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

Tue Apr 24 01:19:17 CEST 2012

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
>>>> 
>>>> 
>>>> _______________________________________________
>>>> 
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>>>> 
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>>>> 
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>>>> 
>>>> 
>>>> 
>>> _______________________________________________
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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
>> 
> 