After updating to R-2.11.1, I no longer have this problem. Thanks. Matt
On Thu, Sep 2, 2010 at 2:08 AM, Henrik Bengtsson <h...@stat.berkeley.edu>wrote: > 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/ > -- 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. 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