I used select command to get information from "org.Hs.eg.db" package, consider code bellow :
library(org.Hs.eg.db)
select(org.Hs.eg.db,key="GAPDH",columns = c("ENTREZID"),keytype = "SYMBOL")
but after run it, I received error :
Warning message: In readChar(con, 5L, useBytes = TRUE) : cannot open compressed file '', probable reason 'No such file or directory' Error in get(load(file)) : error in evaluating the argument 'x' in selecting a method for function 'get': Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
I have no idea what to do.
also the output of sessionInfo() after running library(org.Hs.eg.db) is as follow :
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
locale:
[1] C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods
[9] base
other attached packages:
[1] org.Hs.eg.db_3.0.0 RSQLite_1.0.0 DBI_0.3.1
[4] AnnotationDbi_1.28.2 GenomeInfoDb_1.2.5 IRanges_2.0.1
[7] S4Vectors_0.4.0 Biobase_2.26.0 BiocGenerics_0.12.1
loaded via a namespace (and not attached):
[1] BBmisc_1.9 BatchJobs_1.6 BiocParallel_1.0.3
[4] Biostrings_2.34.1 GenomicAlignments_1.2.2 GenomicFeatures_1.18.7
[7] GenomicRanges_1.18.4 RCurl_1.95-4.5 Rsamtools_1.18.3
[10] XML_3.98-1.1 XVector_0.6.0 base64enc_0.1-2
[13] biomaRt_2.22.0 bitops_1.0-6 brew_1.0-6
[16] checkmate_1.5.2 codetools_0.2-11 digest_0.6.8
[19] fail_1.2 foreach_1.4.2 iterators_1.0.7
[22] rtracklayer_1.26.3 sendmailR_1.2-1 stringr_0.6.2
[25] tools_3.1.2 zlibbioc_1.12.0
Thanks for updating with the sessionInfo, are you running R from the terminal and did you try running it in "vanilla mode"? In the terminal you just type:
R --vanillaWhat is the output of
traceback()after the error is thrown?Something strange is going on ... if the vanilla trick doesn't work, you could also try to reinstall a couple of the relevant packages, perhaps:
R> library("BiocInstaller") R> biocLite(c('AnnotationDbi', 'org.Hs.eg.db'))I'm using RStudio not from terminal.
how can I run it in vanilla mode? I typed "R --vanilla" in the terminal a text that was about version of my R, copyright, ... printed.
the output of traceback() is as follow :
7: get(load(file)) 6: .warnAboutManyToOneRelationships(cols) 5: .legacySelect(x, keys, cols, keytype, jointype) 4: .select(x, keys, columns, keytype, jointype = jointype) 3: .selectWarnJT(x, keys, columns, keytype, jointype = jointype, kt = kt, ...) 2: select(org.Hs.eg.db, key = "GAPDH", columns = "UNIPROT", keytype = "SYMBOL") 1: select(org.Hs.eg.db, key = "GAPDH", columns = "UNIPROT", keytype = "SYMBOL")Yes, in the terminal, you type:
And then you see the R copyright notice followed by the R prompt:
At that prompt you can type commands so try again your initial commands:
library(org.Hs.eg.db) select(org.Hs.eg.db,key="GAPDH",columns = c("ENTREZID"),keytype = "SYMBOL")If that doesn't work, then try reinstalling packages as suggested above.
It also appears that some of your packages are "too new" for your version of R/Bioconductor.
So you should either update to R-3.2.0 and Bioconductor 3.1, or run
source("http://bioconductor.org/biocLite.R") biocValid()...and run the commands that are suggested.
Thanks for your help. the problem solved :)
Can you please update your question by copy/pasting the output from
sessionInfo()after you've runlibrary(org.Hs.eg.db)?You might also try starting R like so:
R --vanillain case you've got some.Rdatafile that is being loaded on startup that might be hosing something.