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hemberg-lab / SC3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
http://bioconductor.org/packages/SC3
GNU General Public License v3.0
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Error in silhouette.default(clusts, diss) : object 'sildist' not found #40

Closed tweirick closed 7 years ago

tweirick commented 7 years ago

I see you are trying to address this in some of the commits, but I am getting the following error when running the example vignette. I have tried running this in a number of ways including the Bioconductor and development branches. Any ideas?

Error in silhouette.default(clusts, diss) : object 'sildist' not found Error in silhouette.default(clusts, diss) : object 'sildist' not found Error in silhouette.default(clusts, diss) : object 'sildist' not found Error in checkForRemoteErrors(val) : 3 nodes produced errors; first error: Error in silhouette.default(clusts, diss) : object 'sildist' not found

sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.2 LTS

Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

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 stats graphics grDevices utils datasets methods
[8] base

other attached packages: [1] SC3_1.5.2 scater_1.4.0 ggplot2_2.2.1
[4] Biobase_2.36.2 BiocGenerics_0.22.0 knitr_1.16

loaded via a namespace (and not attached): [1] bitops_1.0-6 matrixStats_0.52.2 devtools_1.13.3
[4] bit64_0.9-7 doParallel_1.0.10 RColorBrewer_1.1-2
[7] httr_1.2.1 tools_3.4.1 doRNG_1.6.6
[10] R6_2.2.2 KernSmooth_2.23-15 vipor_0.4.5
[13] DBI_0.7 lazyeval_0.2.0 colorspace_1.3-2
[16] withr_2.0.0 gridExtra_2.2.1 bit_1.1-12
[19] curl_2.8.1 compiler_3.4.1 git2r_0.19.0
[22] pkgmaker_0.22 labeling_0.3 caTools_1.17.1
[25] scales_0.4.1 mvtnorm_1.0-6 DEoptimR_1.0-8
[28] robustbase_0.92-7 stringr_1.2.0 digest_0.6.12
[31] rrcov_1.4-3 pkgconfig_2.0.1 htmltools_0.3.6
[34] WriteXLS_4.0.0 limma_3.32.5 rlang_0.1.1
[37] RSQLite_2.0 BiocInstaller_1.26.0 shiny_1.0.3
[40] bindr_0.1 gtools_3.5.0 dplyr_0.7.2
[43] RCurl_1.95-4.8 magrittr_1.5 Matrix_1.2-10
[46] Rcpp_0.12.12 ggbeeswarm_0.6.0 munsell_0.4.3
[49] S4Vectors_0.14.3 viridis_0.4.0 stringi_1.1.5
[52] edgeR_3.18.1 zlibbioc_1.22.0 rhdf5_2.20.0
[55] gplots_3.0.1 plyr_1.8.4 grid_3.4.1
[58] blob_1.1.0 gdata_2.18.0 shinydashboard_0.6.1 [61] lattice_0.20-35 locfit_1.5-9.1 tcltk_3.4.1
[64] rjson_0.2.15 rngtools_1.2.4 reshape2_1.4.2
[67] codetools_0.2-15 biomaRt_2.32.1 stats4_3.4.1
[70] XML_3.98-1.9 glue_1.1.1 data.table_1.10.4
[73] httpuv_1.3.5 foreach_1.4.3 gtable_0.2.0
[76] assertthat_0.2.0 mime_0.5 xtable_1.8-2
[79] e1071_1.6-8 pcaPP_1.9-72 class_7.3-14
[82] viridisLite_0.2.0 tibble_1.3.3 pheatmap_1.0.8
[85] iterators_1.0.8 AnnotationDbi_1.38.2 registry_0.3
[88] beeswarm_0.2.3 memoise_1.1.0 IRanges_2.10.2
[91] tximport_1.4.0 bindrcpp_0.2 cluster_2.0.6
[94] ROCR_1.0-7

wikiselev commented 7 years ago

Hi, could you please follow the steps from #36 and reinstall the cluster package:

install.packages("cluster")

Then if you restart your R session and load SC3 again - do you get the same error?

tweirick commented 7 years ago

Sorry about that, I totally missed the closed issues. Following the steps in #36 fixed the issue.