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wsciekly.maciek
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10
@wscieklymaciek-17486
Last seen 6.0 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
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?