[BioC] ggbio: error when updating to current release version
Martin Morgan
mtmorgan at fhcrc.org
Wed Apr 18 17:39:22 CEST 2012
On 4/18/2012 5:36 AM, Juan L. Mateo wrote:
> 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.
Did your original attempt to install ggbio indicate that some specific
packages were out of date and need to be updated? biocLite is supposed
to catch these things, so that guessing at which packages are out of
date (via Vince's sessionInfo()!) is not necessary.
Martin
> 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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>>
>
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--
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
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