[BioC] Problems with affy on Ubuntu 10.10: "extended" option in sub/R missing

[Martin Morgan]

On 01/29/2011 01:15 PM, January Weiner wrote:
> Dear Martin,
> 
> thank you so much. This seems to have been the problem. I relied on
> the fact that many packages report a problem with R version when they
> are loaded, and usually I just updated them whenever I saw the
> respective message ("this package has been build for a different
> version of R") when I loaded them.
> 
> regards,
> 
> j.
> 
> On Sat, Jan 29, 2011 at 8:52 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>> On 01/29/2011 11:01 AM, January Weiner wrote:
>>> Hello,
>>>
>>> I cannot use ReadAffy() in Ubuntu 10.10 (it works in Ubuntu 10.04).
>>>
>>>> ab <- ReadAffy()
>>> Error in sub("^/?([^/]*/)*", "", filenames, extended = TRUE) :
>>>   unused argument(s) (extended = TRUE)
>>>
>>> The reason is that the sub() function from R lacks the optional
>>> argument "extended":
>>
>> Hi January --
>>
>> This is likely a version mismatch between your R and Bioc packages;
>> follow instructions at
>>
>> http://bioconductor.org/install/index.html#update-bioconductor-packages
>>
>> and
>>
>> source("http://bioconductor.org/biocLite.R")
>> update.packages(repos=biocinstallRepos(), ask=FALSE, checkBuilt=TRUE)
>>
>> Or update your R and create a fresh bioc install.
>>
>> Martin
>>
>>>
>>>> a <- rep( "a", 10 )
>>>> sub( "a", "b", a )
>>>  [1] "b" "b" "b" "b" "b" "b" "b" "b" "b" "b"
>>>> sub( "a", "b", a, extended=TRUE )
>>> Error in sub("a", "b", a, extended = TRUE) :
>>>   unused argument(s) (extended = TRUE)
>>>
>>> No such errors occur in Ubuntu 10.04.
>>>
>>> The R version that comes with Ubuntu 10.10 is 2.11.1:
>>>
>>>> sessionInfo()
>>> R version 2.11.1 (2010-05-31)
>>> i686-pc-linux-gnu
>>>
>>> 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=C              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] affy_1.22.1   Biobase_2.4.1
>>>
>>> loaded via a namespace (and not attached):
>>> [1] affyio_1.12.0        preprocessCore_1.6.0
>>>
>>>
>>> In Ubuntu 10.04, the version of R is 2.10.1
>>>
>>> My question: is that a general problem with R 2.11.1, or a problem
>>> with Ubuntu? Is anyone aware of that problem? I am trying to figure
>>> out what would be the easiest way of getting back the 2.10.1 version
>>> (short of deinstalling all R packages and libraries and manually
>>> reinstalling them again), I will post a solution if I find an easy
>>> one.

On windows it is usual to install pre-built packages; on linux packages
are usually built by the R that is doing the installation. So if the R
is told to build and install the wrong package, there is no warning.
Using biocLite avoids this problem. You could put

options(repos=c(CRAN="http://cran.fhrcr.org"))
utils::setRepositories(ind=1:6)
old.packages()

in ~/.Rprofile to be alerted of all currently installed packages that
are out of date (though this might get irritating with a slow internet
connection / large number of packages.

Martin

>>>
>>> best regards,
>>>
>>> j.
>>>
>>
>>
>> --
>> Computational Biology
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>>
>> Location: M1-B861
>> Telephone: 206 667-2793
>>
> 
> 
> 


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793