I am using the GO.db package in R (v3.3.2) to access information about the Gene Ontology. I can see by running the GO.db command that my annotations are outdated. (I know there are a newer set of annotations released in 2017).
> GO.db
GODb object:
| GOSOURCENAME: Gene Ontology
| GOSOURCEURL: ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
| GOSOURCEDATE: 2016-Sep21
| Db type: GODb
| package: AnnotationDbi
| DBSCHEMA: GO_DB
| GOEGSOURCEDATE: 2016-Sep26
| GOEGSOURCENAME: Entrez Gene
| GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
| DBSCHEMAVERSION: 2.1
I've tried uninstalling and reinstalling the package, but the GOSOURCEDATE value remains unchanged.
I want to find out what sequence of R commands will allow me to load the newer annotations. Do I need to install a newer version of R?
The Bioconductor version information is as follows:
> BiocInstaller::biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
The output of the sessionInfo command is as follows (includes a lot of unrelated packages that my application also loads.
> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
locale:
[1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 LC_MONETARY=English_Canada.1252
[4] LC_NUMERIC=C LC_TIME=English_Canada.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] cowplot_0.8.0 ggplot2_2.2.1 xlsx_0.5.7 xlsxjars_0.6.1 rJava_0.9-8
[6] reshape2_1.4.2 metap_0.8 GO.db_3.4.0 annotate_1.52.1 XML_3.98-1.9
[11] org.Hs.eg.db_3.4.0 AnnotationDbi_1.36.2 IRanges_2.8.2 S4Vectors_0.12.2 Biobase_2.34.0
[16] BiocGenerics_0.20.0 homologene_1.0 magrittr_1.5 tidyr_0.7.1 dplyr_0.7.3
[21] readr_1.1.1 tmod_0.31
loaded via a namespace (and not attached):
[1] beeswarm_0.2.3 purrr_0.2.3 lattice_0.20-34 colorspace_1.3-2 htmltools_0.3.6 blob_1.1.0
[7] rlang_0.1.2 glue_1.1.1 DBI_0.7 bit64_0.9-7 RColorBrewer_1.1-2 bindrcpp_0.2
[13] bindr_0.1 plyr_1.8.4 pca3d_0.10 stringr_1.2.0 munsell_0.4.3 gtable_0.2.0
[19] htmlwidgets_0.9 memoise_1.1.0 knitr_1.17 httpuv_1.3.5 Rcpp_0.12.12 xtable_1.8-2
[25] scales_0.5.0 jsonlite_1.5 mime_0.5 bit_1.1-12 ellipse_0.3-8 hms_0.3
[31] digest_0.6.12 stringi_1.1.5 tagcloud_0.6 shiny_1.0.5 grid_3.3.2 tools_3.3.2
[37] bitops_1.0-6 rgl_0.98.1 lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.3.4 RSQLite_2.0
[43] pkgconfig_2.0.1 assertthat_0.2.0 R6_2.2.2 plotwidgets_0.4
I couldn't find your question on the support site, so I can give you one here.
It seems that you are using Bioconductor version 3.4. It appears that all of your annotation packages are out-of-date. If you want to use the current release annotations, you will have to update your version of R to the current release version (3.4.1) and then run the command BiocInstaller::biocLite("biocUpgrade").