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

[Dan Tenenbaum]

----- 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