STRINGdb: enrichment function raises error
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Entering edit mode
@wscieklymaciek-17486
Last seen 2.9 years ago

Dear All,

I am writing a script that uses STRINGdb library. When I call:

enrichmentGO_Process <- string_db$get_enrichment(genes$STRING_id, category = "Process", methodMT = "fdr", iea = TRUE)

I get an error:

Loading required package: tcltk
Error in result_create(conn@ptr, statement) : no such table: ann
Calls: <Anonymous>
Execution halted

The point is that I am using anaconda cloud to create a virtual environment for that script. I am pulling version 1.20.0.

So I am wondering now, Is this error internal to the library or is the package @ anaconda broken?
Kind Regards,

 

sessionInfo():

R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: ......snakemake/conda/cb6d406e/lib/R/lib/libRblas.so
LAPACK: .......snakemake/conda/cb6d406e/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] biomaRt_2.36.1  STRINGdb_1.20.0 optparse_1.6.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0           compiler_3.4.1       RColorBrewer_1.1-2  
 [4] plyr_1.8.4           tools_3.4.1          prettyunits_1.0.2   
 [7] progress_1.2.0       bitops_1.0-6         digest_0.6.18       
[10] bit_1.1-12           RSQLite_2.1.1        memoise_1.1.0       
[13] rlang_0.3.0.1        pkgconfig_2.0.2      png_0.1-7           
[16] igraph_1.2.2         DBI_1.0.0            parallel_3.4.1      
[19] proto_1.0.0          httr_1.3.1           stringr_1.3.1       
[22] hms_0.4.2            IRanges_2.14.12      S4Vectors_0.18.3    
[25] gtools_3.8.1         caTools_1.17.1.1     stats4_3.4.1        
[28] bit64_0.9-7          getopt_1.20.2        Biobase_2.40.0      
[31] R6_2.2.2             sqldf_0.4-10         plotrix_3.7-3       
[34] hash_2.2.6           AnnotationDbi_1.42.1 XML_3.98-1.10       
[37] gsubfn_0.7           gdata_2.18.0         blob_1.1.1          
[40] magrittr_1.5         gplots_3.0.1         BiocGenerics_0.26.0
[43] assertthat_0.2.0     KernSmooth_2.23-15   stringi_1.2.4       
[46] RCurl_1.95-4.11      crayon_1.3.4         chron_2.3-53       
STRINGdb stringdb gene set enrichment analysis software error go • 429 views
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Entering edit mode

Have you tried the latest version of R and the package to see if this problem is solved on the newest version? Also, could you add the traceback() call to see where does this error originate?

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