[Bioc-devel] failure to load affycoretools in R-beta

[James MacDonald]

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