Re: [aroma.affymetrix] Problems updating aroma.affymetrix
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Error in stop(ex$message) : Your version (0.9.1) of aroma.affymetrix is out of date.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 --
Re: [aroma.affymetrix] Problems updating aroma.affymetrix
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.eduwrote: 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
