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MassBank / RMassBank

Playground for experiments on the official http://bioconductor.org/packages/devel/bioc/html/RMassBank.html
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Build fail on Bioc #308

Closed meowcat closed 2 years ago

meowcat commented 2 years ago

https://master.bioconductor.org/checkResults/3.15/bioc-LATEST/RMassBank/nebbiolo1-buildsrc.html

I don't know yet what it is, it spontaneously started without any change by our side. I thought it was intermittent and would disappear, but it's still here after a week. Will look at it.

(Ignore the install errors on Win and Mac as they are issues of dependencies ChemmineOB/ChemmineR and will resolve)

sneumann commented 2 years ago

Hi, on windows and Mac the complaint is on ERROR: dependency 'ChemmineOB' is not available and check_built() locally gives 

   Error: processing vignette 'RMassBank.Rmd' failed with diagnostics:
   Unable to interpret the SMILES-strings for ID(s) 2817 2818 2819 2820 2821 2822 2823 2824 2825 2826 2827 2828 2829 2830 2758

Minimal example to reproduce:

library(RMassBank)
library(RMassBankData)
loadList(system.file("list/NarcoticsDataset.csv", package="RMassBankData"))

I also find issues which might be related:

RMassBank::getMolecule("CCO")
Error in set.atom.types(mol) : could not find function "set.atom.types"

I have an older installation with rcdk_3.5.0, rcdklibs_2.3, RMassBank_3.0.0 where library(RMassBank); RMassBank::getMolecule("CCO") works. A previously broken installation was fixed by reinstalling rcdk_3.6.0 rcdklibs_2.3. Build machines have the same versions: http://bioconductor.org/checkResults/3.15/bioc-LATEST/nebbiolo1-R-instpkgs.html , so there must be something else.

Yours, Steffen

meowcat commented 2 years ago

This seems to be old