loading scran package
1
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Entering edit mode
TJ • 0
@tj-18752
Last seen 19 months ago
Stanford University

Hi,

I'm looking to use the scran package for scRNAseq analysis. I've used this previously without issues, but now whenever I try to load the library, I get the following error:

Error: package or namespace load failed for ‘scran’:
object ‘.assignIndicesToWorkers’ is not exported by 'namespace:scater'

I removed scran then tried re-installing it. I was then asked to update a few packages, which I did. Then I ran into an error with hdf5r installation, but was ultimately able to get past this by installing it using homebrew at the command line. I then re-installed scran which went through without errors (v1.16.0), but I still get the same message as above whenever I try to load the library. Any guidance would be much appreciated. Thanks!

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] SingleCellExperiment_1.12.0 SummarizedExperiment_1.20.0 Biobase_2.50.0             
 [4] GenomicRanges_1.42.0        GenomeInfoDb_1.26.1         IRanges_2.24.0             
 [7] S4Vectors_0.28.0            BiocGenerics_0.36.0         MatrixGenerics_1.2.0       
[10] matrixStats_0.58.0         

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6                rsvd_1.0.3                locfit_1.5-9.4           
 [4] lattice_0.20-41           assertthat_0.2.1          R6_2.5.0                 
 [7] ggplot2_3.3.3             pillar_1.4.7              sparseMatrixStats_1.2.0  
[10] zlibbioc_1.36.0           rlang_0.4.10              irlba_2.3.3              
[13] Matrix_1.3-2              BiocNeighbors_1.8.1       BiocParallel_1.24.1      
[16] igraph_1.2.6              RCurl_1.98-1.2            munsell_0.5.0            
[19] beachmat_2.6.1            tinytex_0.29              DelayedArray_0.16.0      
[22] vipor_0.4.5               compiler_4.0.2            BiocSingular_1.6.0       
[25] xfun_0.21                 pkgconfig_2.0.3           ggbeeswarm_0.6.0         
[28] tidyselect_1.1.0          gridExtra_2.3             tibble_3.0.6             
[31] GenomeInfoDbData_1.2.4    edgeR_3.30.3              viridisLite_0.3.0        
[34] withr_2.4.1               crayon_1.4.1              dplyr_1.0.4              
[37] bitops_1.0-6              grid_4.0.2                gtable_0.3.0             
[40] lifecycle_0.2.0           DBI_1.1.1                 magrittr_2.0.1           
[43] scales_1.1.1              dqrng_0.2.1               cli_2.3.0                
[46] scuttle_1.0.2             XVector_0.30.0            viridis_0.5.1            
[49] limma_3.46.0              scater_1.18.3             DelayedMatrixStats_1.12.0
[52] ellipsis_0.3.1            vctrs_0.3.6               generics_0.1.0           
[55] tools_4.0.2               glue_1.4.2                beeswarm_0.2.3           
[58] purrr_0.3.4               colorspace_2.0-0          sessioninfo_1.1.1
scran installation • 1.0k views
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2
Entering edit mode
@martin-morgan-1513
Last seen 2 days ago
United States

Make sure that you are using the current version of Bioconductor, and that all packages are up-to-date.

> BiocManager::version()
[1] '3.12'
> BiocManager::valid()
[1] TRUE

If valid() does not return TRUE, update your packages as it describes.

Are you installing scran with BiocManager::install("scran") ? it should install version 1.18.5, not 1.16.0, for Bioconductor version 3.12.

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0
Entering edit mode

This worked, thank you! I had BiocManager v 3.11.

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