Error running init(sclvm,Y=Y,tech_noise = tech_noise) #27
Description
I got this error message when running the example in the vignette and running on my own dataset:
Error in python.exec(paste(objName, " = scLVM(Y,geneID=geneID,tech_noise=tech_noise)", : The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
I'm pretty sure I installed every dependency correctly.
python.exec("import sys; print(sys.version)") 2.7.10 (default, Feb 7 2017, 00:08:15) [GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.34)]
and calling python --version in command window get
Python 2.7.10
R session info:
sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] org.Mm.eg.db_3.4.1 AnnotationDbi_1.38.1 scLVM_0.99.3 rPython_0.0-6 RJSONIO_1.3-0
[6] DESeq2_1.16.1 SummarizedExperiment_1.6.3 DelayedArray_0.2.7 matrixStats_0.52.2 GenomicRanges_1.28.4
[11] GenomeInfoDb_1.12.2 IRanges_2.10.2 S4Vectors_0.14.3 gplots_3.0.1 statmod_1.4.30
[16] genefilter_1.58.1 cellrangerRkit_1.1.0 Rmisc_1.5 plyr_1.8.4 lattice_0.20-35
[21] bit64_0.9-7 bit_1.1-12 ggplot2_2.2.1 RColorBrewer_1.1-2 Biobase_2.36.2
[26] BiocGenerics_0.22.0 Matrix_1.2-10
loaded via a namespace (and not attached):
[1] bitops_1.0-6 httr_1.2.1 rprojroot_1.2 tools_3.4.1 backports_1.1.0
[6] R6_2.2.2 irlba_2.2.1 DT_0.2 rpart_4.1-11 KernSmooth_2.23-15
[11] Hmisc_4.0-3 DBI_0.7 lazyeval_0.2.0 colorspace_1.3-2 nnet_7.3-12
[16] gridExtra_2.2.1 compiler_3.4.1 htmlTable_1.9 plotly_4.7.0 checkmate_1.8.3
[21] caTools_1.17.1 scales_0.4.1 stringr_1.2.0 digest_0.6.12 foreign_0.8-69
[26] rmarkdown_1.6 XVector_0.16.0 base64enc_0.1-3 pkgconfig_2.0.1 htmltools_0.3.6
[31] htmlwidgets_0.9 rlang_0.1.1 RSQLite_2.0 bindr_0.1 jsonlite_1.5
[36] BiocParallel_1.10.1 gtools_3.5.0 acepack_1.4.1 dplyr_0.7.2 RCurl_1.95-4.8
[41] magrittr_1.5 GenomeInfoDbData_0.99.0 Formula_1.2-2 Rcpp_0.12.12 munsell_0.4.3
[46] stringi_1.1.5 yaml_2.1.14 zlibbioc_1.22.0 rhdf5_2.20.0 Rtsne_0.13
[51] grid_3.4.1 blob_1.1.0 gdata_2.18.0 splines_3.4.1 annotate_1.54.0
[56] locfit_1.5-9.1 knitr_1.16 geneplotter_1.54.0 XML_3.98-1.9 glue_1.1.1
[61] evaluate_0.10.1 latticeExtra_0.6-28 data.table_1.10.4 gtable_0.2.0 purrr_0.2.2.2
[66] tidyr_0.6.3 assertthat_0.2.0 xtable_1.8-2 survival_2.41-3 viridisLite_0.2.0
[71] tibble_1.3.3 pheatmap_1.0.8 memoise_1.1.0 bindrcpp_0.2 cluster_2.0.6