Question: error using package : Error in get(load(file)) :
gravatar for tina.khajeh
4.6 years ago by
Iran, Islamic Republic Of
tina.khajeh0 wrote:

I used select command to get information from "" package, consider code bellow : 

select(,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( is as follow :


        R version 3.1.2 (2014-10-31)
       Platform: x86_64-apple-darwin13.4.0 (64-bit)

       [1] C

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

       other attached packages:
       [1]   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 select • 912 views
ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by tina.khajeh0

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', ''))


ADD REPLYlink written 4.6 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(, key = "GAPDH", columns = "UNIPROT", keytype = "SYMBOL")
           1: select(, key = "GAPDH", columns = "UNIPROT", keytype = "SYMBOL")
ADD REPLYlink written 4.6 years ago by tina.khajeh0

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:


select(,key="GAPDH",columns = c("ENTREZID"),keytype = "SYMBOL")

If that doesn't work, then try reinstalling packages as suggested above.


ADD REPLYlink written 4.6 years ago by Dan Tenenbaum8.2k

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


...and run the commands that are suggested.

ADD REPLYlink written 4.6 years ago by Dan Tenenbaum8.2k

Thanks for your help. the problem solved :)

ADD REPLYlink written 4.6 years ago by tina.khajeh0

Can you please update your question by copy/pasting the output from sessionInfo() after you've run library(

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 4.6 years ago by Steve Lianoglou12k
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