Hi Matt. Another point to mention is that you should update your version of R ... 2.7.x is >2.5 years old, which is a long time in R. I'd recommend 2.11.x ..
Cheers, Mark On 2010-09-02, at 2:51 PM, Pierre Neuvial wrote: > [Forwarding this to the list so that others can read this thread] > > Pierre > > On Wed, Sep 1, 2010 at 12:57 PM, Matt <matt.kowg...@gmail.com> wrote: >> Hi Pierre, >> >> Thanks for the reply. I guess it's a problem with the source because what >> you say is exactly what I did and I get the error message shown. >> >> Best, >> Matt >> >> On Wed, Sep 1, 2010 at 3:20 PM, Pierre Neuvial <pie...@stat.berkeley.edu> >> wrote: >>> >>> Hi Matt, >>> >>> You want to *update* the package, not *patch* it: the difference >>> between updates and patches is explained at >>> http://aroma-project.org/howtos/updateOrPatch. >>> >>> So, to update aroma.affymetrix, do: >>> >>> source("http://aroma-project.org/hbLite.R";); >>> hbInstall("aroma.affymetrix"); >>> >>> as explained at http://aroma-project.org/install >>> >>> Hope this helps, >>> >>> Pierre. >>> >>> On Wed, Sep 1, 2010 at 10:08 AM, Matt <matt.kowg...@gmail.com> wrote: >>>> Hi there, >>>> >>>> I'd like to update my version of aroma.affymetrix, current version in >>>> use 0.9.1, so that I can utilize the new CN processing method. I >>>> followed the instructions on the site but I get the following error >>>> message >>>> >>>> Patching /home/matthew/.Rpatches/aroma.affymetrix/20080508/ >>>> WeightsFile.R >>>> Failed to source: >>>> http://www.braju.com/R//patches/aroma.affymetrix/download.R >>>> Error in stop(ex$message) : >>>> Your version (0.9.1) of aroma.affymetrix is out of date. Please >>>> update. >>>> In addition: There were 11 warnings (use warnings() to see them) >>>>> sessionInfo() >>>> R version 2.7.0 Under development (unstable) (2008-01-21 r44087) >>>> x86_64-unknown-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 datasets utils >>>> methods >>>> [8] base >>>> >>>> other attached packages: >>>> [1] Biobase_2.0.1 aroma.affymetrix_0.9.1 >>>> aroma.apd_0.1.7 >>>> [4] R.huge_0.2.0 digest_0.4.2 >>>> aroma.light_1.16.1 >>>> [7] affxparser_1.12.2 R.rsp_0.3.6 >>>> R.cache_0.3.0 >>>> [10] R.utils_1.5.0 R.oo_1.7.3 R.methodsS3_1.2.0 >>>> >>>> >>>> How can I fix this? >>>> >>>> Thanks for any help. >>>> Mattt >>>> >>>> -- >>>> 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/ >> >> > > -- > 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/ ------------------------------ Mark Robinson, PhD (Melb) Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robin...@garvan.org.au e: mrobin...@wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 ------------------------------ ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________ -- 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/
