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 ...

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@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@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@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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