[BioC] package availability for R3.01
Martin Morgan
mtmorgan at fhcrc.org
Thu Sep 5 17:21:25 CEST 2013
On 09/05/2013 07:12 AM, E.M. Lodder wrote:
> Thanks all for the input!
> For the moment I'll just use the older version of R in paralel to the new one just to annotate.
It would be really helpful to understand what difficulty you are encountering,
especially if it is on 'our' end. It would help to see the full transcript of
the session where you try to install the hgu133plus2.db package, followed by the
output of sessionInfo(). This will tell us for instance what specific file your
R version is trying to download (this should also be downloadable from a web
browser; please check that this is the case) as well as your operating system
and locale, all of which have sometimes caused problems. Also a common problem
is installation when your institution uses a proxy; this would cause problems
with installing a CRAN package as well, so something like
install.packages("ggplot2") and / or biocLite("ggplot2") would also fail; I
think the solution to the proxy issue is discussed on the help page
?download.packages.
Here's my session, on a linux system from the command line
R --vanilla --silent
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.12 (BiocInstaller 1.10.3), ?biocLite for help
> biocLite("hgu133plus2.db")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1.
Installing package(s) 'hgu133plus2.db'
trying URL
'http://bioconductor.org/packages/2.12/data/annotation/src/contrib/hgu133plus2.db_2.9.0.tar.gz'
Content type 'application/x-gzip' length 2147816 bytes (2.0 Mb)
opened URL
==================================================
downloaded 2.0 Mb
* installing *source* package ‘hgu133plus2.db’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (hgu133plus2.db)
The downloaded source packages are in
‘/tmp/RtmpZ1HWPZ/downloaded_packages’
> sessionInfo()
R version 3.0.1 Patched (2013-08-11 r63538)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.10.3
loaded via a namespace (and not attached):
[1] tools_3.0.1
Martin
>
> Elisabeth
>
> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon at uw.edu]
> Sent: donderdag 5 september 2013 15:49
> To: E.M. Lodder
> Cc: 'Diego Diez'; bioconductor at r-project.org
> Subject: Re: [BioC] package availability for R3.01
>
> Hi Elisabeth,
>
> On Thursday, September 05, 2013 8:28:34 AM, E.M. Lodder wrote:
>> Hi Diego,
>>
>> Sorry I didn't copy that in the example, but I did install it first, it gives exactly the same error message.
>
> You must not have installed the hgu133plus2.db package, because it is available, and can be installed. As an example, here is my R-3.0.1 sessionInfo after installing the package:
>
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] hgu133plus2.db_2.9.0 org.Hs.eg.db_2.9.0 RSQLite_0.11.4
> [4] DBI_0.2-7 AnnotationDbi_1.22.6 Biobase_2.20.1
> [7] BiocGenerics_0.6.0 BiocInstaller_1.10.3
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.18.3 stats4_3.0.1 tools_3.0.1
>
>
>>
>> Does anyone know the reason for not allowing these packages in newer versions of BioC?
>> I guess many people like me will have older datasets they may want to reanalyse.
>> The contents of these kind of reference packages is not code which I can understand may refer to obsolete functions etc. but just reference data, for the annotation of the probe names so I don't really understand why they would not just be taken along.
>
> The Illumina package you are wanting to install was made by Mark Dunning, who contributed it to BioC. He has evidently stopped creating this package for us (which has to happen each release), although he is still making other packages. You might contact him directly, or look on the website he cites
> (http://compbio.sysbiol.cam.ac.uk/Resources/Annotation/index.html) to see what the deal is with that package.
>
> Or you could just install the 'regular' illuminaMousev2.db' package and use that instead.
>
> We cannot arbitrarily take annotation packages along, because the underlying infrastructure can and does change with each successive release. Unless the package is rebuilt using the newest versions of R and requisite BioC packages, there is no guarantee that a given old package will continue to work correctly.
>
> That said, there is nothing preventing you from installing the old package version into your new version of R. In addition, there is nothing preventing you from installing an old version of R and then installing the old annotation package using biocLite(). Except that you will then be on your own, and should not expect anybody to give you support, as we only support current versions of packages, and certainly don't support old versions of packages installed in current BioC installations.
>
> Best,
>
> Jim
>
>
>>
>> Elisabeth
>>
>> -----Original Message-----
>> From: kurai.yousei at gmail.com [mailto:kurai.yousei at gmail.com] On Behalf
>> Of Diego Diez
>> Sent: donderdag 5 september 2013 10:51
>> To: E.M. Lodder
>> Cc: Marc Carlson; bioconductor at r-project.org
>> Subject: Re: [BioC] package availability for R3.01
>>
>> The link you include with illuminaMousev2BeadID.db is for bioconductor
>> 2.6 (i.e. a release several years old). It seems that package does not exist anymore in Bioconductor (since version 2.9, now we are in 2.12).
>> As for hgu133plus2.db, you have to install it first (you only tried to install illuminaMousev2BeadID.db in your example code). Try:
>>
>> biocLite("hgu133plus2.db")
>> library(hgu133plus2.db)
>>
>> HTH,
>>
>> Diego
>>
>>
>> On Thu, Sep 5, 2013 at 5:29 PM, E.M. Lodder <e.m.lodder at amc.uva.nl> wrote:
>>>
>>> Hi all,
>>>
>>> I'm afraid that doesn't answer my question, both packages are available through the bioconductor website:
>>>
>>> http://bioconductor.org/packages/2.6/data/annotation/html/illuminaMou
>>> s
>>> ev2BeadID.db.html
>>> and
>>> http://bioconductor.org/packages/release/data/annotation/html/hgu133p
>>> l
>>> us2.db.html
>>>
>>> but give this same error message when installing:
>>>
>>>> Warning message:
>>>> package 'illuminaMousev2BeadID.db' is not available (for R version
>>>> 3.0.1)
>>>
>>> any more ideas?
>>>
>>> Elisabeth
>>>
>>>
>>> -----Original Message-----
>>> From: bioconductor-bounces at r-project.org
>>> [mailto:bioconductor-bounces at r-project.org] On Behalf Of Marc Carlson
>>> Sent: woensdag 4 september 2013 22:21
>>> To: bioconductor at r-project.org
>>> Subject: Re: [BioC] package availability for R3.01
>>>
>>> Hi Elisabeth,
>>>
>>> That package "illuminaMousev2BeadID.db" is not a bioconductor package and I don't think it ever has been a bioconductor package. Perhaps someone in the past made a custom package for you and then named it that? In any case, you can look at this vignette if you need to repeat that process:
>>>
>>> http://www.bioconductor.org/packages/release/bioc/vignettes/Annotatio
>>> n
>>> Forge/inst/doc/SQLForge.pdf
>>>
>>>
>>> As for the "hgu133plus2.db" package, you can get that package using
>>> biocLite() as it is a bioconductor package. If you want to see a list of all the annotation packages for the latest release you can find it here:
>>>
>>> http://www.bioconductor.org/packages/release/BiocViews.html#___Annota
>>> t
>>> ionData
>>>
>>>
>>>
>>> Marc
>>>
>>>
>>>
>>>
>>> On 09/04/2013 12:39 PM, E.M. Lodder wrote:
>>>> Hi All,
>>>>
>>>> Just a quick question I just updated my R to 3.01 and wanted to reinstall some of the packages I was using.
>>>> Now I do get the following error message:
>>>>
>>>>> source("http://bioconductor.org/biocLite.R")
>>>>> biocLite("illuminaMousev2BeadID.db")
>>>> BioC_mirror: http://bioconductor.org Using Bioconductor version 2.12
>>>> (BiocInstaller 1.10.3), R version 3.0.1.
>>>> Installing package(s) 'illuminaMousev2BeadID.db'
>>>> Warning message:
>>>> package 'illuminaMousev2BeadID.db' is not available (for R version
>>>> 3.0.1)
>>>>> library("hgu133plus2.db",character.only = TRUE)
>>>> Error in library("hgu133plus2.db", character.only = TRUE) :
>>>> there is no package called 'hgu133plus2.db'
>>>>> library("illuminaMousev2BeadID.db", character.only = TRUE)
>>>> Error in library("illuminaMousev2BeadID.db", character.only = TRUE) :
>>>> there is no package called 'illuminaMousev2BeadID.db'
>>>> Any ideas on how to fix this? Or should I just operate with two different versions of R in parallel for the moment?
>>>>
>>>> Thanks!
>>>>
>>>> Elisabeth
>>>> ________________________________
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>>>
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>> ________________________________
>>
>> AMC Disclaimer : http://www.amc.nl/disclaimer
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