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kuwisdelu / matter

Out-of-core statistical computing and signal processing
http://www.cardinalmsi.org
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argument data is missing with no default #13

Closed MASHUOA closed 1 year ago

MASHUOA commented 1 year ago

Hi, there, As I was loading the Imzml data, I found this:

        mz <- matter_list(path=file,
            type=Ctypeof(mz.ibdtype),
            offset=mzData(info)[["external offset"]],
            extent=mzData(info)[["external array length"]])
        intensity <- matter_list(path=file,
            type=Ctypeof(intensity.ibdtype),
            offset=intensityData(info)[["external offset"]],
            extent=intensityData(info)[["external array length"]])

will trigger the error message: argument "data" is missing with no default

Best, George

kuwisdelu commented 1 year ago

Can you confirm the version of matter you are using and the exact function call (with parameters) that you used?

The source code suggests you are using the updated Cardinal 3.0 but I can't replicate this issue with the updated matter 2.0.

MASHUOA commented 1 year ago

I see. I was using Cardinal 2.X. After an installation through: remotes::install_github("kuwisdelu/Cardinal") It's working now. Best, George

kuwisdelu commented 1 year ago

Ah, yes. The Github branches are the development versions of Cardinal and matter (and will therefore sometimes break), so you will need to make sure they are updated and in sync. The stable version is the Bioconductor release.

MASHUOA commented 1 year ago

I see. I found people have to use a specified (latest) version of BiocManager to make Cardinal 3.0 available: BiocManager::install(version = "3.16") If a pc was pre-installed with BiocManager (3.1.5, e.g.), it might only be able to get the Cardinal 2. X. Many thanks, George