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rformassspectrometry / MsBackendMsp

Mass Spectrometry Data Backend for MSP Files
https://rformassspectrometry.github.io/MsBackendMsp/
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MsBackendMsp not on bioconda channel #11

Open zmahnoor14 opened 2 years ago

zmahnoor14 commented 2 years ago

Hello,

I have been using Spectra and MsBackends for my Metabolome Identification Workflow.

I had previously downloaded MsBackendMsp with R4.1. Now, I want to create a conda package and it would be easier for installations using conda if this package is already on some conda channel, since I want to use the stable R version 4.1.1 for now instead of the R devel (which currently hosts the MsBackendMsp package).

On Anaconda, only MsBackendMgf and msbackendmassbank are available.

With the Docker container, however, MsBackend can be installed with Dockerfile, although the R version installed by default is 4.1.1. MSP_Docker.zip

I have added docker and yml file here that I used to install MsBackendMsp, without using R-devel version. Is there a possibility to install this package using conda?

Best regards, Mahnoor

zmahnoor14 commented 2 years ago

I checked the versions and installations in the jupyter notebook

sneumann commented 2 years ago

Ok, after downloading the ZIP and docker build -t msptest . I can docker run --rm -it msptest bash and source activate msbackendmspTest . This includes R version 4.1.1 (2021-08-10) and

Indeed installing BiocManager::install("MsBackendMsp") gives package ‘MsBackendMsp’ is not available for Bioconductor version '3.14' since the package only appeared in BioC-3.15: https://bioconductor.org/packages/devel/bioc/html/MsBackendMsp.html BioC releases are always tied to the R version, so in R-4.1.1 the BiocManager::install() will always grab packages from BioC 3.14.

=> If you stick with R version 4.1.1 (2021-08-10) the only choice is to obtain MsBackendMsp (and its dependencies!) from 3.15 manually. => The Bioconda team is creating packages from BioC on an irregular basis, latest is only BioC-3.14 e.g. https://anaconda.org/bioconda/bioconductor-spectra/ , so you'll have to wait there.

Yours, Steffen