| library("devtools") # with_lib(), install_github() | |
| tmp_lib <- file.path(tempdir(), ".lib") | |
| dir.create(tmp_lib) | |
| cran_pkg <- function(pkg, tmp_lib = tmp_lib){ | |
| ## upgrade or downgrade a package here | |
| ## following example is upgrading to bleeding edge devel version | |
| with_lib(tmp_lib, install.packages(pkg, repos = "http://cran.rstudio.com")) | |
| ## but this could also be a downgrade to the CRAN/released version! |
I recently got an email from Kurt Hornik from CRAN stating that a single line of code was causing poppr to fail in R-devel. Since installing R-devel is a pain on OSX, I decided to use a docker container. Ted Hart has a good blog on it here.
On mac, I followed the instructions to install docker starting here.
I ran this once and have never had to run it again:
I am a contributor to NESCent's Population Genetics in R repository. The idea behind this repository is that people would be able to construct short vignettes for genetic analysis in R that can be displayed on the Population Genetics Info Website. Of course, the submissions would need to be pull requests from other users that would have forked the repository. For beginners, updating a fork is not a simple task. It requires that you fetch the upstream branch and then merge that branch into your head.
One problem: neither the OSX nor Windows GUIs have the ability to synch a fork from upstream, meaning that the contributors would have to know some command line options. This isn't a terrible thing all in all, because OSX has a Terminal app and users can access the shell from the Windows GUI. I recently attempted to test things on a w
| plot_mlg_stats <- function(x, type = "p", palette = rainbow, ...){ | |
| layout(matrix(1:6, nrow = 2)) | |
| if (is.list(x)){ | |
| minmax <- matrix(numeric(0), nrow = 2, ncol = 8, | |
| dimnames = list(c("min", "max"), | |
| rownames(x[[1]]))) | |
| minmax["min", ] <- apply(vapply(x, function(i) apply(i, 1, min), numeric(8)), 1, min) | |
| minmax["max", ] <- apply(vapply(x, function(i) apply(i, 1, max), numeric(8)), 1, max) | |
| pal <- match.fun(palette) | |
| cols <- pal(length(x)) |
| # This file's location is ~/.R/Makevars | |
| # Default variables (no omp support): | |
| # CXX=clang++ | |
| # CC=clang | |
| # I followed the instructions at http://hpc.sourceforge.net/ to install gcc 4.9 | |
| CC=/usr/local/bin/gcc | |
| CXX=/usr/local/bin/g++ | |
| FC=/usr/local/bin/gfortran | |
| F77=/usr/local/bin/gfortran |
| resort_microsat <- function(x){ | |
| # Gather all alleles, convert to numeric, and reorder | |
| alls <- adegenet::alleles(x) | |
| alln <- lapply(alls, as.numeric) | |
| alln <- lapply(alln, order) | |
| # Loop over the names and paste together the locus name and the sorted alleles. | |
| alls <- lapply(names(alls), function(i) paste(i, alls[[i]][ alln[[i]] ], sep = ".")) | |
| # Convert to a vector an match the name to the column names of the data matrix. |
| # test that skeleton | |
| snippet tt | |
| test_that("${1:stuffworks}", { | |
| ${2:skip_on_cran()} | |
| }) | |
| # add a header line | |
| snippet hl | |
| #==============================================================================# | |
| ${0} |
root@e40c958b33f6:/# RD CMD check --as-cran poppr_*.tar.gz
* using log directory ‘//poppr.Rcheck’
| # 2015-12-06 10:55:45 PST ---------------------------------- | |
| # This script will allow you to update your fork of the | |
| # NESCent popgenInfo page without having to interact with | |
| # the command line. Note: you do not need to install git | |
| # for this particular script to work, but it is necessary | |
| # to use pull/commit/push through Rstudio. | |
| library("git2r") | |
| # Do this once and then open the Rproject file ------------ | |
| # clone(url = "", |
| "INRA63.167","INRA63.171","INRA63.173","INRA63.175","INRA63.177","INRA63.179","INRA63.181","INRA63.183","INRA63.185","INRA5.137","INRA5.139","INRA5.141","INRA5.143","INRA5.145","INRA5.147","INRA5.149","ETH225.137","ETH225.139","ETH225.141","ETH225.143","ETH225.145","ETH225.147","ETH225.149","ETH225.151","ETH225.153","ETH225.155","ETH225.157","ETH225.159","ILSTS5.182","ILSTS5.184","ILSTS5.186","ILSTS5.190","ILSTS5.194","HEL5.149","HEL5.151","HEL5.153","HEL5.155","HEL5.157","HEL5.159","HEL5.161","HEL5.163","HEL5.165","HEL5.167","HEL5.169","HEL1.101","HEL1.103","HEL1.105","HEL1.107","HEL1.109","HEL1.111","HEL1.113","HEL1.115","HEL1.117","INRA35.102","INRA35.104","INRA35.106","INRA35.108","INRA35.110","INRA35.114","INRA35.120","ETH152.181","ETH152.187","ETH152.191","ETH152.193","ETH152.195","ETH152.197","ETH152.199","ETH152.201","ETH152.203","ETH152.205","ETH152.207","ETH152.209","INRA23.193","INRA23.197","INRA23.199","INRA23.201","INRA23.203","INRA23.205","INRA23.207","INRA23.209","INRA23.211","INRA23.213","INRA |