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

Wed Apr 18 17:44:30 CEST 2012

Hi,
I came to this problem when I was updating all my bioconductor packages 
(biocLite(character(), ask=FALSE)) and I had already the previous 
version of ggbio installed and working. The update was all right but for 
ggbio.

Best,
Juan

On 04/18/2012 05:39 PM, Martin Morgan wrote:
> 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 packages were out of date and need to be updated?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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>
>