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

[Dan Tenenbaum]

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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>