umr1283 / flashpcar

Fast Principal Component Analysis of Large-Scale Genome-Wide Data

UMR 1283 - Project Template

You can install umr1283 with:

remotes::install_github("umr1283/umr1283")

The default project directory architecture from umr1283::create_project (compatible with RStudio Project Wizard) is as follow:

library(umr1283)
create_project(path = "my-project", analyst_name = "UMR1283")

tree -a my-project
#> my-project/
#> ├── data
#> ├── .devcontainer
#> │   ├── devcontainer.json
#> │   └── Dockerfile
#> ├── docs
#> ├── .gitignore
#> ├── logs
#> ├── my-project.Rproj
#> ├── outputs
#> ├── README.md
#> ├── renv
#> ├── reports
#> ├── .Rprofile
#> ├── scripts
#> │   ├── 00-targets.R
#> │   ├── _dependencies.R
#> │   └── tar-utils
#> ├── _targets
#> └── _targets.R
#> 
#> 10 directories, 9 files

---

Getting help

If you encounter a clear bug, please file a minimal reproducible example on GitHub.
For questions and other discussion, please open a discussion on GitHub.

flashpcar's Issues

Check issues

── R CMD check results ──────────────────────────────────── flashpcaR 2.1.1 ────
Duration: 2m 56.4s

❯ checking for missing documentation entries ... WARNING
  Undocumented code objects:
    ‘plot2d’
  Undocumented data sets:
    ‘hm3.chr1’
  All user-level objects in a package should have documentation entries.
  See chapter ‘Writing R documentation files’ in the ‘Writing R
  Extensions’ manual.

❯ checking Rd \usage sections ... WARNING
  Undocumented arguments in documentation object 'plot2d.cv.scca'
    ‘...’
  
  Functions with \usage entries need to have the appropriate \alias
  entries, and all their arguments documented.
  The \usage entries must correspond to syntactically valid R code.
  See chapter ‘Writing R documentation files’ in the ‘Writing R
  Extensions’ manual.

❯ checking for hidden files and directories ... NOTE
  Found the following hidden files and directories:
    .github
  These were most likely included in error. See section ‘Package
  structure’ in the ‘Writing R Extensions’ manual.

❯ checking installed package size ... NOTE
    installed size is 37.4Mb
    sub-directories of 1Mb or more:
      libs  36.3Mb

❯ checking R code for possible problems ... NOTE
  plot2d.cv.scca: no visible binding for global variable ‘.data’
    (/home/runner/work/flashpcaR/flashpcaR/check/flashpcaR.Rcheck/00_pkg_src/flashpcaR/R/scca.R:733-743)
  plot2d.cv.scca: no visible binding for global variable ‘r’
    (/home/runner/work/flashpcaR/flashpcaR/check/flashpcaR.Rcheck/00_pkg_src/flashpcaR/R/scca.R:733-743)
  Undefined global functions or variables:
Error: Error: R CMD check found WARNINGs
    .data r
Execution halted

❯ checking compiled code ... NOTE
  File ‘flashpcaR/libs/flashpcaR.so’:
    Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
      Object: ‘data.o’
  
  Compiled code should not call entry points which might terminate R nor
  write to stdout/stderr instead of to the console, nor use Fortran I/O
  nor system RNGs.
  
  See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.

❯ checking for detritus in the temp directory ... NOTE
  Found the following files/directories:
    ‘RtmpB8p6VWhumanht-12_v3_0_r3_11283641_a_txt.zip’

0 errors ✔ | 2 warnings ✖ | 5 notes ✖