These are the libraries I'm loading:
suppressMessages( library( tidyverse ) )suppressMessages( library( data.table ) )suppressMessages( library( magrittr )suppressMessages( library( neo4r ) )
(I need tidyverse , data.table and magrittr to parse the output of call_neo4j )
The connection is set up like this :
con <- neo4j_api$new( url = 'http://localhost:7474' , user = 'neo4j' , password = 'NeO4J' )
And I execute the queries like this:
res = neo4r::call_neo4j( Q , con , type = 'graph' )
When Q = 'MATCH a=(p1:Protein)-[r:CURATED_INTERACTS_WITH]-(p2:Protein) RETURN a;' , the query works as expected . However, when I use Q = 'MATCH a=(p1:Protein)-[r:COMPILED_INTERACTS_WITH]-(p2:Protein) RETURN a;' after a few seconds I get the following error:
Error in readBin(content, character()) : R character strings are limited to 2^31-1 bytes
If I introduce a limit to that second query , like so Q = 'MATCH a=(p1:Protein)-[r:COMPILED_INTERACTS_WITH]-(p2:Protein) RETURN a LIMIT 25;', the the query works as expected.
Any idea what causes that error and how to solve it ?
Here is the output of sessionInfo():
`> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS
I'm using neo4r to query a Neo4J database that runs via a docker container (Ref: https://ckg.readthedocs.io/en/latest/intro/getting-started-with-docker.html ).
These are the libraries I'm loading:
suppressMessages( library( tidyverse ) )suppressMessages( library( data.table ) )suppressMessages( library( magrittr )suppressMessages( library( neo4r ) )(I need tidyverse , data.table and magrittr to parse the output of call_neo4j )
The connection is set up like this :
con <- neo4j_api$new( url = 'http://localhost:7474' , user = 'neo4j' , password = 'NeO4J' )And I execute the queries like this:
res = neo4r::call_neo4j( Q , con , type = 'graph' )When
Q = 'MATCH a=(p1:Protein)-[r:CURATED_INTERACTS_WITH]-(p2:Protein) RETURN a;', the query works as expected . However, when I useQ = 'MATCH a=(p1:Protein)-[r:COMPILED_INTERACTS_WITH]-(p2:Protein) RETURN a;'after a few seconds I get the following error:Error in readBin(content, character()) : R character strings are limited to 2^31-1 bytesIf I introduce a limit to that second query , like so
Q = 'MATCH a=(p1:Protein)-[r:COMPILED_INTERACTS_WITH]-(p2:Protein) RETURN a LIMIT 25;', the the query works as expected.Any idea what causes that error and how to solve it ?
Here is the output of
sessionInfo(): `> sessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.6 LTSMatrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] neo4r_0.1.1 magrittr_2.0.3 data.table_1.14.6 forcats_0.5.2 stringr_1.5.0
[6] dplyr_1.0.10 purrr_1.0.1 readr_2.1.3 tidyr_1.2.1 tibble_3.1.8
[11] ggplot2_3.4.0 tidyverse_1.3.2
loaded via a namespace (and not attached): [1] Rcpp_1.0.9 lubridate_1.9.0 assertthat_0.2.1 digest_0.6.31 utf8_1.2.2
[6] mime_0.12 R6_2.5.1 cellranger_1.1.0 backports_1.4.1 reprex_2.0.2
[11] evaluate_0.19 httr_1.4.4 pillar_1.8.1 rlang_1.0.6 curl_5.0.0
[16] googlesheets4_1.0.1 readxl_1.4.1 rstudioapi_0.14 rmarkdown_2.19 googledrive_2.0.0
[21] munsell_0.5.0 shiny_1.7.4 broom_1.0.2 compiler_4.1.2 httpuv_1.6.8
[26] modelr_0.1.10 xfun_0.36 pkgconfig_2.0.3 htmltools_0.5.4 tidyselect_1.2.0
[31] attempt_0.3.1 fansi_1.0.3 crayon_1.5.2 tzdb_0.3.0 dbplyr_2.2.1
[36] withr_2.5.0 later_1.3.0 grid_4.1.2 jsonlite_1.8.4 xtable_1.8-4
[41] gtable_0.3.1 lifecycle_1.0.3 DBI_1.1.3 scales_1.2.1 stringi_1.7.12
[46] cli_3.6.0 fs_1.5.2 promises_1.2.0.1 xml2_1.3.3 ellipsis_0.3.2
[51] generics_0.1.3 vctrs_0.5.1 tools_4.1.2 glue_1.6.2 hms_1.1.2
[56] fastmap_1.1.0 yaml_2.3.6 timechange_0.2.0 colorspace_2.0-3 gargle_1.2.1
[61] rvest_1.0.3 knitr_1.41 haven_2.5.1`