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

[Peter Haverty]

Somewhere in GO.db a direct call to the ls .Internal is being made
(probably a speed hack) apparently.  The API for .Internal(ls()) has
changed in R 3.2.0. This call should be replaced with "names", which now
works on environments in R 3.2.0, and is way faster than the direct call to
.Internal(ls()) too.

Regards,

Pete

____________________
Peter M. Haverty, Ph.D.
Genentech, Inc.
phaverty at gene.com

On Fri, Apr 17, 2015 at 1:53 PM, Sergei Ryazansky <s.ryazansky at gmail.com>
wrote:

> 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 ÎÅ ÕÄÁÌÏÓØ × loadNamespace() ÄÌÑ 'GO.db',
> ÐÏÄÒÏÂÎÏÓÔÉ:
>   ×ÙÚÏ×: ls(envir, all.names = TRUE)
>   ÏÛÉÂËÁ: 2 ÁÒÇÕÍÅÎÔÁ ÐÅÒÅÄÁÎÙ × .Internal(ls), Á ÔÒÅÂÕÅÔÓÑ 3ïÛÉÂËÁ:
> ÎÅ ÕÄÁÌÁÓØ ÚÁÇÒÕÚËÁ ÐÁËÅÔÁ ÉÌÉ ÐÒÏÓÔÒÁÎÓÔ×Á ÉÍÅÎ ÄÌÑ '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?
>
>
> --
> *Sincerely,*
> *Sergei Ryazansky, PhD*
> *IMG RAS, Moscow*
>
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>
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