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cole-trapnell-lab / garnett

Automated cell type classification
MIT License
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<simpleError: 'coef.cv.glmnet' is not an exported object from 'namespace:glmnet'> #32

Closed yejg2017 closed 4 years ago

yejg2017 commented 4 years ago

When I run my dataset with pretrained classifier,and I got this error

hpliner commented 4 years ago

Thanks for the report. Looks like the latest version of glmnet no longer exports that function. I have just pushed a fix, go ahead and reinstall according to the instructions on the website. Reopen if that doesn't fix it!

SathiyaNManivannan commented 4 years ago

Still getting the error after reinstalling as per the website instruction

hpliner commented 4 years ago

@SathiyaNManivannan Can you post your sessionInfo where you're still getting the error?

hpliner commented 4 years ago

I'm going to close, reply or reopen if this continues to be an issue.

vswarup commented 4 years ago

I am having the same problem and seems like the issue has not been resolved. Kindly help, my R sessionInfo()

R version 3.6.2 (2019-12-12) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: Ubuntu 18.04.4 LTS

Matrix products: default BLAS/LAPACK: /home/vivek/anaconda3/lib/libopenblasp-r0.3.8.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] splines stats4 parallel stats graphics grDevices utils [8] datasets methods base

other attached packages: [1] garnett_0.2.8 monocle3_0.2.1 [3] SingleCellExperiment_1.8.0 SummarizedExperiment_1.16.0 [5] DelayedArray_0.12.0 BiocParallel_1.20.0 [7] matrixStats_0.55.0 GenomicRanges_1.38.0 [9] GenomeInfoDb_1.22.0 org.Hs.eg.db_3.10.0 [11] AnnotationDbi_1.48.0 IRanges_2.20.0 [13] S4Vectors_0.24.0 Seurat_3.1.4 [15] monocle_2.14.0 DDRTree_0.1.5 [17] irlba_2.3.3 VGAM_1.1-2 [19] ggplot2_3.2.1 Biobase_2.46.0 [21] BiocGenerics_0.32.0 Matrix_1.2-18 [23] HSMMSingleCell_1.4.0