I want to get similarity between any two concept in MeSH database. with meshSim method in meshes package.
library(meshes)
library(MeSH.db)
meshdatabase <- meshdata("MeSH.db")
and I get following error:
Error in rsqlite_send_query(conn@ptr, statement) : basic_string::resize
My session info:
R version 3.3.2 (2016-10-31)
Platform: i686-pc-linux-gnu (32-bit)
Running under: Ubuntu precise (12.04.5 LTS)
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] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] meshes_1.0.0 DOSE_3.0.9 MeSH.db_1.7.0
[4] MeSHDbi_1.10.0 BiocGenerics_0.20.0
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.36.0 BiocParallel_1.8.1 splines_3.3.2
[4] digest_0.6.10 scales_0.4.1 assertthat_0.1
[7] grid_3.3.2 stringr_1.1.0 S4Vectors_0.12.0
[10] fgsea_1.0.2 fastmatch_1.0-4 RSQLite_1.1
[13] munsell_0.4.3 qvalue_2.6.0 GOSemSim_2.0.2
[16] tibble_1.2 DBI_0.5-1 DO.db_2.9
[19] igraph_1.0.1 ggplot2_2.2.0 plyr_1.8.4
[22] Biobase_2.34.0 data.table_1.9.8 stats4_3.3.2
[25] GO.db_3.4.0 stringi_1.1.2 magrittr_1.5
[28] reshape2_1.4.2 gtable_0.2.0 colorspace_1.3-1
[31] tools_3.3.2 gridExtra_2.2.1 IRanges_2.8.1
[34] lazyeval_0.2.0 memoise_1.0.0 Rcpp_0.12.8
meshes
mesh.db