[Workshop] Using the recount2 resource and related tools

[lcolladotor]

BioC2019 repository: https://github.com/LieberInstitute/recountWorkshop2019

Deadlines

• [x] May 27: initial draft of workshop, as the vignette of a stand-alone R package in your own GitHub repo. The workshop does not have to be complete, but it be installable.
• [x] June 10: complete workshop submitted. Only bugfixes / refinements should be made after this point.
• [ ] June 17: All workshops complete and building without error. No new commits to contributor repos will be incorporated.

Related

BioC2017 workshop version repository: https://github.com/LieberInstitute/recountWorkshop

[lcolladotor]

May 29th update (from this commit https://github.com/LieberInstitute/recountWorkshop2019/commit/75c1b8928f53d4f4ba1bbd8c1e495f7d356b53a8):

$ R CMD build --keep-empty-dirs --no-resave-data recountWorkshop2019
Loading required package: colorout
* checking for file ‘recountWorkshop2019/DESCRIPTION’ ... OK
* preparing ‘recountWorkshop2019’:
* 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 ‘recountWorkshop2019_0.99.0.tar.gz’

$ R CMD check --no-vignettes --timings recountWorkshop2019_0.99.0.tar.gz
Loading required package: colorout
* using log directory ‘/Users/lcollado/Dropbox/Code/recountWorkshop2019.Rcheck’
* using R version 3.6.0 (2019-04-26)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘recountWorkshop2019/DESCRIPTION’ ... OK
* this is package ‘recountWorkshop2019’ version ‘0.99.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘recountWorkshop2019’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 239.0Mb
  sub-directories of 1Mb or more:
    doc        4.7Mb
    extdata  234.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/lcollado/Dropbox/Code/recountWorkshop2019.Rcheck/00check.log’
for details.

[lcolladotor]

Hi,

Is there something else I should do?

Best, Leo

[seandavi]

Nope. You are good to go.

On Tue, Jun 18, 2019 at 1:31 PM Leonardo Collado-Torres < notifications@github.com> wrote:

Hi,

Is there something else I should do?

Best, Leo

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