Hello,
Here are the items to help narrow it down.
Short example:
library(aroma.affymetrix)
library(Repitools)
annotation <- data.frame(chr = rep("chr1", 3), start = c(781253, 850983,
885829), end = c(783614, 869824, 890958), strand = rep('+', 3))
cdf <- AffymetrixCdfFile$byChipType("Hs_PromPR_v02")
cdfU <- getUniqueCdf(cdf)
cel.set <- AffymetrixCelSet$byName("FaK9Ac", cdf = cdf)
MATNormalise <- MatNormalization(cel.set)
csN <- process(MATNormalise)
csNU <- convertToUnique(csN)
surround.scores <- featureScores(csNU, annotation, up = 5000, down = 2000, freq
= 500, chrs = paste("chr", c(1:22, 'X', 'Y', 'M'), sep = '')) # Function in
Repitools.
Error:
readUnits.AffymetrixCdfFile(): Updating cache
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "trim", for signature
"character"
R Session:
R version 2.13.0 (2011-04-13)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8
LC_COLLATE=en_AU.UTF-8 LC_MONETARY=C
[6] LC_MESSAGES=en_AU.UTF-8 LC_PAPER=en_AU.UTF-8 LC_NAME=C
LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomicRanges_1.4.8 IRanges_1.10.6 Repitools_0.99.24
aroma.affymetrix_2.1.9 affxparser_1.24.0
[6] aroma.apd_0.2.0 R.huge_0.3.0 aroma.core_2.1.5
aroma.light_1.20.0 matrixStats_0.2.2
[11] R.rsp_0.6.2 R.cache_0.5.1 R.filesets_1.1.0
digest_0.5.0 R.utils_1.7.8
[16] R.oo_1.8.1 R.methodsS3_1.2.1
loaded via a namespace (and not attached):
[1] Biobase_2.11.10 Biostrings_2.19.18 BSgenome_1.19.6
---- Original message ----
>Date: Fri, 2 Sep 2011 05:50:13 -0700
>From: aroma-affymetrix@googlegroups.com (on behalf of Henrik Bengtsson
><henrik.bengts...@aroma-project.org>)
>Subject: Re: [aroma.affymetrix] Function Clash With IRanges
>To: aroma-affymetrix@googlegroups.com
>
>Hi,
>
>thanks for this. The issue with the trim() clash with IRanges was
>(supposed to be) dealt with in aroma.core v1.0.6 [2009-05-14]:
>
>o BUG FIX: Now aroma.core works with the IRanges and grid packages,
> regardless on the order they were loaded.
>
>and the comments in the code show that this especially done regarding
>trim(). The fix is that aroma.core makes sure IRanges will always come
>after R.oo in the search() path. So, I'm interesting in getting more
>details about your case. Could you please:
>
>1. Produce a minimum example that gives this error.
>2. Show exactly what error you get.
>3. Report your sessionInfo() after you get the error.
>
>Thanks,
>
>Henrik
>
>
>On Fri, Sep 2, 2011 at 2:00 AM, Dario Strbenac <dario.gar...@gmail.com> wrote:
>> When loading aroma.affymetrix, then calling a function that has
>> require(GenomicRanges) in it, that has AromaCellPositionFile
>> $byChipType(getChipType(cdf)), I get an error because IRanges has a
>> trim method too, and the aroma method eventually calls trim(tags).
>>
>> Should this be R.oo::trim(tags) in the next release ?
>>
>> I have IRanges 1.10.6, aroma.affymetrix 2.1.9 and R.oo_1.8.1 in R
>> 2.13.0.
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
>> version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> To post to this group, send email to aroma-affymetrix@googlegroups.com
>> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>>
>
>--
>When reporting problems on aroma.affymetrix, make sure 1) to run the latest
>version of the package, 2) to report the output of sessionInfo() and
>traceback(), and 3) to post a complete code example.
>
>
>You received this message because you are subscribed to the Google Groups
>"aroma.affymetrix" group with website http://www.aroma-project.org/.
>To post to this group, send email to aroma-affymetrix@googlegroups.com
>To unsubscribe and other options, go to http://www.aroma-project.org/forum/
--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
