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

[Dan Tenenbaum]

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.

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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