[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.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")???????? ?????????? ??????: AnnotationDbi???????? ?????????? ??????: stats4???????? ?????????? ??????: GenomeInfoDb???????? ?????????? ??????: S4Vectors???????? ?????????? ??????: IRanges
??????????? ?????: ?AnnotationDbi?
The following object is masked from ?package:GenomeInfoDb?:

    species
???????? ?????????? ??????: DBIError : .onLoad ?? ??????? ?
loadNamespace() ??? 'GO.db', ???????????:
  ?????: ls(envir, all.names = TRUE)
  ??????: 2 ????????? ???????? ? .Internal(ls), ? ????????? 3??????:
?? ??????? ???????? ?????? ??? ???????????? ???? ??? ?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 ?? ??????? ? loadNamespace() ???
'GO.db', ???????????:
  ?????: ls(envir, all.names = TRUE)
  ??????: 2 ????????? ???????? ? .Internal(ls), ? ????????? 3??????:
?? ??????? ???????? ?????? ??? ???????????? ???? ??? ?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*

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

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

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