriburl =
contriburl, :
installation of package 'qvalue' had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, contriburl =
contriburl, :
installation of package 'tkWidgets' had non-zero exit status
> sessionInfo()
R version 2.6.0 beta (2007-09-18 r42895) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] limma_2.11.13 affy_1.15.9 preprocessCore_0.99.18 [4] affyio_1.5.11 Biobase_1.15.33 graph_1.15.20 loaded via a namespace (and not attached): [1] cluster_1.11.8 rcompgen_0.1-15
> require(affycoretools)
Loading required package: affycoretools Loading required package: GOstats Loading required package: GO.db Error: package 'AnnotationDbi' 0.1.15 was found, but >= 0.99.1 is required by 'GO.db' Enter a frame number, or 0 to exit 1: require(affycoretools) 2: library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = 3: .getRequiredPackages2(pkgInfo) 4: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.lo 5: .getRequiredPackages2(pkgInfo) 6: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.lo 7: .getRequiredPackages2(pkgInfo) Selection:
James W. MacDonald, MS Biostatistician UMCCC cDNA and Affymetrix Core University of Michigan 1500 E Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623