drisso/zinbwave

Can't run zinbwave in R

Closed this issue · 3 comments

yingzhang121 commented

Hi, dear developers,

I can't run zinbwave as you instructed (https://bioconductor.org/packages/release/bioc/vignettes/zinbwave/inst/doc/intro.html#zinb-wave):

x37_zinb <- zinbwave(sce37, K=2, epsilon=1000)
Error in zinbwave(sce37, K = 2, epsilon = 1000) :
could not find function "zinbwave"

Below is my 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 10.13.4

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] 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] magrittr_1.5 SingleCellExperiment_1.2.0 SummarizedExperiment_1.10.0
[4] DelayedArray_0.6.0 BiocParallel_1.14.0 matrixStats_0.53.1
[7] Biobase_2.40.0 GenomicRanges_1.32.0 GenomeInfoDb_1.16.0
[10] IRanges_2.14.1 S4Vectors_0.18.1 BiocGenerics_0.26.0

loaded via a namespace (and not attached):
[1] pcaPP_1.9-73 Rcpp_0.12.16 compiler_3.5.0 XVector_0.20.0
[5] iterators_1.0.9 bitops_1.0-6 tools_3.5.0 zlibbioc_1.26.0
[9] digest_0.6.15 bit_1.1-12 memoise_1.1.0 annotate_1.58.0
[13] zinbwave_1.2.0 RSQLite_2.1.0 lattice_0.20-35 pspline_1.0-18
[17] foreach_1.4.4 Matrix_1.2-14 DBI_1.0.0 mvtnorm_1.0-7
[21] GenomeInfoDbData_1.1.0 copula_0.999-18 genefilter_1.62.0 glmnet_2.0-16
[25] bit64_0.9-7 locfit_1.5-9.1 grid_3.5.0 ADGofTest_0.3
[29] AnnotationDbi_1.42.0 survival_2.42-3 XML_3.98-1.11 limma_3.36.0
[33] blob_1.1.1 edgeR_3.22.0 codetools_0.2-15 splines_3.5.0
[37] stabledist_0.7-1 softImpute_1.4 xtable_1.8-2 numDeriv_2016.8-1
[41] gsl_1.9-10.3 RCurl_1.95-4.10

Best,
Ying

drisso commented

Are you sure you loaded the zinbwave package?

zinbwave appears in the loaded via a namespace (and not attached): section. Adding

library(zinbwave)

should solve it.

yingzhang121 commented

I did run library(zinbwave) before I ran the command.

Oh, I see the problem. I installed magrittr package in the same active R session. So R session has been restarted.

Thanks.

  • Ying
drisso commented

No problem! Glad it was an easy fix!