Hi Mark,
I think a much easier and safer way to update is as follows:
source("http://www.bioconductor.org/biocLite.R")
## I just have the above in my .Rprofile file, so biocLite() is always
there for me.
biocLite("Biobase")
repos <- biocReposList()
update.packages(repos=repos, ask=FALSE)
this will get all CRAN and BioC packages, and got me correctly updated
this morning.
Probably the problem with your script is you are hitting the IL mirror,
and it might be out of synch with fhcrc. Try the above and see if it helps.
Best,
Jim
Mark W Kimpel wrote:
Jim,
I don't understand it, but you are correct. Below is the function I have
been using to get updates, using the IL mirror (formatting is as pretty
as I can make it for email). Basically, the function tests to see if it
has been >7 days since my last update, and, if so, updates from all
repositories. I can also force updates with the argument force = TRUE,
which I did several times last night. In fact, I know that many things
updated, because that was when the original error began occurring. I
have never received an error from this function.
When I the function last night, several times, AnnotationDbi was not
updating; this morning, it and several other BioC packages (oligo,
annotate for example) updated.
Is there something wrong with my function? Is it possible that several
of the updates had just not propagated to the IL mirror? I don't want to
use this function if it is wrong or unreliable, but it is convenient.
Here's the function:
##############################################################
my.update.packages.func <- function(force = FALSE){
require(utils)
old.wd <- getwd()
setwd("~/")
last.update.error <- try(load(file = ".Rupdate.date"), TRUE)
if(inherits(last.update.error, "try-error"))
{last.update <- as.POSIXct("2007-01-01")} else {
load(file = ".Rupdate.date")}
#if .Rupdate.date does not exist or can't load, update
if(force) {last.update <- as.POSIXct("2007-01-01")}
#allow to force updates
current.time <- Sys.time()
time.diff <- current.time - last.update
if(
(
(units(time.diff) == "days")
&&
(time.diff[[1]][1] >= 7)
) ||
inherits(last.update.error, "try-error")
)
{ #then update
update.packages(ask = FALSE) #all CRAN packages
update.packages(repos="http://www.bioconductor.org/packages/2.1/bioc",
ask = FALSE) #main BioC repos
update.packages(repos="http://www.bioconductor.org/packages/2.1/data/annotation",
ask = FALSE)
update.packages(repos="http://www.bioconductor.org/packages/2.1/data/experiment",
ask = FALSE)
update.packages(repos="http://www.bioconductor.org/packages/2.1/extra",
ask = FALSE)
update.packages(repos="http://www.omegahat.org/R", ask = FALSE)
update.packages(repos="http://www.stats.ox.ac.uk/pub/RWin", ask = FALSE)
last.update <- current.time
local(save(last.update, file = ".Rupdate.date"))
print("packages updated")
} else {
print("packages do not need updated")}
setwd(old.wd)
}
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, & Mobile & VoiceMail
(317) 663-0513 Home (no voice mail please)
******************************************************************
James MacDonald wrote:
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