----- Original Message ----- > From: "Sergei Ryazansky" <s.ryazan...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: bioc-devel@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 < 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel