tag:blogger.com,1999:blog-7556813435224291579.post436477855064425169..comments2023-03-23T10:46:08.543+00:00Comments on One R Tip A Day: R Upgrade on Mac Os X 10.5.5 (Leopard)Paolohttp://www.blogger.com/profile/01969817827028660433noreply@blogger.comBlogger17125tag:blogger.com,1999:blog-7556813435224291579.post-46483689719608523402014-04-07T08:22:38.727+01:002014-04-07T08:22:38.727+01:00Feel free to use the code on your blog: just put a...Feel free to use the code on your blog: just put a link to the original post.<br />Paolohttps://www.blogger.com/profile/01969817827028660433noreply@blogger.comtag:blogger.com,1999:blog-7556813435224291579.post-32912418843420770252014-04-06T21:39:17.195+01:002014-04-06T21:39:17.195+01:00Hi there Paolo, thanks for your useful post! I tri...Hi there Paolo, thanks for your useful post! I tried this in my OS X 10.7.5 Lion and it seems like it worked! Do you mind if I put your code in my own blog? (with some minor comments for my particular case).SLAVhttps://www.blogger.com/profile/07887473747566478388noreply@blogger.comtag:blogger.com,1999:blog-7556813435224291579.post-3573154085512382012013-10-22T13:30:01.085+01:002013-10-22T13:30:01.085+01:00Hi Gareth! Thanks for visiting my blog! I hope you...Hi Gareth! Thanks for visiting my blog! I hope you find something useful for you! See you soon in person! :-)Paolohttps://www.blogger.com/profile/01969817827028660433noreply@blogger.comtag:blogger.com,1999:blog-7556813435224291579.post-71370051363430451532013-10-22T08:09:55.796+01:002013-10-22T08:09:55.796+01:00Paolo! It is Gareth the student of Luca. I just ha...Paolo! It is Gareth the student of Luca. I just had to fix this and found your blog. Bioinformatics is a small world so I'm saying hello to people when I run into them on forums from now on!Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-7556813435224291579.post-50823384079628024252013-10-14T14:27:35.366+01:002013-10-14T14:27:35.366+01:00Dear Marianne, I'm glad this old post it is st...Dear Marianne, I'm glad this old post it is still useful to someone! Nowadays I completely switch to Linux and I don't have access to a Mac. In any case i think the install.packages() function is redundant: you can use directly biocLite to install CRAN as well as bioconductor packages.Paolohttps://www.blogger.com/profile/01969817827028660433noreply@blogger.comtag:blogger.com,1999:blog-7556813435224291579.post-58125503623524299152013-10-14T11:04:32.857+01:002013-10-14T11:04:32.857+01:00Thank you, this is very helpful!
I think though ...Thank you, this is very helpful! <br /><br />I think though that if I go through the commands in the order that you write them, this one:<br /><br />for (i in 1:length(missing)) biocLite(missing[i])<br /><br />... installs all the packages from biocLite. So running <br /><br />install.packages(missing)<br /><br />first might make more sense. I'm not sure, I haven't tried this.<br /><br />Anyway, updated R and all packages there -> happy. Many thanks!Mariannehttp://promberger.info/linuxnoreply@blogger.comtag:blogger.com,1999:blog-7556813435224291579.post-84925379735593259282013-08-26T08:06:16.373+01:002013-08-26T08:06:16.373+01:00I'm happy it is of some use to you! :-)I'm happy it is of some use to you! :-)Paolohttps://www.blogger.com/profile/01969817827028660433noreply@blogger.comtag:blogger.com,1999:blog-7556813435224291579.post-24120114501474712732012-02-05T07:26:15.526+00:002012-02-05T07:26:15.526+00:00I like the sarcasm. I don' like so much commen...I like the sarcasm. I don' like so much comments suggesting alternative strategies without indicate the context in which you can apply them.<br />The procedure you suggest works almost certainly between minor revisions: e.g., upgrade from R-2.14.0 to R-2.14.1. Nevertheless try to upgrade 'your way' from let's say R-2.9.0 to R-2.14.1! I think you'll have a surprise! My post is meant to explain an upgrade workflow which works FOR ME with the particular configuration (hardware/software) described. It seems to be useful to other people too and I'm glad for that! If anybody (maybe using his real name, nobody bites on this blog ;-) ) want to post a more general, reliable and fast pipeline I'll be more than happy to update the post.Paolohttps://www.blogger.com/profile/01969817827028660433noreply@blogger.comtag:blogger.com,1999:blog-7556813435224291579.post-15080348196856712682012-02-04T21:30:58.938+00:002012-02-04T21:30:58.938+00:00Thank you so much for this. So much easier than c...Thank you so much for this. So much easier than copying my entire suite of library files and moving them back into the new R directory...Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-7556813435224291579.post-5465456660955591812011-09-16T09:25:41.788+01:002011-09-16T09:25:41.788+01:00It seems (not sure) that some component of the pre...It seems (not sure) that some component of the previous version (R.2.12.0) are still in place. I suggest to wipe completely the old version (as stated at the beginning of the post) and try again to install R from scratch. Remember that this procedure works (at least for me) on Mac OS X 10.5. I can't guarantee this will work on Mac OS X 10.6 or 10.7 as well.Paolohttps://www.blogger.com/profile/01969817827028660433noreply@blogger.comtag:blogger.com,1999:blog-7556813435224291579.post-37572389663088391072011-09-16T07:51:58.142+01:002011-09-16T07:51:58.142+01:00Hi,
Thanks for the post. When trying to install...Hi,<br /><br />Thanks for the post. When trying to install bioconductor packages using, I get the following error:<br />>source("http://bioconductor.org/biocLite.R")<br />Error in file(file, "r", encoding = encoding) : <br /> internet routines cannot be loaded<br />In addition: Warning message:<br />In file(file, "r", encoding = encoding) :<br /> unable to load shared object '/Library/Frameworks/R.framework/Resources/modules/x86_64/internet.so':<br /> dlopen(/Library/Frameworks/R.framework/Resources/modules/x86_64/internet.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libR.dylib<br /> Referenced from: /Library/Frameworks/R.framework/Resources/modules/x86_64/internet.so<br /> Reason: Incompatible library version: internet.so requires version 2.13.0 or later, but libR.dylib provides version 2.12.0<br /><br />Any advice would be appreciated!Katiehttps://www.blogger.com/profile/15789677710819881212noreply@blogger.comtag:blogger.com,1999:blog-7556813435224291579.post-80308199503363357832011-04-15T11:31:40.343+01:002011-04-15T11:31:40.343+01:00@JC Thanks for your contribution!@JC Thanks for your contribution!Paolohttps://www.blogger.com/profile/01969817827028660433noreply@blogger.comtag:blogger.com,1999:blog-7556813435224291579.post-28275723845622818432011-04-15T10:12:01.319+01:002011-04-15T10:12:01.319+01:00Thanks, very useful indeed.. I also suggest to us...Thanks, very useful indeed.. I also suggest to use chooseBioCmirror() after sourcing "biocLite.R".. depending on your location and the installed packages (Hs map size is around 800Mb) the upgrade running time can be drastically reduced.<br /><br />jCUnknownhttps://www.blogger.com/profile/05846837713319069201noreply@blogger.comtag:blogger.com,1999:blog-7556813435224291579.post-24126994318270551382011-03-17T09:33:35.227+00:002011-03-17T09:33:35.227+00:00Troppo gentile! The door is always open! ;-)Troppo gentile! The door is always open! ;-)Paolohttps://www.blogger.com/profile/01969817827028660433noreply@blogger.comtag:blogger.com,1999:blog-7556813435224291579.post-21304315849124115862011-03-16T21:59:59.905+00:002011-03-16T21:59:59.905+00:00Grazie mille, with such good daily tips I'll ...Grazie mille, with such good daily tips I'll be back here tommorrow!Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-7556813435224291579.post-70241597987660970552009-08-01T18:17:58.319+01:002009-08-01T18:17:58.319+01:00You're welcome! :-)You're welcome! :-)Paolohttps://www.blogger.com/profile/01969817827028660433noreply@blogger.comtag:blogger.com,1999:blog-7556813435224291579.post-36115322066978060452009-07-31T16:13:40.070+01:002009-07-31T16:13:40.070+01:00Thanks! This is extremely helpful!Thanks! This is extremely helpful!Anonymousnoreply@blogger.com