[BioC] ggbio and R-2.14.0

[Vincent Carey]

I don't believe I've seen a sessionInfo() result from your system.  I
just installed ggbio
in R 2.14 with the following sessionInfo:

> sessionInfo()
R version 2.14.0 Patched (2011-11-09 r57622)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.iso88591       LC_NUMERIC=C
 [3] LC_TIME=en_US.iso88591        LC_COLLATE=en_US.iso88591
 [5] LC_MONETARY=en_US.iso88591    LC_MESSAGES=en_US.iso88591
 [7] LC_PAPER=C                    LC_NAME=C
 [9] LC_ADDRESS=C                  LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso88591 LC_IDENTIFICATION=C

attached base packages:
[1] grid      stats     graphics  grDevices datasets  tools     utils
[8] methods   base

other attached packages:
 [1] ggbio_1.0.1         ggplot2_0.8.9       proto_0.3-9.2
 [4] reshape_0.8.4       plyr_1.7.1          biovizBase_1.0.0
 [7] weaver_1.20.0       codetools_0.2-8     digest_0.5.1
[10] BiocInstaller_1.2.1

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.16.2  Biobase_2.14.0        biomaRt_2.10.0
 [4] Biostrings_2.22.0     bitops_1.0-4.1        BSgenome_1.22.0
 [7] colorspace_1.1-0      DBI_0.2-5             dichromat_1.2-4
[10] GenomicFeatures_1.7.1 GenomicRanges_1.6.2   gridExtra_0.9
[13] IRanges_1.12.1        munsell_0.3           RColorBrewer_1.0-5
[16] RCurl_1.7-0           Rsamtools_1.7.1       RSQLite_0.10.0
[19] rtracklayer_1.14.2    scales_0.1.0          stringr_0.6
[22] XML_3.4-3             zlibbioc_1.0.0

I suggest you manually push your system as close to this configuration
as you can.
As individual packages fail, you need to figure out why.  Detailed
error messages can be
reported back to the list if necessary.

On Mon, Jan 16, 2012 at 4:26 PM, Weiner, Michael <weinerm at ccf.org> 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 Some of your packages are out of date, and some additional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?
>
> Thanks
> Michael Weiner
>
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