[BioC] ggbio and R-2.14.0

[Martin Morgan]

On 01/16/2012 01:26 PM, Weiner, Michael wrote:
> From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
>> Hi Michael
>>
>> Some of your packages are out of date, and some additional
> dependencies
>> need to be installed. You should
>>
>>     source("http://bioconductor.org/biocLite.R")
>>     biocLite(character()) ## to update old packages
>>     biocLite('ggbio")     ## to install new pkg and dependencies
>>
>> It looks like perhaps other packages have not been installed
> correctly;
>> I'd guess at biocLite('GenomicFeatures') as another step to iterate if
>
>> ggbio continues to fail to install.
>>
>> Martin
>
> Nope, unfortunately the biocLite(character()) downloads a bunch of packages and installs some, but then fails with a bunch as in the following:
>
> There were 50 or more warnings (use warnings() to see the first 50)
>> warnings()
> Warning messages:
> 1: In install.packages(update[instlib == l, "Package"], l,  ... :
>    installation of package âabcâ had non-zero exit status
> 2: In install.packages(update[instlib == l, "Package"], l,  ... :
>    installation of package âadabagâ had non-zero exit status
> 3: In install.packages(update[instlib == l, "Package"], l,  ... :
>    installation of package âadehabitatLTâ had non-zero exit status
> 4: In install.packages(update[instlib == l, "Package"], l,  ... :
>    installation of package âalphahullâ had non-zero exit status
>
> and loads of others :( Any other suggestions perhaps?

Each of these packages would have failed more explicitly earlier in the 
installation process; you could biocLite('abc') to see what the details 
are, and repeat... The errors could be any number of things.

These look like they are alphabetical, and that there are a lot of them. 
I guess you have something like 'all of CRAN' installed, which means 
that you've tasked yourself with managing a very large number of 
packages and their system dependencies. Yikes.

In some ways I feel like you've got yourself in a mess, e.g., 
incompatible versions of many packages, perhaps installed for unintended 
versions of R. The way forward might be to figure out, e.g., on a clean 
system, how you should have proceeded, and then work back to cleaning up 
your full system. A basic starting point is to make sure that packages 
are installed in R version-specific directories.

If you wanted to back-track to the initial problem, then

** preparing package for lazy loading

Error in library(pkg, character.only = TRUE, logical.return = TRUE, 
lib.loc = lib.loc) :

   package âbitopsâ does not have a NAMESPACE and should be re-installed

here you could biocLite('bitops') which will re-install bitops, 
presumably with a NAMESPACE.

ERROR: lazy loading failed for package ârtracklayerâ

* removing â/usr/lib64/R/library/rtracklayerâ

and here biocLite('rtracklayer'). If this fails then track down what the 
problems are, because without rtracklayer you can't proceed

ERROR: dependency ârtracklayerâ is not available for package 
âGenomicFeaturesâ

* removing â/usr/lib64/R/library/GenomicFeaturesâ

... and so on.

For what it's worth, the troubles you are having are NOT normal but 
reflect some earlier inappropriate installation. Normally, (e.g., on a 
clean R system) source('http://bioconductor.org/biocLite.R'); 
biocLite('ggbio') would just work.

Martin



>
> Thanks
> Michael Weiner
>
> ===================================
>
>   Please consider the environment before printing this e-mail
>
> Cleveland Clinic is ranked one of the top hospitals
> in America by U.S.News&  World Report (2010).
> Visit us online at http://www.clevelandclinic.org for
> a complete listing of our services, staff and
> locations.
>
>
> Confidentiality Note:  This message is intended for use\...{{dropped:13}}
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793