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

James MacDonald jmacdon at med.umich.edu
Thu Sep 20 21:22:31 CEST 2007


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



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