[BioC] Trouble installing BiocGenerics

[Andreas Leha]

Hi Vincent,


Vincent Carey <stvjc at channing.harvard.edu>
writes:

> can i suggest that you start with a fresh R --vanilla session? -- you have
> some packages such as filehash attached that seem to be causing some
> conflicts.
>

that did the trick.  Should have tried before posting.

Thanks a lot!

Regards,
Andreas




>
> On Sun, Jan 19, 2014 at 7:21 PM, Andreas Leha <
> andreas.leha at med.uni-goettingen.de> wrote:
>
>> Hi all,
>>
>> I have troubles installing (better: loading) BiocGenerics.  See below
>> [fn:1].
>>
>> What am I to do here?
>>
>> Regards,
>> Andreas
>>
>>
>> [fn:1]
>>
>> sessionInfo()
>> R version 3.0.2 (2013-09-25)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>>
>> locale:
>>  [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C
>>  [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8
>>  [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=C
>>  [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C
>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> Footnotes:
>>
>> [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] andRstuff_1.0    devtools_1.3     tikzDevice_0.7.0 filehash_2.2-1
>>
>> loaded via a namespace (and not attached):
>>  [1] digest_0.6.3   evaluate_0.4.7 grid_3.0.2     httr_0.2
>> memoise_0.1
>>  [6] parallel_3.0.2 plyr_1.8       RCurl_1.95-4.1 stringr_0.6.2
>>  tools_3.0.2
>> [11] whisker_0.3-2
>> > source("http://bioconductor.org/biocLite.R")
>> Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help
>> > biocLite("BiocGenerics")
>> BioC_mirror: http://bioconductor.org
>> Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2.
>> Installing package(s) 'BiocGenerics'
>> trying URL '
>> http://bioconductor.org/packages/2.13/bioc/src/contrib/BiocGenerics_0.8.0.tar.gz
>> '
>> Content type 'application/x-gzip' length 30969 bytes (30 Kb)
>> opened URL
>> ==================================================
>> downloaded 30 Kb
>>
>> * installing *source* package ‘BiocGenerics’ ...
>> ** R
>> ** inst
>> ** preparing package for lazy loading
>> Warning: class "connection" is defined (with package slot ‘filehash’) but
>> no metadata object found to revise subclass information---not exported?
>>  Making a copy in package ‘BiocGenerics’
>> Warning: subclass "file" of class "connection" is not local and cannot be
>> updated for new inheritance information; consider setClassUnion()
>> Creating a new generic function for ‘append’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘as.data.frame’ in package
>> ‘BiocGenerics’
>> Creating a new generic function for ‘as.vector’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘rbind’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘duplicated’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘anyDuplicated’ in package
>> ‘BiocGenerics’
>> Creating a new generic function for ‘eval’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘pmax’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘pmin’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘pmax.int’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘pmin.int’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘Reduce’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘Filter’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘Find’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘Map’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘Position’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘get’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘mget’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘is.unsorted’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘lapply’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘sapply’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘mapply’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘match’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘order’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘paste’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘rank’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘rep.int’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘rownames’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘colnames’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘union’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘intersect’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘setdiff’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘sort’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘table’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘tapply’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘unique’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘unlist’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘xtabs’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘clusterCall’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘clusterApply’ in package
>> ‘BiocGenerics’
>> Creating a new generic function for ‘clusterApplyLB’ in package
>> ‘BiocGenerics’
>> Creating a new generic function for ‘clusterEvalQ’ in package
>> ‘BiocGenerics’
>> Warning in getPackageName(environment(fdef)) :
>>   Created a package name, ‘2014-01-20 01:16:35’, when none found
>> Creating a new generic function for ‘clusterExport’ in package
>> ‘BiocGenerics’
>> Creating a new generic function for ‘clusterMap’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘parLapply’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘parSapply’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘parApply’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘parRapply’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘parCapply’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘parLapplyLB’ in package ‘BiocGenerics’
>> Creating a new generic function for ‘parSapplyLB’ in package ‘BiocGenerics’
>> ** help
>> *** installing help indices
>> ** building package indices
>> ** testing if installed package can be loaded
>> Error in namespaceExport(ns, exports) : undefined exports: .__C__file
>> Error: loading failed
>> * DONE (BiocGenerics)
>>
>> The downloaded source packages are in
>>         ‘/tmp/Rtmp3P1KdF/downloaded_packages’
>>
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