destiny
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Version issue Matrix package (v1.5-1)
Hi developers, I tried running the DiffusionMap() function on the "guo" dummy dataset:
data(guo)
dm_guo <- DiffusionMap(guo)
However, this throws the following error:
Error: as(<dsCMatrix>, "dsTMatrix") is deprecated since Matrix 1.5-0; do as(., "TsparseMatrix") instead
Traceback is as follows:
- warning.(gettextf("as(<%s>, "%s") is deprecated since Matrix 1.5-0; do %s instead", cln1, cln2, deparse1(.as.via.virtual(Class1, Class2, quote(.)))), call. = FALSE, domain = NA)
- Matrix.DeprecatedCoerce(cd1, cd2)
- asMethod(object)
- as(d2, "dsTMatrix")
- no_censoring(dists, sigma, cb)
- verbose_timing(verbose, "Calculating transition probabilities", { if (censor) censoring(imputed_data, sigma, dists, censor_val, ...
- transition_probabilities(imputed_data, sigma, knn$dist_mat, censor, censor_val, censor_range, missing_range, verbose)
- DiffusionMap(guo)
This seems to be an issue with the latest version of the Matrix package, version 1.5-1.
Any idea how I could solve this issue?
Thanks in advance,
Basiel
It’s a warning, not an error, so you just need to stop using options(warn=2)
to turn warnings into errors, then you can ignore it.
Thank you for notifying me, I’ll make sure a future version of destiny doesn’t use deprecated APIs anymore
Thank you for your swift response!
Setting options(Matrix.warnDeprecatedCoerce = 0)
resolved the issue.