Yes, I did the upgrading of Bioconductor as well, but the result was the
same:
> library("BiocInstaller", lib.loc="~/Rlibs")Bioconductor version 3.0
> (BiocInstaller 1.16.2), ?biocLite for help
> biocLite()BioC_mirror: http://bioconductor.orgUsing Bioconductor version 3.0
> (BiocInstaller 1.16.2), R version 3.2.0.Old packages: 'manipulate'Update
> all/some/none? [a/s/n]: n
> library("GO.db")Загрузка требуемого пакета: AnnotationDbiЗагрузка требуемого
> пакета: stats4Загрузка требуемого пакета: GenomeInfoDbЗагрузка требуемого
> пакета: S4VectorsЗагрузка требуемого пакета: IRanges
Присоединяю пакет: ‘AnnotationDbi’
The following object is masked from ‘package:GenomeInfoDb’:
species
Загрузка требуемого пакета: DBIError : .onLoad не удалось в
loadNamespace() для 'GO.db', подробности:
вызов: ls(envir, all.names = TRUE)
ошибка: 2 аргумента переданы в .Internal(ls), а требуется 3Ошибка:
не удалась загрузка пакета или пространства имен для ‘GO.db’
2015-04-18 0:11 GMT+03:00 Dan Tenenbaum <dtene...@fredhutch.org>:
>
>
> ----- Original Message -----
> > From: "Sergei Ryazansky" <s.ryazan...@gmail.com>
> > To: bioc-devel@r-project.org
> > Sent: Friday, April 17, 2015 1:53:41 PM
> > Subject: [Bioc-devel] Error after upgrading to R 3.2.0 with loading of
> GO.db: 2 arguments passed to .Internal(ls)
> > which requires 3
> >
> > Hello everyone,
> >
> > after updating to fresh R 3.2.0 from R 3.1.3, GO.db, org.Dm.eg.db and
> > org.Hs.eg.db are failed to load (sorry for non-english environment):
> >
> > >library("GO.db")Error : .onLoad не удалось в loadNamespace() для
> > >'GO.db', подробности:
> > вызов: ls(envir, all.names = TRUE)
> > ошибка: 2 аргумента переданы в .Internal(ls), а требуется 3Ошибка:
> > не удалась загрузка пакета или пространства имен для ‘GO.db’
> >
> >
> > > traceback()2: stop(gettextf("package or namespace load failed for
> > > %s", sQuote(package)),
> > call. = FALSE, domain = NA)
> > 1: library("GO.db")
> >
> >
> > >sessionInfo()R version 3.2.0 (2015-04-16)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> > Running under: Ubuntu 14.10
> >
> > locale:
> > [1] LC_CTYPE=ru_RU.UTF-8 LC_NUMERIC=C
> > LC_TIME=ru_RU.UTF-8
> > [4] LC_COLLATE=ru_RU.UTF-8 LC_MONETARY=ru_RU.UTF-8
> > LC_MESSAGES=ru_RU.UTF-8
> > [7] LC_PAPER=ru_RU.UTF-8 LC_NAME=C
> > LC_ADDRESS=C
> > [10] LC_TELEPHONE=C LC_MEASUREMENT=ru_RU.UTF-8
> > LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats4 parallel stats graphics grDevices utils
> > datasets methods
> > [9] base
> >
> > other attached packages:
> > [1] BiocInstaller_1.16.2 RSQLite_1.0.0 DBI_0.3.1
> > AnnotationDbi_1.28.2
> > [5] GenomeInfoDb_1.2.5 IRanges_2.0.1 S4Vectors_0.4.0
> > GEOquery_2.32.0
> > [9] Biobase_2.26.0 BiocGenerics_0.12.1
> >
> > loaded via a namespace (and not attached):
> > [1] Rcpp_0.11.5 MASS_7.3-40 munsell_0.4.2
> > colorspace_1.2-6 stringr_0.6.2
> > [6] plyr_1.8.1 tools_3.2.0 grid_3.2.0 gtable_0.1.2
> > digest_0.6.8
> > [11] reshape2_1.4.1 ggplot2_1.0.1 bitops_1.0-6
> > RCurl_1.95-4.5
> > scales_0.2.4
> > [16] XML_3.98-1.1 proto_0.3-10
> >
> >
> > Are there any way to fix this?
> >
>
> After you upgrade to R-3.2.0 you need to upgrade all your packages with:
>
> library(BiocInstaller)
> biocLite()
>
> Dan
>
>
> >
> > --
> > *Sincerely,*
> > *Sergei Ryazansky, PhD*
> > *IMG RAS, Moscow*
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
--
*Sincerely,*
*Sergei Ryazansky, PhD*
*IMG RAS, Moscow*
[[alternative HTML version deleted]]
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