search

Irrationone / cellassign

Automated, probabilistic assignment of cell types in scRNA-seq data
Other
191 stars 79 forks source link

Documentation workflow does not work with conda install #80

Open keithgmitchell opened 3 years ago

keithgmitchell commented 3 years ago

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)

keithgmitchell commented 3 years ago

Bump?

regiopires commented 2 years ago

Please,

Any solution for this issue?

Best regards.

At.te