cellassign
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Irrationone
Documentation workflow does not work with conda install
The example data does not load.
> library(cellassign)
> library(SingleCellExperiment)
> data(example_sce)
> data(example_marker_mat)
Warning message:
In data(example_marker_mat) : data set 'example_marker_mat' not found
The conda session info does not match that from the documentation.
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 16.04.7 LTS
Matrix products: default
BLAS/LAPACK: /afs/genomecenter.ucdavis.edu/software/anaconda3/4.8.3/lssc0-linux/envs/cellassign-0.99.2/lib/libopenblasp-r0.3.10.so
locale:
[1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US
[4] LC_COLLATE=en_US LC_MONETARY=en_US LC_MESSAGES=en_US
[7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] SingleCellExperiment_1.12.0 SummarizedExperiment_1.20.0
[3] Biobase_2.50.0 GenomicRanges_1.42.0
[5] GenomeInfoDb_1.26.0 IRanges_2.24.0
[7] S4Vectors_0.28.0 BiocGenerics_0.36.0
[9] MatrixGenerics_1.2.0 matrixStats_0.57.0
[11] cellassign_0.99.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4.6 whisker_0.4 XVector_0.30.0
[4] magrittr_1.5 zlibbioc_1.36.0 lattice_0.20-41
[7] tools_4.0.3 grid_4.0.3 tfruns_1.4
[10] tensorflow_2.2.0 Matrix_1.2-18 GenomeInfoDbData_1.2.4
[13] base64enc_0.1-3 bitops_1.0-6 RCurl_1.98-1.2
[16] glue_1.4.2 DelayedArray_0.16.0 compiler_4.0.3
[19] reticulate_1.18 jsonlite_1.7.1
In addition, I believe the cell by gene matrix was not working with the cellassign call but since the example data was not working it has been difficult to detect what the issue is. It seemed to work fine with R 3.6 but I do not believe things are working with the conda install (R 4.0)
