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

Juan L. Mateo juan.mateo at cos.uni-heidelberg.de
Wed Apr 18 18:01:20 CEST 2012 

Hi,

I don't know which one (or ones) of the new packages is essential 
because I installed all of them at once and not one by one to check the 
result of trying to update ggbio.
Since this problem could not be reproduced, I guess that it is a 
specific misconfiguration of my system but I can't tell which.

After I run the update command non of my packages were outdated, apart 
from ggbio, so everything went fine even for the packages that ggbio 
1.0.4 depends on.

Best,
Juan

On 04/18/2012 05:46 PM, Martin Morgan wrote:
> 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 package was out-of-date after biocLite(character(), ask=FALSE) that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 packages were out of date and need to be updated?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
>>>>>
>>>>> _________________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at r-project.org <mailto:Bioconductor at r-project.org>
>>>>> https://stat.ethz.ch/mailman/__listinfo/bioconductor
>>>>> <https://stat.ethz.ch/mailman/listinfo/bioconductor>
>>>>> Search the archives:
>>>>> http://news.gmane.org/gmane.__science.biology.informatics.__conductor
>>>>> <http://news.gmane.org/gmane.science.biology.informatics.conductor>
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
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>>>
>>>
>
>

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