[BioC] problem with loading DESeq after upgrading from R 2.14 to R 2.15

Mon Apr 23 23:30:01 CEST 2012

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
>>> 
>>> 
>>> _______________________________________________
>>> 
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>>> 
>>> Bioconductor at r-project.org
>>> 
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>>> 
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>> 
>>> 
>>> 
>> _______________________________________________
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> 
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
> 