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# Adapted from https://github.com/tmatta/lsasim/issues/50#issue-2254039296

# Package, Data and subset
remotes::install_github("tmatta/lsasim", "issue-50")
#> Using GitHub PAT from the git credential store.
#> Skipping install of 'lsasim' from a github remote, the SHA1 (28b71cf3) has not changed since last install.
#>   Use `force = TRUE` to force installation
library(lsasim)
#> This is lsasim 2.1.4-1713963651

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# Setup
remotes::install_github("tmatta/lsasim", "issue-50")
#> Using GitHub PAT from the git credential store.
#> Downloading GitHub repo tmatta/lsasim@issue-50
#> 
#> ── R CMD build ─────────────────────────────────────────────────────────────────
#> * checking for file ‘/tmp/RtmpCKm8ak/remotes9c8f72a0c9f7/tmatta-lsasim-940c83a/DESCRIPTION’ ... OK
#> * preparing ‘lsasim’:
#> * checking DESCRIPTION meta-information ... OK

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# Loading package ==============================================================
library("MADMMplasso")
message(paste("MADMMplasso version", packageVersion("MADMMplasso")))

# Loading data =================================================================
CRC_data <- readRDS("aux/CRC_data_300.rds") # change this manually, I won't bother with commandArgs()
X23 <- CRC_data$x

# log2 transfermation f or the expression levels
X1 <- (X23)

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# Setup ========================================================================
rm(list = ls())
devtools::install_github("ocbe-uio/MADMMplasso", force = TRUE)
#> Downloading GitHub repo ocbe-uio/MADMMplasso@HEAD
#> 
#> ── R CMD build ─────────────────────────────────────────────────────────────────
#> * checking for file ‘/tmp/Rtmpr2fzD2/remotes149907717ef58/ocbe-uio-MADMMplasso-9896eeb/DESCRIPTION’ ... OK
#> * preparing ‘MADMMplasso’:
#> * checking DESCRIPTION meta-information ... OK

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# Simulations to address https://github.com/ocbe-uio/permChacko/issues/13

# Setup =================================================================
remotes::install_github("ocbe-uio/permChacko@issue-13")
runs <- 1000L
results <- matrix(
  NA, nrow = runs, ncol = 6L,
  dimnames = list(
    "run" = seq_len(runs),
    "p_values" = c(

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Input

R CMD check --use-valgrind --no-build-vignettes --no-manuals BayesMallows_2.0.1.tar.gz

Note: use --no-manual instead of --use-manuals (invalid option) next time!

Output

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Building cellmigRation vignettes
--- re-building ‘cellmigRation.Rmd’ using rmarkdown
Bioconductor
  version
  3.12
  (BiocManager
  1.30.10), R
  4.0.4
  (2021-02-15)
Installing

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Code from tmatta/lsasim#40

Assumptions that make code work

library(lsasim)
n_items <- 30

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testInstallation:
	@echo -e "If you can see this, Make has been installed successfully"

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---
title: "Title"
author: Waldir Leoncio
institute: "Oslo Centre for Biostatistics and Epidemiology"
date: "2020-09-11"
output:
  xaringan::moon_reader:
    nature:
      highlightLanguage: r
      highlightLines: true