Doesn't work with more recent versions of biodb

[elliotfontaine]

Hi.

Versions in README.md should be more strict: the script fails with versions of biodb that don't expose the biodb::BiodbLogger class anymore. For exemple it fails with biodb 1.10.0

R packages:

getopt >= 1.20.0.
biodb >= 1.2.0rc2. # this should be more strict

[elliotfontaine]

It doesn't even work with biodb 1.2.0. Which version do you use on W4M ?

[pkrog]

Hi @elliotfontaine ,

If I understand well you are trying to run the script as a standalone script, not inside a Galaxy instance, right ?
As you see, the instructions are rather old, since it makes reference to R version 3.5. Are you using this version of R ?

[elliotfontaine]

Hi @pkrog ,
Yes I'm trying to use the script on its own. I was using R 4.3.3 when I tried it.
I believe the main issue is that the script uses a old interface of biodb, which exposed biodb::BiodbLogger et biodb::Biodb. It was only the case in 1.2.0rc, which sadly isn't on bioconductor/bioconda because it's a release candidate.

[elliotfontaine]

I'm gonna try again with versions described in lcmsmatching.xml.

<requirements>
		<requirement type="package" version="1.2.2">r-biodb</requirement>
		<requirement type="package" version="1.20.0">r-getopt</requirement>
		<requirement type="package" version="0.2_15">r-codetools</requirement> <!-- R_VERSION="0.2-15" IMPORTANT Do not remove, used by travis_install_deps.sh script. --> <!-- codetools package is needed because of the following error when running Galaxy on Travis-CI in planemo tests: "code for methods in class “HtmlWriter” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)". -->
		
</requirements>

[pkrog]

Je regarde de mon côté si je peux mettre à jour pour la dernière version de biodb sur Bioconductor.

[pkrog]

It fails with biodb 1.2.2 and R 4.4.1. Because of old code that passed with older versions of R:

DEBUG[2024-07-18 12:49:12.8530194759369][BiodbFactory::getFactory()] : Creating new connector mass.csv.file for database class mass.csv.file, with base URL "./res/filedb/filedb-rtsec.tsv".   
Error in !is.null(colname) && !is.na(colname) :                                                                                                                                                
  'length = 4' in coercion to 'logical(1)'                                                                                                                                                     
Calls: get.db.conn -> <Anonymous>                                                                                                                                                              
Execution halted                                                                                                                                                                               

I tried to upgrade lcmsmatching to latest version of biodb in Bioconductor. But it is too much work.
If you have some notions of R language, I would suggest to use the latest biodb package directly by installing it from Bioconductor. See https://www.bioconductor.org/packages/release/bioc/html/biodb.html.
Included vignettes will show you how to use it.

[elliotfontaine]

Thanks !