Hi, if you are following Pierre's advice and still getting *that* error message my best guess is that you are getting an error while installing one of the packages that aroma.affymetrix depends on, which in turn probably will fail the installation of aroma.affymetrix itself. The reason why one of the required packages didn't install, may because your R version is far too old. So, update R, then retry again.
More details: The installation code - hbInstall() - assumes that the installation went well and at the end tries to download and install patches. Since it did install well, you'll get that error on a too old version. I've updated that piece of the code not to try to patch if installation failed. Hope this helps Henrik On Wed, Sep 1, 2010 at 10:03 PM, Mark Robinson <mrobin...@wehi.edu.au> wrote: > 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/ > -- 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/
