[Bioc-devel] Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3

[Sergei Ryazansky]

Thanks, it fixed the issue.

2015-04-18 0:24 GMT+03:00 Dan Tenenbaum <dtenenba at fredhutch.org>:

>
>
> ----- Original Message -----
> > From: "Sergei Ryazansky" <s.ryazansky at gmail.com>
> > To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> > Cc: bioc-devel at r-project.org
> > Sent: Friday, April 17, 2015 2:18:00 PM
> > Subject: Re: [Bioc-devel] Error after upgrading to R 3.2.0 with loading
> of GO.db: 2 arguments passed to .Internal(ls)
> > which requires 3
> >
> >
> > 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.org Using Bioconductor
> > > version 3.0 (BiocInstaller 1.16.2), R version 3.2.0.
>
>
> biocLite() should update itself to version 1.18.1 and then install from
> the proper place.
>
> We'll look into that, but try this:
>
> Start R with
>
> R --vanilla
>
> Then:
>
> remove.packages("BiocInstaller")
> source("http://bioconductor.org/biocLite.R")
> biocLite()
>
> Dan
>
>
>
>  Old packages:
> > > 'manipulate' Update all/some/none? [a/s/n]: n
> > > library("GO.db") Загрузка требуемого пакета: AnnotationDbi Загрузка
> > > требуемого пакета: stats4 Загрузка требуемого пакета: GenomeInfoDb
> > > Загрузка требуемого пакета: S4Vectors Загрузка требуемого пакета:
> > > IRanges Присоединяю пакет: ‘AnnotationDbi’ The following object is
> > > masked from ‘package:GenomeInfoDb’:
> >
> >     species Загрузка требуемого пакета: DBI 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 3 Ошибка:
> >   не удалась загрузка пакета или пространства имен для ‘GO.db’
> >
> >
> >
> >
> >
> > 2015-04-18 0:11 GMT+03:00 Dan Tenenbaum < dtenenba at fredhutch.org > :
> >
> >
> >
> >
> >
> >
> > ----- Original Message -----
> > > From: "Sergei Ryazansky" < s.ryazansky at gmail.com >
> > > To: bioc-devel at 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 at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >
> >
> >
> >
> >
> > --
> >
> >
> >
> > Sincerely,
> > Sergei Ryazansky, PhD
> > IMG RAS, Moscow
>



-- 
*Sincerely,*
*Sergei Ryazansky, PhD*
*IMG RAS, Moscow*

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