Semantic Similarity against all MeSH categories

Question

[rzjfr]

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

Answer 1

[Guangchuang Yu]

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

[Leandro Lima]

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.

[steve]

"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

[Leandro Lima]

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

[steve]

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.