concerns/questions about error messages in call to revolver_plt_dendogram

[githubuserincyte]

I've been running some vignette code (specifically this code https://github.com/caravagn/revolver.misc/blob/master/vignette_plotting_functions/vignette_plotting_functions.md) . During the issue of a command to plot a dendrogram ( see console output below), I encounter an error. Has anybody observed this error message in a call to revolver_plt_dendogram?

> revolver_plt_dendogram(Breast.fit, type = 'clonality')
 [ REVOLVER Plot: Dendrogram of REVOLVER clusters ]
         Dendogram = 1
         Dendogram type = rectangle
         Output file =  N/A
Error in cluster::agnes(dist(features$occurrences.clonal.subclonal), method = x$cluster$hc.method) :
  object 'twins' not found
> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 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=en_US.UTF-8
 [9] LC_ADDRESS=en_US.UTF-8        LC_TELEPHONE=en_US.UTF-8
[11] LC_MEASUREMENT=en_US.UTF-8    LC_IDENTIFICATION=en_US.UTF-8

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

other attached packages:
[1] revolver_0.1.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.18          RColorBrewer_1.1-2    pillar_1.3.0
 [4] compiler_3.4.4        DEoptimR_1.0-8        plyr_1.8.4
 [7] R.methodsS3_1.7.1     R.utils_2.7.0         tools_3.4.4
[10] viridis_0.5.1         class_7.3-14          iterators_1.0.10
[13] prabclus_2.2-6        dendextend_1.8.0      mclust_5.4.1
[16] nlme_3.1-124          tibble_1.4.2          gtable_0.2.0
[19] lattice_0.20-33       viridisLite_0.3.0     mgcv_1.8-11
[22] pkgconfig_2.0.2       rlang_0.2.2           Matrix_1.2-3
[25] igraph_1.2.2          foreach_1.4.4         parallel_3.4.4
[28] mvtnorm_1.0-8         rJava_0.9-10          gridExtra_2.3
[31] trimcluster_0.1-2.1   cluster_2.0.3         xlsxjars_0.6.1
[34] fpc_2.1-11.1          stats4_3.4.4          diptest_0.75-7
[37] grid_3.4.4            nnet_7.3-12           robustbase_0.93-2
[40] flexmix_2.3-14        pio_0.1.0             pheatmap_1.0.10
[43] purrr_0.2.5           ggplot2_3.0.0         kernlab_0.9-27
[46] magrittr_1.5          whisker_0.3-2         scales_1.0.0
[49] codetools_0.2-14      modeltools_0.2-22     MASS_7.3-45
[52] dynamicTreeCut_1.63-1 permute_0.9-4         colorspace_1.3-2
[55] xlsx_0.6.1            lazyeval_0.2.1        munsell_0.5.0
[58] doParallel_1.0.11     vegan_2.5-2           crayon_1.3.4
[61] R.oo_1.22.0
>

A google search of some of the message turned up this URL https://stackoverflow.com/questions/46592133/package-cluster-does-not-work-with-r-x64-3-4-1 . revolver requires R 3.4 or greater (according to the DESCRIPTION file https://github.com/caravagn/revolver/blob/master/DESCRIPTION ) . Would this command (revolver_plt_dendogram(Breast.fit, type = 'clonality')) proceed without an error in R v3.4 but an error then emerge in 3.4.4 (as I am currently using?) Is R version 3.4 strictly required to use this ? Does anybody know if a specific version of "vegan" is required?

If anyone has been able to successfully use this function (revolver_plt_dendogram(Breast.fit, type = 'clonality')) can they by chance run "sessionInfo" and post their output?

[caravagn]

Hi,

I can succesfully run it with

R version 3.4.2 (2017-09-28) revolver_0.1.1 cluster_2.0.6

You have a crash with cluster_2.0.3, could that be the reason?

Giulio

---

sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: OS X El Capitan 10.11.6

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_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] revolver_0.1.1

loaded via a namespace (and not attached): [1] modeltools_0.2-22 tidyselect_0.2.4 purrr_0.2.5 kernlab_0.9-26
[5] lattice_0.20-35 colorspace_1.3-2 stats4_3.4.2 viridisLite_0.3.0
[9] mgcv_1.8-20 yaml_2.1.19 rlang_0.2.1 R.oo_1.22.0
[13] pillar_1.3.0 R.utils_2.6.0 glue_1.3.0 prabclus_2.2-6
[17] RColorBrewer_1.1-2 fpc_2.1-11.1 bindrcpp_0.2.2 foreach_1.4.4
[21] bindr_0.1.1 plyr_1.8.4 robustbase_0.93-0 munsell_0.5.0
[25] gtable_0.2.0 R.methodsS3_1.7.1 mvtnorm_1.0-8 codetools_0.2-15
[29] knitr_1.20 permute_0.9-4 pio_0.1.0 doParallel_1.0.11
[33] flexmix_2.3-14 parallel_3.4.2 class_7.3-14 DEoptimR_1.0-8
[37] trimcluster_0.1-2.1 Rcpp_0.12.18 scales_0.5.0 diptest_0.75-7
[41] vegan_2.5-2 gridExtra_2.3 ggplot2_3.0.0.9000 dplyr_0.7.6
[45] grid_3.4.2 tools_3.4.2 magrittr_1.5 lazyeval_0.2.1
[49] tibble_1.4.2 dynamicTreeCut_1.63-1 cluster_2.0.6 crayon_1.3.4
[53] whisker_0.3-2 pkgconfig_2.0.1 dendextend_1.8.0 Matrix_1.2-11
[57] pheatmap_1.0.10 MASS_7.3-47 assertthat_0.2.0 rstudioapi_0.7
[61] viridis_0.5.1 iterators_1.0.10 R6_2.2.2 mclust_5.4
[65] nlme_3.1-131 nnet_7.3-12 igraph_1.2.1 compiler_3.4.2

[elifirem]

Hi,

I have a similar error with the functions revolver_plt_dendogram and revolver_plt_compare_dendograms although for me it says function not found. I am using:

R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

revolver_0.1.6
cluster_2.0.7-1
vegan_2.5-3 

Irem

[caravagn]

Hi @elifirem, my bad :) Luckily @ttriche fixed with a pull request my spelling error of the word dendrogram, which was originally missing an 'r'.

It should work with the current version using the correct name.

See this commit

[elifirem]

Oh sorry the functions works fine, you're right! Best