[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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