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

[Dan Tenenbaum]

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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