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Question: error using org.Hs.eg.db package : Error in get(load(file)) :
0
gravatar for tina.khajeh
2.6 years ago by
Iran, Islamic Republic Of
tina.khajeh0 wrote:

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

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by tina.khajeh0
2

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 --vanilla

What 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'))

 

ADD REPLYlink written 2.6 years ago by Steve Lianoglou12k

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")
ADD REPLYlink written 2.6 years ago by tina.khajeh0
1

Yes, in the terminal, you type:

R --vanilla

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.

 

ADD REPLYlink written 2.6 years ago by Dan Tenenbaum ♦♦ 8.2k

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.

ADD REPLYlink written 2.6 years ago by Dan Tenenbaum ♦♦ 8.2k

Thanks for your help. the problem solved :)

ADD REPLYlink written 2.6 years ago by tina.khajeh0

Can you please update your question by copy/pasting the output from sessionInfo() after you've run library(org.Hs.eg.db)?

You might also try starting R like so: R --vanilla in case you've got some .Rdata file that is being loaded on startup that might be hosing something.

ADD REPLYlink written 2.6 years ago by Steve Lianoglou12k
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