[BioC] rtracklayer fails to load in the new Bioconductor devel branch

[Martin Morgan]

On 11/02/2011 01:47 PM, Ivan Gregoretti wrote:
> Hello Bioconductorians,
>
> I just downloaded and installed the new R-devel (without problems) but
> rtracklayer fails to load.
>
> It started by asking me to recompile bitops, which I did.
> Unfortunately, the problem persists. Please see below.

update packages via

   source('http://bioconductor.org/biocLite.R')
   biocLite(character())

Martin

>
> Can anybody think of a solution?
>
> Thank you,
>
> Ivan
>
>
>
> $ R --vanilla
>
> R Under development (unstable) (2011-11-01 r57541)
> Copyright (C) 2011 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>    Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>> library(rtracklayer)
> Loading required package: RCurl
> Loading required package: bitops
> Error : classes "file", "connection" are not exported by 'namespace:Biostrings'
> Error: package/namespace load failed for ‘rtracklayer’
>> sessionInfo()
> R Under development (unstable) (2011-11-01 r57541)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] RCurl_1.6-10   bitops_1.0-4.1
>
> loaded via a namespace (and not attached):
> [1] Biostrings_2.23.0   BSgenome_1.23.0     GenomicRanges_1.7.0
> [4] IRanges_1.13.0      tools_2.15.0        XML_3.4-3
> [7] zlibbioc_1.1.0
>
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