[BioC] Affy 1.5.8 functions not working on Mac OS X 10.3
Robert Gentleman
rgentlem at fhcrc.org
Tue Jan 25 20:57:25 CET 2005
On Jan 25, 2005, at 9:35 AM, Chad Wayne wrote:
> I appreciate you taking the time to answer my questions.
>
>>
>> On Jan 24, 2005, at 12:55 PM, Chad Wayne wrote:
>>
>>> It was recommended that I post this problem to the mailing list. I
>>> am unable to get affy to work, e.g. the library loads into R, but
>>> the functions don't seem to work. I was hoping someone may have seen
>>> this problem before and may have a solution. I am working in the
>>> correct working directory.
>>>
>>> I am using version v2.0.1 of R with the default Bioconductor package
>>> installed. Current package of Affy is 1.5.8. I am using Mac OS X
>>> 10.3.7 and running X11 (X11 1.0 - XFree86 4.3.0). This is a shared
>>> environment and all packages were installed in the top library, not
>>> in the User library.
>>>
>>> On prompt:
>>> > load("/nnn/nnn/nnn/timecourse.RData")
>>
>>> > library(affy)
>>> Loading required package: Biobase
>>> Loading required package: tools
>>> Loading required package: reposTools
>>
>> So, if you go
>> search()
>> at this point you should get something like:
>> > search()
>> [1] ".GlobalEnv" "package:affy" "package:reposTools"
>> [4] "package:Biobase" "package:tools" "package:methods"
>> [7] "package:stats" "package:graphics" "package:grDevices"
>> [10] "package:utils" "package:datasets" "Autoloads"
>> [13] "package:base"
>>
>> The important things are for affy and Biobase to be there (at least
>> given what you are saying below)
>>
>
> I loaded affy and did the search as you suggested:
>
> > library(affy)
> Loading required package: Biobase
> Loading required package: tools
> Loading required package: reposTools
> > search()
> [1] ".GlobalEnv" "package:affy" "package:reposTools"
> [4] "package:Biobase" "package:tools" "package:methods"
> [7] "package:stats" "package:graphics" "package:grDevices"
> [10] "package:utils" "package:datasets" "Autoloads"
> [13] "package:base"
>
> Appears to be there along with biobase.
>
>
>>> > ReadAffy(widget=T)
>>> Error: couldn't find function "ReadAffy"
>>> > ReadAffy()
>>> Error: couldn't find function "ReadAffy"
>>> > pData(eset)
>>> Error: couldn't find function "pData"
>>>
>>
>>
>> You can also try something like
>> ls("package:affy")
>>
>> which should show about 116 things (mostly functions) and one should
>> be ReadAffy.
>>
>
> I also performed the ls("package:affy") and retrieved 116 items. I
> attempted again to try the ReadAffy function and it failed.
>
Hmm, this seems really odd. So a whole bunch of questions in the
hopes that one of them sheds some light on what your problem is.
Basically, if the library is attached and the function is listed, it is
there (or ought to be). Please show the entire transcript of you
session (in answering the questions below, not just the part you want
to) [possibly skipping to the end, as I now suspect that you do not
have enough system software installed - we should think about how to
find that out more automatically]
If you just type ReadAffy, what happens?
what if you type the name of one of the other functions (in any of the
packages)?
what is .libPaths() reporting?
>> If not, then the installation is not correct. Are you sure they have
>> global read permission etc on the R library directory and all
>> contents? Have you checked to see if there are any files
>> in those directories?
>>
>
> Do I need to go to terminal to change the permissions or is there a
> nice simple way to check permissions and change them accordingly if
> that is the problem. Sorry that this appears so dense, but I haven't
> quite got the hang of the unix side of OsX yet.
>
I doubt I was right about that; but there is nothing special going on
on OS X, you do need a lot of stuff installed though - and that might
be your problem.
try this:
> capabilities()
jpeg png tcltk X11 http/ftp sockets libxml fifo
TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
cledit IEEE754 iconv
TRUE TRUE TRUE
And in particular you are going to need X11 and tcltk (and you want
most of the others). The R FAQ for OS X provides explicit details on
how to do this.
Robert
> Thanks again,
>
> Chad.
>
>> Robert
>>
>>> I've also attempted to "start from scratch" from the original .cel
>>> files and get the same type of error message that the function
>>> couldn't be found.
>>>
>>> I have checked to ensure that affy is installed and loaded, and
>>> based on the Package Manager, it is .
>>>
>>>
>>> I've also tried using limma (v1.8.10), and had no problems, other
>>> than I can't read in the eset.
>>>
>>> > packageDescription("limma", field="Version")
>>> [1] "1.8.10"
>>> > packageDescription("affy", field="Version")
>>> [1] "1.5.8"
>>> > version
>>> _
>>> platform powerpc-apple-darwin6.8
>>> arch powerpc
>>> os darwin6.8
>>> system powerpc, darwin6.8
>>> status
>>> major 2
>>> minor 0.1
>>> year 2004
>>> month 11
>>> day 15
>>> language R
>>>
>>>
>>> Thanks for the assistance.
>>>
>>> Chad Wayne
>>>
>>> Chad M. Wayne, Ph. D.
>>> Baylor College of Medicine
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>
>>>
>> +---------------------------------------------------------------------
>> ------------------+
>> | Robert Gentleman phone: (206) 667-7700
>> |
>> | Head, Program in Computational Biology fax: (206) 667-1319 |
>> | Division of Public Health Sciences office: M2-B865
>> |
>> | Fred Hutchinson Cancer Research Center
>> |
>> | email: rgentlem at fhcrc.org
>> |
>> +---------------------------------------------------------------------
>> ------------------+
>>
>>
>
>
+-----------------------------------------------------------------------
----------------+
| Robert Gentleman phone: (206) 667-7700
|
| Head, Program in Computational Biology fax: (206) 667-1319 |
| Division of Public Health Sciences office: M2-B865
|
| Fred Hutchinson Cancer Research Center
|
| email: rgentlem at fhcrc.org
|
+-----------------------------------------------------------------------
----------------+
More information about the Bioconductor
mailing list