Just to let you guys know that the tips suggested by Jim work gracefully, and I would recommend all R users (at least Unix users) to follow that when upgrading their R! Thanks very much. On 2012-04-23, at 5:30 PM, Yue Li wrote: > Thanks Jim! That seems more automated upgrade. So basically we reinstall all existing packages that are NOT "Part of R 2.14.1" when upgrading to "Part of R 2.15". > > I will try that out and let you guys know how that goes! > > > On 2012-04-23, at 5:23 PM, James W. MacDonald wrote: > >> >> >> On 4/23/2012 5:17 PM, Dan Tenenbaum wrote: >>> On Mon, Apr 23, 2012 at 2:11 PM, Yue Li<gorillayue at="" gmail.com=""> wrote: >>>> Any helps on not having to manually re-install the packages for each R >>>> upgrade would be greatly appreciated! I followed this post but apparently >>>> not be able to make the upgrade seamless ... >>>> >>> I echo Steve in saying this is not really recommended. >>> For a given version of R, you should be using the appropriate version >>> of Bioconductor. >>> >>> If it makes it easier, you can go into R 2.14 and get a list of the >>> packages you have installed with >>> pkgs<- installed.packages()[,"Package"] >>> >>> You can then take this list and use it as an argument to biocLite() in R 2.15. >>> However, the list will include packages that are part of R so these >>> will not install properly. >> >> Or alternatively, >> >> x <- installed.packages() >> y <- row.names(x)[-grep("Part", x[,11])] >> >> Then you can write that out and scan() it back into your new R version. >> >> Best, >> >> Jim >> >> >> >> >>> >>> Dan >>> >>> >>>> https://stat.ethz.ch/pipermail/r-sig-mac/2008-August/005276.html >>>> >>>> >>>> On 2012-04-23, at 4:54 PM, Dan Tenenbaum wrote: >>>> >>>> On Mon, Apr 23, 2012 at 1:47 PM, Yue Li<gorillayue at="" gmail.com=""> wrote: >>>> >>>> Hi Dan, >>>> >>>> >>>> By "all of the packages", I meant the packages installed for R 2.14 not all >>>> of the packages from CRAN or Bioconductors. >>>> >>>> >>>> They work fine under terminal as shown below and most work fine in R GUI >>>> except for DESeq and DEXSeq ... >>>> >>>> >>>> OK, thanks for the clarification. >>>> >>>> Dan >>>> >>>> >>>> >>>> Yue >>>> >>>> >>>> On 2012-04-23, at 4:39 PM, Dan Tenenbaum wrote: >>>> >>>> >>>> Hi Yue, >>>> >>>> >>>> On Mon, Apr 23, 2012 at 1:10 PM, Yue Li<gorillayue at="" gmail.com=""> wrote: >>>> >>>> Hi Steve, >>>> >>>> >>>> Thanks for prompt reply! It's just that having to re-install all of the >>>> packages for every upgrade of R is also a hassle, don't u think? But you're >>>> right that installing it improperly is even disastrous like what I am >>>> experiencing now. >>>> >>>> >>>> When you say "all of the packages," what do you mean? You only need to >>>> >>>> install the packages that you work with. There is no requirement to >>>> >>>> install all of them. >>>> >>>> >>>> Dan >>>> >>>> >>>> >>>> >>>> >>>> I wish in the future, someone could just make the upgrade of R as easy as >>>> upgrading iTunes or something like that. >>>> >>>> >>>> Yue >>>> >>>> >>>> >>>> On 2012-04-23, at 3:53 PM, Steve Lianoglou wrote: >>>> >>>> >>>> Hi, >>>> >>>> >>>> The way you are trying to maintain your libraries is generally frowned >>>> >>>> upon. You shouldn't be trying to use R-2.14 packages with your R-2.14 >>>> >>>> install. You are exposing yourself to weird and hard to explain >>>> >>>> problems. >>>> >>>> >>>> Look at the error message you are getting: >>>> >>>> >>>> On Mon, Apr 23, 2012 at 3:36 PM, Yue Li<yueli at="" cs.toronto.edu=""> wrote: >>>> >>>> [snip] >>>> >>>> Loading required package: locfit >>>> >>>> locfit 1.5-7 2012-03-22 >>>> >>>> Error in dyn.load(file, DLLpath = DLLpath, ...) : >>>> >>>> unable to load shared object '/Library/RLib/RSQLite/libs/x86_64/RSQLite.so': >>>> >>>> dlopen(/Library/RLib/RSQLite/libs/x86_64/RSQLite.so, 6): Library not loaded: >>>> /Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libR.dylib >>>> >>>> Referenced from: /Library/RLib/RSQLite/libs/x86_64/RSQLite.so >>>> >>>> Reason: image not found >>>> >>>> Error: package/namespace load failed for ?DESeq? >>>> >>>> >>>> Your trying to load a package from your 2.14 repo ... I'm not sure why >>>> >>>> this works from the terminal and not the GUI (are you sure you are >>>> >>>> firing up 2.15 from the terminal?), but I'm also not too inclined to >>>> >>>> smoke this out, because ... well, you shouldn't be doing this ;-) and >>>> >>>> also it will likely take you less time to just install things "the >>>> >>>> normal way". >>>> >>>> >>>> If you really have some compelling reason to have a custom library >>>> >>>> structure, I like the way the bioc folks suggest developers to keep >>>> >>>> bioc-devel package separate from bioc-release (now that R is on an >>>> >>>> annual release cycle), eg: >>>> >>>> >>>> http://www.bioconductor.org/developers/useDevel/ >>>> >>>> >>>> You could imagine having R-2.14 and R-2.15 in separate dirs instead of >>>> >>>> 2.15-release and 2.15-devel if working w/ devel libraries isn't your >>>> >>>> cup of tea -- but note they still keep different versions different. >>>> >>>> >>>> Anyway, the "normal" R install does this for you anyway on OS X, so >>>> >>>> dollars-to-donuts you'll have less hassles just going "the normal" >>>> >>>> route, and installing the package you need via biocLite again in your >>>> >>>> "clean" 2.15 library path will likely cost less time than trying to >>>> >>>> debug your custom library path woes. >>>> >>>> >>>> HTH, >>>> >>>> -steve >>>> >>>> >>>> >>>> -- >>>> >>>> Steve Lianoglou >>>> >>>> Graduate Student: Computational Systems Biology >>>> >>>> | Memorial Sloan-Kettering Cancer Center >>>> >>>> | Weill Medical College of Cornell University >>>> >>>> Contact Info: http://cbio.mskcc.org/~lianos/contact >>>> >>>> >>>> _______________________________________________ >>>> >>>> Bioconductor mailing list >>>> >>>> Bioconductor at r-project.org >>>> >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> >