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Semantic Similarity against all MeSH categories

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

1 answer

please follow the vignette, meshdata works for species specific data.

This error is actually coming from RSQLite. I got a similar problem, when using GEOmetadb.

Error in rsqlite_send_query(conn@ptr, statement) : basic_string::_M_replace_aux

The problem was that for some reason the sqlite file was with size=0. I downloaded the file again, created the connection again and now it's working.

"sqlite file was with size=0" can you explain what you mean by this? I am getting the exact same error with RSQLite, but cannot figure out what the message means or what the error might be

What's the size of your file? Did you try to download again?

I solved this issue, the error was that the 'column' name in my SQLite db had '.' in the name after being read in by R. So, before importing my R dataframe into RSQLite, I first had to replace the '.' in the colnames with '_', and that solved the issue.

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