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Question: org.Rn,eg.db not yet available for R version 3.3.3
0
gravatar for Bohdan Khomtchouk
4 months ago by
Stanford University
Bohdan Khomtchouk10 wrote:

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  
ADD COMMENTlink modified 4 months ago by Peter Langfelder1.3k • written 4 months ago by Bohdan Khomtchouk10
1
gravatar for Peter Langfelder
4 months ago by
United States
Peter Langfelder1.3k wrote:

Try again with

org.Rn.eg.db

instead of

org.Rn,eg.db

note the dot instead of comma...

 

ADD COMMENTlink written 4 months ago by Peter Langfelder1.3k

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 REPLYlink written 4 months ago by Bohdan Khomtchouk10
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