Error running netDx vignette locally

[ajfricke]

Description

When running the netDx vignette locally in docker, the process is automatically killed and does not complete.

Steps to recreate

1. Pull the "shraddhapai/netdx:v1.3.1" docker image
2. Run docker run -it -v /Users/{yourusername}/projects/netDx/output:/results shraddhapai/netdx:1.3.1 /bin/bash
3. Run cd netDx/vignettes
4. Run R and type rmarkdown::render("BuildPredictor.Rmd")

sessionInfo() Output

R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so

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=C
 [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] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BiocManager_1.30.10

loaded via a namespace (and not attached):
[1] compiler_4.0.3 tools_4.0.3    knitr_1.30     xfun_0.19

Output from Running Vignette

Bioconductor version 3.12 (BiocManager 1.30.10), ?BiocManager::install for help
> rmarkdown::render("BuildPredictor.Rmd")


processing file: BuildPredictor.Rmd
  |.                                                                     |   2%
   inline R code fragments

  |..                                                                    |   3%
label: unnamed-chunk-1 (with options)
List of 1
 $ eval: logi FALSE

  |....                                                                  |   5%
  ordinary text without R code

  |.....                                                                 |   7%
label: unnamed-chunk-2 (with options)
List of 1
 $ eval: logi FALSE

  |......                                                                |   8%
  ordinary text without R code

  |.......                                                               |  10%
label: unnamed-chunk-3 (with options)
List of 1
 $ eval: logi TRUE

  |........                                                              |  12%
  ordinary text without R code

  |.........                                                             |  13%
label: unnamed-chunk-4 (with options)
List of 1
 $ eval: logi TRUE

  |..........                                                            |  15%
  ordinary text without R code

  |............                                                          |  17%
label: unnamed-chunk-5 (with options)
List of 1
 $ eval: logi TRUE

  |======================================================================| 100%
  |.............                                                         |  18%
  ordinary text without R code

  |..............                                                        |  20%
label: unnamed-chunk-6 (with options)
List of 1
 $ eval: logi TRUE

  |...............                                                       |  22%
  ordinary text without R code

  |................                                                      |  23%
label: unnamed-chunk-7 (with options)
List of 1
 $ eval: logi TRUE

  |..................                                                    |  25%
  ordinary text without R code

  |...................                                                   |  27%
label: unnamed-chunk-8 (with options)
List of 1
 $ eval: logi TRUE

  |....................                                                  |  28%
  ordinary text without R code

  |.....................                                                 |  30%
label: unnamed-chunk-9 (with options)
List of 1
 $ eval: logi TRUE

  |......................                                                |  32%
  ordinary text without R code

  |.......................                                               |  33%
label: unnamed-chunk-10 (with options)
List of 1
 $ eval: logi TRUE

  |........................                                              |  35%
  ordinary text without R code

  |..........................                                            |  37%
label: unnamed-chunk-11 (with options)
List of 1
 $ eval: logi TRUE

  |...........................                                           |  38%
  ordinary text without R code

  |............................                                          |  40%
label: unnamed-chunk-12 (with options)
List of 1
 $ eval: logi TRUE

  |.............................                                         |  42%
  ordinary text without R code

  |..............................                                        |  43%
label: unnamed-chunk-13 (with options)
List of 1
 $ eval: logi TRUE

  |................................                                      |  45%
  ordinary text without R code

  |.................................                                     |  47%
label: unnamed-chunk-14
  |..................................                                    |  48%
  ordinary text without R code

  |...................................                                   |  50%
label: unnamed-chunk-15 (with options)
List of 1
 $ eval: logi TRUE

Bioconductor version 3.12 (BiocManager 1.30.10), ?BiocManager::install for help
Killed