[BioC] ggbio: error when updating to current release version
Martin Morgan
mtmorgan at fhcrc.org
Wed Apr 18 17:46:53 CEST 2012
On 4/18/2012 8:44 AM, Juan L. Mateo wrote:
> 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.
I guess I'm trying to understand why biocLite didn't update the packages
that ggbio depends on, and why you had to do that manually? Which
package was out-of-date after biocLite(character(), ask=FALSE) that
needed to be updated manually?
Martin
>
> 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 packages were out of date and need to be updated?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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>>
>>
--
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
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