Comments (3)
from icellr.
It failed again. The same error as before.
from icellr.
It's the version of SCRAN.
Here is my session info. If you install it in R 3.5 it should work.
You need a version of scran that has the fastMNN function. Mine is scran_1.10.2
In the near future I will fix this. But for now, let me know if this fixes the error!
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux
Matrix products: default
BLAS: /gpfs/share/apps/R/3.5.1/lib64/R/lib/libRblas.so
LAPACK: /gpfs/share/apps/R/3.5.1/lib64/R/lib/libRlapack.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] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] scran_1.10.2 SingleCellExperiment_1.4.1
[3] SummarizedExperiment_1.12.0 DelayedArray_0.8.0
[5] matrixStats_0.55.0 Biobase_2.42.0
[7] GenomicRanges_1.34.0 GenomeInfoDb_1.18.2
[9] IRanges_2.16.0 S4Vectors_0.20.1
[11] BiocGenerics_0.28.0 BiocParallel_1.16.6
loaded via a namespace (and not attached):
[1] statmod_1.4.32 beeswarm_0.2.3 locfit_1.5-9.1
[4] tidyselect_0.2.5 reshape2_1.4.3 purrr_0.3.3
[7] HDF5Array_1.10.1 lattice_0.20-38 rhdf5_2.26.2
[10] colorspace_1.4-1 viridisLite_0.3.0 rlang_0.4.0
[13] pillar_1.4.2 glue_1.3.1 GenomeInfoDbData_1.2.0
[16] plyr_1.8.4 stringr_1.4.0 zlibbioc_1.28.0
[19] munsell_0.5.0 gtable_0.3.0 vipor_0.4.5
[22] scater_1.10.1 BiocNeighbors_1.0.0 Rcpp_1.0.2
[25] edgeR_3.24.3 scales_1.0.0 limma_3.38.3
[28] XVector_0.22.0 gridExtra_2.3 ggplot2_3.2.1
[31] stringi_1.4.3 dplyr_0.8.3 grid_3.5.1
[34] tools_3.5.1 bitops_1.0-6 magrittr_1.5
[37] RCurl_1.95-4.12 lazyeval_0.2.2 tibble_2.1.3
[40] dynamicTreeCut_1.63-1 crayon_1.3.4 pkgconfig_2.0.3
[43] Matrix_1.2-17 DelayedMatrixStats_1.4.0 ggbeeswarm_0.6.0
[46] assertthat_0.2.1 viridis_0.5.1 Rhdf5lib_1.4.3
[49] R6_2.4.0 igraph_1.2.4.1 compiler_3.5.1
from icellr.
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from icellr.