org.Rn,eg.db not yet available for R version 3.3.3
1
0
Entering edit mode
@bohdan-khomtchouk-9617
Last seen 6.5 years ago
Stanford University

Hello, it looks like org.Rn,eg.db (and others like it) are not yet available for R version 3.3.3:

> biocLite("org.Rn,eg.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.3 (2017-03-06).
Installing package(s) ‘org.Rn,eg.db’
Warning message:
package ‘org.Rn,eg.db’ is not available (for R version 3.3.3) 

Here is my sessionInfo() for reference:

> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X Yosemite 10.10.5

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
 [1] splines   stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] GEOmetadb_1.32.2           RSQLite_2.0                GEOquery_2.38.4           
 [4] geneXtendeR_1.0.2          data.table_1.10.4          mygene_1.8.0              
 [7] GenomicFeatures_1.24.5     AnnotationDbi_1.34.4       DEGseq_1.26.0             
[10] samr_2.0                   matrixStats_0.52.2         impute_1.46.0             
[13] qvalue_2.4.2               PoissonSeq_1.1.2           combinat_0.0-8            
[16] BiocInstaller_1.22.3       baySeq_2.6.0               perm_1.0-0.0              
[19] abind_1.4-5                EBSeq_1.12.0               testthat_1.0.2            
[22] blockmodeling_0.1.9        DESeq2_1.12.4              SummarizedExperiment_1.2.3
[25] Biobase_2.32.0             edgeR_3.14.0               limma_3.28.21             
[28] dplyr_0.7.1                gplots_3.0.1               shinyapps_0.4.1.8         
[31] shiny_1.0.3                bindrcpp_0.2               rtracklayer_1.32.2        
[34] GenomicRanges_1.24.3       GenomeInfoDb_1.8.7         IRanges_2.6.1             
[37] S4Vectors_0.10.3           BiocGenerics_0.18.0        devtools_1.13.2           

loaded via a namespace (and not attached):
 [1] backports_1.1.0         Hmisc_4.0-3             plyr_1.8.4              lazyeval_0.2.0         
 [5] BiocParallel_1.6.6      ggplot2_2.2.1           digest_0.6.12           htmltools_0.3.6        
 [9] gdata_2.18.0            magrittr_1.5            checkmate_1.8.3         memoise_1.1.0          
[13] cluster_2.0.6           Biostrings_2.40.2       annotate_1.50.1         colorspace_1.3-2       
[17] blob_1.1.0              crayon_1.3.2            RCurl_1.95-4.8          jsonlite_1.5           
[21] roxygen2_6.0.1          genefilter_1.54.2       bindr_0.1               survival_2.41-3        
[25] glue_1.1.1              gtable_0.2.0            zlibbioc_1.18.0         XVector_0.12.1         
[29] scales_0.4.1            DBI_0.7                 Rcpp_0.12.11            xtable_1.8-2           
[33] htmlTable_1.9           foreign_0.8-69          bit_1.1-12              Formula_1.2-2          
[37] sqldf_0.4-11            htmlwidgets_0.9         httr_1.2.1              RColorBrewer_1.1-2     
[41] acepack_1.4.1           pkgconfig_2.0.1         XML_3.98-1.9            nnet_7.3-12            
[45] locfit_1.5-9.1          rlang_0.1.1             reshape2_1.4.2          munsell_0.4.3          
[49] tools_3.3.3             gsubfn_0.6-6            stringr_1.2.0           knitr_1.16             
[53] bit64_0.9-7             caTools_1.17.1          mime_0.5                xml2_1.1.1             
[57] biomaRt_2.28.0          curl_2.7                tibble_1.3.3            geneplotter_1.50.0     
[61] stringi_1.1.5           desc_1.1.0              lattice_0.20-35         Matrix_1.2-10          
[65] commonmark_1.2          bitops_1.0-6            httpuv_1.3.5            R6_2.2.2               
[69] latticeExtra_0.6-28     KernSmooth_2.23-15      gridExtra_2.2.1         gtools_3.5.0           
[73] assertthat_0.2.0.9000   chron_2.3-50            proto_1.0.0             rprojroot_1.2          
[77] withr_1.0.2             GenomicAlignments_1.8.4 Rsamtools_1.24.0        grid_3.3.3             
[81] rpart_4.1-11            git2r_0.18.0            base64enc_0.1-3  
R package installation • 956 views
ADD COMMENT
1
Entering edit mode
@peter-langfelder-4469
Last seen 2 days ago
United States

Try again with

org.Rn.eg.db

instead of

org.Rn,eg.db

note the dot instead of comma...

 

ADD COMMENT
0
Entering edit mode

Oops, didn't notice the comma in: A: Returning gene functional annotations with gene symbols as input (using mygene B.  Thanks for the catch!

ADD REPLY

Login before adding your answer.

Traffic: 846 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6