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hms-dbmi / scde

R package for analyzing single-cell RNA-seq data
http://pklab.med.harvard.edu/scde
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scde issue #88

Open mark0237 opened 3 years ago

mark0237 commented 3 years ago

I keep getting this error when trying to run scde.error.models() or knn on the data from the scde tutorial.

Error in checkSlotAssignment(object, name, value) : assignment of an object of class “expression” is not valid for slot ‘defineComponent’ in an object of class “FLXMRglmC”; is(value, "expressionOrfunction") is not TRUE

I have already tried to downgrade to the flexmix_2.3-13 version. I also reinstalled the latest version of SCDE several time. Unfortunately I cannot downgrade SCDE because my mac does not allow to do it from the Terminal.

Literally, I have been with SCDe issues for hours. Please, help.

mark0237 commented 3 years ago

It is a pity I cannot get to use this package with my data as well. I found it perfect for what I would like to analyze since I am not really an expert on scRNA seq data.

mark0237 commented 3 years ago

Hi there!

I CANT BELIEVE I COULD FINALLY SOLVE THIS PROBLEM!

I HAVE (RE)-INSTALLED THE FOLLOWING VERSIONS

gfortran 10.2 for Catalina (macOS 10.15) https://github.com/fxcoudert/gfortran-for-macOS/releases/tag/10.2

RCCARMADILLO OLDER VERSION install.packages("https://cran.r-project.org/src/contrib/Archive/RcppArmadillo/RcppArmadillo_0.9.900.3.0.tar.gz", repos=NULL, type="source")

SCDE VERSION 1.99.1 AND FLEXMIX 2.3-13 OLD require(devtools) devtools::install_version('flexmix', '2.3-13') devtools::install_github('hms-dbmi/scde', build_vignettes = FALSE)

I HOPE THIS WILL BE OF A HELP FOR SOMEONE WHO HAVE BEEN STRUGGLING FOR HOURS AS ME

oyshilin commented 2 years ago

I'm facing this problem as well, is this method useful for windows user?