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

[Yue Li]

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 ...

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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