[BioC] ggbio: error when updating to current release version

Juan L. Mateo juan.mateo at cos.uni-heidelberg.de
Wed Apr 18 14:36:06 CEST 2012


Hi Vincent,

If I install manually all the packages that are listed in your 
sessionInfo I can install ggbio but with warnings. These warnings remain 
when I load the module.
Appart from that I have tested several functions of ggbio and they seem 
to work properly.

Thanks for the answer
Juan

 > 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'
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’
Warning in FUN(X[[1L]], ...) :
   Created a package name, ‘2012-04-18 13:53:39’, when none found
** help
*** installing help indices
** building package indices
** installing vignettes
    ‘intro.Rnw’
** testing if installed package can be loaded
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

* DONE (ggbio)

The downloaded source packages are in
	‘/tmp/Rtmp3FIBAU/downloaded_packages’
Warning message:
installed directory not writable, cannot update packages 'ggbio'
 > library(ggbio)
Loading required package: ggplot2

Attaching package: ‘ggbio’

The following object(s) are masked from ‘package:ggplot2’:

     geom_rect, geom_segment, stat_identity, xlim

Warning messages:
1: found methods to import for function ‘as.list’ but not the generic 
itself
2: found methods to import for function ‘aggregate’ but not the generic 
itself
3: found methods to import for function ‘as.table’ but not the generic 
itself
4: found methods to import for function ‘complete.cases’ but not the 
generic itself
5: found methods to import for function ‘cor’ but not the generic itself
6: found methods to import for function ‘diff’ but not the generic itself
7: found methods to import for function ‘drop’ but not the generic itself
8: found methods to import for function ‘append’ but not the generic itself
9: found methods to import for function ‘as.data.frame’ but not the 
generic itself
10: found methods to import for function ‘as.list’ but not the generic 
itself
 >


 > 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] ggbio_1.2.8         ggplot2_0.9.0       BiocInstaller_1.4.3

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_2.24.1       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] digest_0.5.2            GenomicFeatures_1.8.1   GenomicRanges_1.8.3
[16] grid_2.15.0             gridExtra_0.9           Hmisc_3.9-3
[19] IRanges_1.14.2          lattice_0.20-6          MASS_7.3-17
[22] Matrix_1.0-6            memoise_0.1             munsell_0.3
[25] plyr_1.7.1              proto_0.3-9.2           RColorBrewer_1.0-5
[28] RCurl_1.91-1            reshape2_1.2.1          Rsamtools_1.8.3
[31] RSQLite_0.11.1          rtracklayer_1.16.1      scales_0.2.0
[34] snpStats_1.6.0          splines_2.15.0          stats4_2.15.0
[37] stringr_0.6             survival_2.36-12        tools_2.15.0
[40] VariantAnnotation_1.2.5 XML_3.9-4


On 04/18/2012 12:38 PM, Vincent Carey wrote:
> 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 at cos.uni-heidelberg.de
> <mailto:juan.mateo at 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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