Hi,
I have been running the mnnCorrect from the SCRAN package without issues, and now wanted to run the fastMNN (scripts downloaded form github; https://github.com/MarioniLab/scran/tree/master/R). However, when calling the fastMNN function ( mnn.out <- do.call(fastMNN, c(original, list(k=20, d=50))) ) I end up getting the error:
Fejl i FUN(X[[i]], ...) : objekt 'cxx_cosine_norm' blev ikke fundet
I can see that "cxx_cosine_norm" is called within the cosineNorm function (out <- .Call(cxx_cosine_norm, X, mode!="l2norm")), which is called within the fastMNN function. I am puzzled as the mnnCorrect calls the same cosineNorm function, without any issues. Does anybody how an suggestion to why the "cxx_cosine_norm" can't be found when called through fastMNN?
All help will be greatly appreciated!
/Tobias
Session info:
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] da_DK.UTF-8/da_DK.UTF-8/da_DK.UTF-8/C/da_DK.UTF-8/da_DK.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocManager_1.30.1 dplyr_0.7.6 Matrix_1.2-14 scran_1.8.2
[5] DropletUtils_1.1.5 scater_1.9.7 SingleCellExperiment_1.3.6 SummarizedExperiment_1.11.5
[9] DelayedArray_0.7.19 BiocParallel_1.14.2 matrixStats_0.53.1 GenomicRanges_1.33.7
[13] GenomeInfoDb_1.17.1 IRanges_2.15.14 S4Vectors_0.19.17 ggplot2_3.0.0
[17] Biobase_2.41.1 BiocGenerics_0.27.1
loaded via a namespace (and not attached):
[1] viridis_0.5.1 dynamicTreeCut_1.63-1 edgeR_3.23.3 viridisLite_0.3.0 DelayedMatrixStats_1.3.4
[6] shiny_1.1.0 assertthat_0.2.0 statmod_1.4.30 GenomeInfoDbData_1.1.0 vipor_0.4.5
[11] pillar_1.3.0 lattice_0.20-35 glue_1.2.0 limma_3.37.3 digest_0.6.15
[16] promises_1.0.1 XVector_0.21.3 colorspace_1.3-2 htmltools_0.3.6 httpuv_1.4.4.2
[21] plyr_1.8.4 pkgconfig_2.0.1 zlibbioc_1.27.0 purrr_0.2.5 xtable_1.8-2
[26] scales_0.5.0 later_0.7.3 tibble_1.4.2 DT_0.4 withr_2.1.2
[31] lazyeval_0.2.1 magrittr_1.5 crayon_1.3.4 mime_0.5 beeswarm_0.2.3
[36] FNN_1.1 tools_3.5.0 data.table_1.11.4 stringr_1.3.1 Rhdf5lib_1.3.1
[41] munsell_0.5.0 locfit_1.5-9.1 bindrcpp_0.2.2 compiler_3.5.0 rlang_0.2.1
[46] rhdf5_2.25.4 grid_3.5.0 RCurl_1.95-4.10 tximport_1.9.8 rstudioapi_0.7
[51] rjson_0.2.20 htmlwidgets_1.2 igraph_1.2.1 bitops_1.0-6 gtable_0.2.0
[56] reshape2_1.4.3 R6_2.2.2 gridExtra_2.3 bindr_0.1.1 stringi_1.2.3
[61] ggbeeswarm_0.6.0 Rcpp_0.12.17 tidyselect_0.2.4
Dear Aron,
Yes I was sourcing through the R files, but seem to have gotten it to work now through the BioC-devel. Thank you very much for the help and for creating and maintaining scran!