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"

lcolladotor

Hola RLadies-Aguascalientes,

Les escribo por si quieren unirse al Slack de la CDSB donde tenemos a gente de todos los demás grupos de RLadies del país. Tenemos un canal llamado #rladies y andamos jugando con un par de ideas. En https://www.r-consortium.org/blog/2020/03/18/cdsb-diversity-and-outreach-hotspot-in-mexico vienen más detalles de nuestra historia y nuestra relación con grupos de RLadies en México.

Si sí, solo necesitaría su(s) correo(s) y nombre(s).

Saludos,
Leo

Leonardo Collado Torres, Ph. D., Research Scientist

lcolladotor

Some of my own notes prior to answering live on the community call

Question: What does it mean to “maintain an R package”?

• deal with questions, you approve/dissapprove changes you receive from others, you end up learning about community guidelines (Bioconductor in my case) as well as R-devel

Question: How do you encourage user feedback and/or manage a firehose of user feedback or requests for help?

• emails: no one really benefits, sure, I can write a blog post about your question but that's a ton of extra work
• private data (unpublished) but the packages we make are open-source and we believe in community building

lcolladotor

## From https://stackoverflow.com/questions/5812493/how-to-add-leading-zeros
x <- 10 ^ (0:5)
library('stringr')

getOption('scipen')
x
str_pad(x, 8, pad = '0')
options(scipen = 999)
getOption('scipen')
x

lcolladotor

## Contains edits related to https://github.com/Bioconductor/Contributions/issues/1191

# Helper to retrieve GTF & GFF3 file urls from Gencode
.gencodeSourceUrls <- function(species, release, filetype, justRunUnitTest)
{
    speciesUrl <- ifelse(species=="Human", "Gencode_human/", "Gencode_mouse/")
    dirurl = paste0(AnnotationHubData:::.gencodeBaseUrl, speciesUrl, "release_", release, "/")
    names(dirurl) <- paste0(species,"_", release)

    fileurls <-AnnotationHubData:::.gencodeFileFromUrl(dirurl)

lcolladotor

> table(!is.na(lcg_alumni$candidate_gscholar_id))

FALSE  TRUE 
  226    47 
> 
> plot(y = !is.na(lcg_alumni$candidate_gscholar_id), x = lcg_alumni$date_finished)