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When running the netDx vignette locally in docker, the process is automatically killed and does not complete.
Steps to recreate
Pull the "shraddhapai/netdx:v1.3.1" docker image
Run docker run -it -v /Users/{yourusername}/projects/netDx/output:/results shraddhapai/netdx:1.3.1 /bin/bash
Run cd netDx/vignettes
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
The text was updated successfully, but these errors were encountered:
Description
When running the netDx vignette locally in docker, the process is automatically killed and does not complete.
Steps to recreate
docker run -it -v /Users/{yourusername}/projects/netDx/output:/results shraddhapai/netdx:1.3.1 /bin/bash
cd netDx/vignettes
rmarkdown::render("BuildPredictor.Rmd")
sessionInfo() Output
Output from Running Vignette
The text was updated successfully, but these errors were encountered: