----- 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") ???????? ?????????? ??????: AnnotationDbi ????????
?????????? ??????: stats4 ???????? ?????????? ??????: GenomeInfoDb
???????? ?????????? ??????: S4Vectors ???????? ?????????? ??????:
IRanges ??????????? ?????: ?AnnotationDbi? The following object is
masked from ?package:GenomeInfoDb?:
species ???????? ?????????? ??????: DBI Error : .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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