unable to load metabolites database

[emiliesecherre]

Hello ! I'm trying to run this code :

utils::download.file("https://ndownloader.figshare.com/files/11438549", "metabolites_20180508.bridge")
locationm = normalizePath("./metabolites_20180508.bridge")
mapperm <- BridgeDbR::loadDatabase(locationm)

and i get this error :

> mapperm <- BridgeDbR::loadDatabase(locationm)
Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,  : 
  org.bridgedb.IDMapperException: Could not connect to database

how can i fix it please ? I add that i'm using bridgedbR in a devtools package, so the metabolitedb file is downloaded inside the package folder. If i download it somewhere else it works

[egonw]

Which version of BridgeDbR are you using? This is not the active repository anymore, but this is: https://github.com/BridgeDb/BridgeDbR

Second, I would also suggest to try to load the most recent metabolite database, which you can find at https://bridgedb.github.io/data/gene_database/

[emiliesecherre]

I'm using BridgeDbR 1.22.0, thank you for the recent databases. Unfortunatly, the issue remain the same : if the file is inside the package i'm creating, the database can't be loaded...

[emiliesecherre]

Edit : Now its not working at all, no matter where i put the .bridge file... Its always the same issue

[egonw]

I'll try to look at it asap. I'm sorry about the trouble :/ (there are a few things overdue I need to finish first...)

[emiliesecherre]

no worries, thank you !

[egonw]

Okay, first attempt to reproduce it failed. It seems to work with BridgeDb 1.23.1 on Debian GNU/Linux.

[egonw]

Okay, works for me with BridgeDb 1.22.0 too. Both were with R 3.6.3. What R version are you using?

[egonw]

Okay, installed R 4.0 and BridgeDbR 1.22, still works :( Okay, I'm starting to get convinced we're looking at a OS-level issue. @emiliesecherre, can you plz tell me your operating system, R version (for completeness, but I guess 4.0), and the value of locationm?

[emiliesecherre]

I have R 4.0.2, BridgeDbR 1.22.0, Windows 10 (last version) and locationm is "C:\Users\Thanael\Documents\promethee\metabo.bridge" (i renamed the metabolite db). The weird thing is that i works only with some folders, like "Downloads" one, but not for others..

[egonw]

Okay, thanks. I was able to reproduce the problem with Java8, Win10, RStudio, and R 3.6.3.

I'll have to do some debugging to figure out what goes wrong. I don't get much info here either :/

[emiliesecherre]

Okay it's just about a package i'm building, i can't use the metabolite db if its inside the package folder.

[egonw]

I have been thinking about this anyway... there are plenty of Bioconductor data packages, but I do not have time to explore how to create those.

PS. I'm doing some updates to the BridgeDb Java code to get some better feedback to get an idea what goes wrong, but did not finish that yet.

[DeniseSl22]

Moved to bridgedb/BridgeDbR#28