search

rsilvabioinfo / ProbMetab

Provides probability ranking to candidate compounds assigned to masses, with the prior assumption of connected sample and additional previous and spectral information modeled by the user.
http://labpib.fmrp.usp.br/methods/probmetab
2 stars 2 forks source link

Problem when installing on R 4.0 #5

Closed geraldocantelli closed 3 years ago

geraldocantelli commented 3 years ago

Hello, I need to install the package ProbMetab on R 4.0 but I found the next error: Skipping 3 packages not available: multtest, RCytoscape, graph The packages multtest and graph are already installed (by Bioconductor::install) and the Rcytoscape seems was updated to another package name version and the one that was called Rcytoscape doesn't allow installation on R 4.0.

Can some one help me please? Best regards, Geraldo Cesar Cantelli Bioinformatic specialist

rsilvabioinfo commented 3 years ago

Hello Geraldo,

The instructions here may help http://labpib.fmrp.usp.br/methods/probmetab/

One option would be to downgrade your R version. If you don't want to go this route, you can download the package on the link above, then, remove Rcytoscape from 'Depends' section and try to install https://github.com/rsilvabioinfo/ProbMetab/blob/master/DESCRIPTION

Rcytoscape is only used at the end of the workflow.

I have to warn you, ProbMetab is no being maintained, I recommend you to use something more updated, such as IPA https://pubs.acs.org/doi/abs/10.1021/acs.analchem.9b02354

Which has the same concept, or https://www.metaboanalyst.ca https://github.com/xia-lab/MetaboAnalystR

which implements 'Mummichog' with a very similar concept.

Cheers, Ricardo

Em ter., 2 de fev. de 2021 às 13:58, geraldocantelli < notifications@github.com> escreveu:

Hello, I need to install the package ProbMetab on R 4.0 but I found the next error: Skipping 3 packages not available: multtest, RCytoscape, graph The packages multtest and graph are already installed (by Bioconductor::install) and the Rcytoscape seems was updated to another package name version and the one that was called Rcytoscape doesn't allow installation on R 4.0.

Can some one help me please? Best regards, Geraldo Cesar Cantelli Bioinformatic specialist

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/rsilvabioinfo/ProbMetab/issues/5, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAN2SA66SBEEB72GTAIAY2DS5AVKPANCNFSM4W7B4VPA .

geraldocantelli commented 3 years ago

Thank you very much Ricardo.