Comments (3)
jorainer
commented on July 18, 2024
Really sorry about these installation problems! We made some quite drastic changes recently, thus all packages need to be the most recent developmental versions. All problems should however go away with the upcoming Bioconductor release.
I guess the installed Spectra package must be too old. Actually, the BiocManager::install("jorainer/MetaboAnnotationTutorials") call should have installed/updated all packages properly, but I guess something must have gone wrong.
Please try the following:
BiocManager::install("RforMassSpectrometry/ProtGenerics")
BiocManager::install("RforMassSpectrometry/MsCoreUtils")
BiocManager::install("RforMassSpectrometry/Spectra")
BiocManager::install("RforMassSpectrometry/MetaboCoreUtils")
BiocManager::install("RforMassSpectrometry/CompoundDb")Installing the packages in that order should fix the installation problems. Please let me know if it's still not working.
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redbluewater
commented on July 18, 2024
Excellent - this works just fine. Thanks for the update and added help. I appreciate it, and I look forward to using this package. Cheers.
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jorainer
commented on July 18, 2024
Great! I'm closing the issue now. Feel free to re-open. And also please let me know if you run into problems or see features/things that could be improved!
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Related Issues (20)
- Create an IonDb with all theoretical adducts for a CompoundDb
- Function to combine/concatenate CompDb databases
- Add an insertCompound function HOT 1
- Availability of functions to create empty CompDB and insert and delete compounds HOT 2
- Seeking suggestions for database development (HMDB version 5) HOT 2
- Pass skipErrors to read.SDFset through compound_tbl_sdf? HOT 4
- Avoid storing the DB connection within the object
- Rename table "compound" into "ms_compound"
- Implement a StandardsDb that extends CompoundDb HOT 11
- Update the MsBackendCompDb HOT 1
- insertIon method HOT 4
- non integer msLevel values HOT 3
- Add possibility to delete (inserted or existing) ions or MS/MS spectra
- Prepare for Bioconductor submission HOT 3
- Arbitrary columns in insertIon
- Transfer of CompoundDb
- Support import from MoNa MSP files HOT 1
- custom Db - spectra and ion Db questions HOT 2
- mass2mz method for CompDb HOT 6
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