Hi, I am unable to confirm a problem; check your additional resources
against the session info below

> sessionInfo()
R version 2.15.0 Patched (2012-03-31 r58891)
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] stats     graphics  grDevices datasets  tools     utils     methods
[8] base

other attached packages:
[1] ggbio_1.2.8         ggplot2_0.9.0       BiocInstaller_1.4.3
[4] weaver_1.22.0       codetools_0.2-8     digest_0.5.2

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.18.0    Biobase_2.16.0          BiocGenerics_0.2.0
 [4] biomaRt_2.12.0          Biostrings_2.24.0       biovizBase_1.3.6
 [7] bitops_1.0-4.1          BSgenome_1.24.0         cluster_1.14.2
[10] colorspace_1.1-1        DBI_0.2-5               dichromat_1.2-4
[13] GenomicFeatures_1.8.0   GenomicRanges_1.8.0     grid_2.15.0
[16] gridExtra_0.9           Hmisc_3.9-3             IRanges_1.14.0
[19] lattice_0.20-6          MASS_7.3-17             Matrix_1.0-6
[22] memoise_0.1             munsell_0.3             plyr_1.7.1
[25] proto_0.3-9.2           RColorBrewer_1.0-5      RCurl_1.91-1
[28] reshape2_1.2.1          Rsamtools_1.8.0         RSQLite_0.11.1
[31] rtracklayer_1.16.0      scales_0.2.0            snpStats_1.6.0
[34] splines_2.15.0          stats4_2.15.0           stringr_0.6
[37] survival_2.36-12        VariantAnnotation_1.2.0 XML_3.9-4
[40] zlibbioc_1.2.0


On Wed, Apr 18, 2012 at 3:39 AM, Juan L. Mateo <
juan.mateo@cos.uni-heidelberg.de> wrote:

> Dear all,
>
> I tried to update the package ggbio from version 1.0.4 to the current
> release version 1.2.8 but there seems to be an error.
> I list below the error output and sessionInfo().
> I tried also to use the development version (1.3.4) but I get the same
> problem.
>
> Best regards
>
>
> > source("http://bioconductor.**org/biocLite.R<http://bioconductor.org/biocLite.R>
> ")
> BiocInstaller version 1.4.3, ?biocLite for help
> >     biocLite("ggbio")
> BioC_mirror: http://bioconductor.org
> Using R version 2.15, BiocInstaller version 1.4.3.
> Installing package(s) 'ggbio'
> trying URL 'http://www.bioconductor.org/**packages/2.10/bioc/src/**
> contrib/ggbio_1.2.8.tar.gz<http://www.bioconductor.org/packages/2.10/bioc/src/contrib/ggbio_1.2.8.tar.gz>
> '
> Content type 'application/x-gzip' length 205262 bytes (200 Kb)
> opened URL
> ==============================**====================
> downloaded 200 Kb
>
> * installing *source* package ‘ggbio’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Warning: found methods to import for function ‘as.list’ but not the
> generic itself
> Warning: found methods to import for function ‘chartr’ but not the generic
> itself
> Warning: found methods to import for function ‘IQR’ but not the generic
> itself
> Warning: found methods to import for function ‘NROW’ but not the generic
> itself
> Warning: found methods to import for function ‘aggregate’ but not the
> generic itself
> Warning: found methods to import for function ‘chartr’ but not the generic
> itself
> Warning: found methods to import for function ‘cor’ but not the generic
> itself
> Creating a new generic function for ‘rescale’ in package ‘ggbio’
> Creating a generic function for ‘summary’ from package ‘base’ in package
> ‘ggbio’
> Creating a generic function for ‘print’ from package ‘base’ in package
> ‘ggbio’
> Creating a new generic function for ‘xlim’ in package ‘ggbio’
> Creating a generic function for ‘update’ from package ‘stats’ in package
> ‘ggbio’
> Creating a new generic function for ‘geom_rect’ in package ‘ggbio’
> Creating a new generic function for ‘geom_segment’ in package ‘ggbio’
> Creating a new generic function for ‘stat_identity’ in package ‘ggbio’
> Error in conformMethod(signature, mnames, fnames, f, fdef, definition) :
>  in method for ‘autoplot’ with signature ‘x="GRanges"’: formal arguments
> (x = "GRanges", ... = "GRanges") omitted in the method definition cannot be
> in the signature
> Error : unable to load R code in package ‘ggbio’
> ERROR: lazy loading failed for package ‘ggbio’
> * removing ‘/usr/local/lib/R/site-**library/ggbio’
> * restoring previous ‘/usr/local/lib/R/site-**library/ggbio’
>
>
>
> > sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-pc-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] BiocInstaller_1.4.3
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.0
>
>
> --
> =============================
> Juan L. Mateo PhD.
> Centre for Organismal Studies (COS) - University of Heidelberg
> Im Neuenheimer Feld 230
> 69120 Heidelberg, Germany
> Tel: 0049 (0)6221 54 6493
> Fax: 0049 (0)6221 54 5639
>
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>

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