search

ceabiodb / biodbHmdb

A biodb extension for connecting to HMDB.
GNU Affero General Public License v3.0
2 stars 0 forks source link

ERROR [18:21:35.705] Database(s) "hmdb.metabolites" is(are) not defined. #14

Open ekaterinaesenkova opened 3 years ago

ekaterinaesenkova commented 3 years ago

I got the following error when I try to create a connector to HMDB metabolites.

conn <- mybiodb$getFactory()$createConn('hmdb.metabolites') ERROR [18:21:35.705] Database(s) "hmdb.metabolites" is(are) not defined. Error in error0("Database(s) \"", paste(db.id[notDefined], collapse = ", "), : Database(s) "hmdb.metabolites" is(are) not defined.

pkrog commented 3 years ago

Thank you for contacting us.

It seems you do not have biodbHmdb package installed. Did you installed both packages biodb and biodbHmdb as explained in the README of https://github.com/pkrog/biodbHmdb?

Please note that the biodb package is currently under submission to Bioconductor, and thus may undergo slight modifications that could impact extension packages like biodbHmdb. Do not hesitate to post new issues.

pkrog commented 3 years ago

I'll transfer this issue to the biodbHmdb package since it concerns it.

ekaterinaesenkova commented 3 years ago

I installed both packages. So I ran the following lines and still got an error. devtools::install_github('pkrog/biodb', dependencies=TRUE) devtools::install_github('pkrog/biodbHmdb', dependencies=TRUE)

mybiodb <- biodb::Biodb() INFO [20:53:17.568] Loading definitions from package biodb version 0.99.6. conn <- mybiodb$getFactory()$createConn('hmdb.metabolites') ERROR [20:53:20.207] Database(s) "hmdb.metabolites" is(are) not defined. Error in error0("Database(s) \"", paste(db.id[notDefined], collapse = ", "), : Database(s) "hmdb.metabolites" is(are) not defined.

pkrog commented 3 years ago

I've made some changes for Bioconductor today, and then retested biodbHmdb after that, it works for me. Would you mind trying again with the new versions (note the change in the instantiation of biodb main class, the function to call is now newInst():

devtools::install_github('pkrog/biodb', dependencies=TRUE)
devtools::install_github('pkrog/biodbHmdb', dependencies=TRUE)
mybiodb <- biodb::newInst()
ekaterinaesenkova commented 3 years ago

Still an error message:

Error: Failed to install 'biodb' from GitHub: (converted from warning) installation of package ‘/tmp/RtmpEOadOs/file1295f64e3434e/biodb_0.99.8.tar.gz’ had non-zero exit status

pkrog commented 3 years ago

Were there any output? I would need the complete output of the install in order to see the exact error that occurred. On which platform are you installing the packages (Windows, Linux, Mac)?