ubuntu 16.04 SC3 1.4.2 or 1.5.1 bugs

[weizhiting]

when i run SC3 on my PC,it comes up a bugs , can not find 'sildist' object.can you help me? my error is Error in silhouette.default(clusts, diss) : can not find object 'sildist';

[wikiselev]

Hi thanks for your message, could you provide your sessionInfo() please?

[weizhiting]

HI, sessionInfo() is R version 3.4.0 (2017-04-21) 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=zh_CN.UTF-8 LC_NUMERIC=C LC_TIME=zh_CN.UTF-8 LC_COLLATE=zh_CN.UTF-8
[5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=zh_CN.UTF-8 LC_PAPER=zh_CN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] SC3_1.5.1

loaded via a namespace (and not attached): [1] Biobase_2.36.2 viridis_0.4.0 edgeR_3.18.1 viridisLite_0.2.0 foreach_1.4.3
[6] gtools_3.5.0 shiny_1.0.3 assertthat_0.2.0 stats4_3.4.0 doRNG_1.6.6
[11] vipor_0.4.5 robustbase_0.92-7 RSQLite_1.1-2 lattice_0.20-35 limma_3.32.2
[16] digest_0.6.12 RColorBrewer_1.1-2 colorspace_1.3-2 htmltools_0.3.6 httpuv_1.3.3
[21] Matrix_1.2-8 plyr_1.8.4 pcaPP_1.9-61 WriteXLS_4.0.0 XML_3.98-1.7
[26] pheatmap_1.0.8 biomaRt_2.32.0 zlibbioc_1.22.0 xtable_1.8-2 mvtnorm_1.0-6
[31] scales_0.4.1 gdata_2.17.0 tibble_1.3.0 pkgmaker_0.22 IRanges_2.10.0
[36] ggplot2_2.2.1 ROCR_1.0-7 BiocGenerics_0.22.0 lazyeval_0.2.0 magrittr_1.5
[41] mime_0.5 memoise_1.1.0 doParallel_1.0.10 gplots_3.0.1 class_7.3-14
[46] beeswarm_0.2.3 shinydashboard_0.5.3 tools_3.4.0 scater_1.4.0 registry_0.3
[51] data.table_1.10.4 matrixStats_0.52.2 stringr_1.2.0 S4Vectors_0.14.0 munsell_0.4.3
[56] locfit_1.5-9.1 cluster_2.0.6 rngtools_1.2.4 AnnotationDbi_1.38.0 compiler_3.4.0
[61] e1071_1.6-8 caTools_1.17.1 rhdf5_2.20.0 grid_3.4.0 RCurl_1.95-4.8
[66] tximport_1.4.0 iterators_1.0.8 rjson_0.2.15 bitops_1.0-6 gtable_0.2.0
[71] codetools_0.2-15 DBI_0.6-1 reshape2_1.4.2 rrcov_1.4-3 R6_2.2.1
[76] gridExtra_2.2.1 dplyr_0.5.0 KernSmooth_2.23-15 ggbeeswarm_0.5.3 stringi_1.1.5
[81] Rcpp_0.12.10 DEoptimR_1.0-8

[wikiselev]

Hi!

Could you please try this this sequence of commands:

library(SC3)
library(scater)
library(cluster, lib.loc = .Library)

and then run SC3? Do you get the error?

[weizhiting]

aha，it really works.thanks!

[wikiselev]

Great, could you please reinstall cluster package:

install.packages("cluster")

and then this:

library(SC3)
library(scater)

and then run SC3 again? Do you get the error now?

[weizhiting]

no, it works ok . But actually i do not know why this works? Anyway,awesome work!

[wikiselev]

The problem is in cluster package, here is a comment from its developer (Martin Maechler):

---

This has (almost) nothing to do with cluster but with the fact that all R packages which use .C() or .Fortran() must be re-installed in R 3.4.0 as long ago announced on the R-devel mailing list and also in the NEWS of R 3.4.0 :

Packages which register native routines for .C or .Fortran need to be re-installed for this version (unless installed with R-devel SVN revision r72375 or later).

So your users (or you) which have problem must accidentally use a version of 'cluster' that was installed with an earlier version of R ... inspite of the fact that cluster is part of every R's version, and there is of course is installed correctly.

---

So, simple reinstallation of cluster package should be enough to fix the issue, as you have just proved. Many thanks for testing it for me! Cheers, Vlad