[BioC] SomaticSignatures

Martin Morgan mtmorgan at fhcrc.org
Wed Apr 2 00:11:03 CEST 2014

I think the errors related to Biostrings

On 04/01/2014 01:13 PM, Huma Asif wrote:

> * installing *source* package ‘BiocParallel’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Error in readRDS(nsInfoFilePath) : error reading from connection
> ERROR: lazy loading failed for package ‘BiocParallel’

I really don't know what is causing this, but can only guess that it is a 
corrupt file from a previous installation attempt. You might try

   rm -rf /home/asif/R/i686-pc-linux-gnu-library/3.1/BiocParallel

> * installing *source* package ‘Biostrings’ ...
> ** libs
> -pc-linux-gnu-library/3.1/XVector/include"   -fpic  -g -O2  -c io_utils.c -o
> io_utils.o
> io_utils.c:18:19: fatal error: bzlib.h: No such file or directory
> compilation terminated.
> gmake: *** [io_utils.o] Error 1

Address this (and perhaps subsequent errors relating to unavailability of 
Biostrings) by installing the system dependency

   sudo apt-get install libbz2-dev

(my understanding is that a revision to the devel version of Biostrings will not 
require this dependency).

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