lcolladotor

##################### Steps for reproducing this problem ######################

## Create a package
usethis::create_package("~/Desktop/testgit")

## Set up git and say yes to the prompts
usethis::use_git()

## Create a file

lcolladotor

## From https://r-graphics.org/recipe-quick-scatter
plot(mtcars$wt, mtcars$mpg)

library(ggplot2)

ggplot(mtcars, aes(x = wt, y = mpg)) +
  geom_point()

## Check structure of the ggplot object

lcolladotor

$ R CMD build --keep-empty-dirs --no-resave-data regionReport
Loading required package: colorout
* checking for file ‘regionReport/DESCRIPTION’ ... OK
* preparing ‘regionReport’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘regionReport_1.21.8.tar.gz’

lcolladotor

## Generate the HTML report
report <- derfinderReport(
    prefix = "report", browse = FALSE,
    nBestRegions = 15, makeBestClusters = TRUE, outdir = "html",
    fullCov = list("21" = genomeDataRaw$coverage), optionsStats = optionsStats
)
## Registered S3 method overwritten by 'GGally':
##   method from   
##   +.gg   ggplot2
## Writing 9 Bibtex entries ... OK

lcolladotor

$ java -jar ~/Desktop/bfg-1.13.0.jar --strip-blobs-bigger-than 600K .

Using repo : /Users/lcollado/Dropbox/Code/spatialLIBD/./.git


This repo has been processed by The BFG before! Will prune repo before proceeding - to avoid unnecessary cleaning work on unused objects...
Completed prune of old objects - will now proceed with the main job!

Scanning packfile for large blobs: 4459
Scanning packfile for large blobs completed in 133 ms.

lcolladotor

### job 1

https://github.com/LieberInstitute/recount3/runs/595989184?check_suite_focus=true

Cache R packages

```bash
/usr/bin/docker exec  75fa6381ecfef7283744d18704e483f121f4b70928e7b61339d45400512ea988 sh -c "cat /etc/*release | grep ^ID"
Running JavaScript Action with default external tool: node12
Cache not found for input keys: Linux-r-biocdocker-bioc-devel-0bb5a4fcc86a585a290e0e47479439bbb3091332b2d4248989d8aea6b193b542, Linux-r-biocdocker-bioc-devel-.

lcolladotor

## Read more about GitHub actions at
## https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/
## which will lead you to
## https://github.com/r-lib/actions/tree/master/examples.
## Also check the reference manual at
## https://help.github.com/en/actions
## I also found this work in progress book
## https://ropenscilabs.github.io/actions_sandbox/
## as well as these two other GitHub actions config files
## https://github.com/seandavi/BiocActions/blob/master/.github/workflows/main.yml

lcolladotor

Hi!

Here’s the recording from my session today with Sang Ho, Kristen and Abby. 

Here are the links and content for several config files I gave Sang Ho throughout the session:

R https://cran.r-project.org/
RStudio https://rstudio.com/products/rstudio/download/#download
JHPCE register: https://jhpce.jhu.edu/register/user/
JHPCE ssh keys: https://jhpce.jhu.edu/knowledge-base/authentication/ssh-key-setup/

lcolladotor

$ R CMD build --keep-empty-dirs --no-resave-data regionReport
Bioconductor version 3.11 (BiocManager 1.30.10), ?BiocManager::install for help
* checking for file ‘regionReport/DESCRIPTION’ ... OK
* preparing ‘regionReport’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘bumphunterExample.Rmd’ using rmarkdown
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata.

lcolladotor

> current <- dir(.libPaths())
> current
  [1] "abind"
  [2] "acepack"
  [3] "ada"
  [4] "additivityTests"
  [5] "ade4"
  [6] "admisc"
  [7] "AER"
  [8] "affy"