# R/qtl2

# Tags

* assigned: pjotrp, alexm
* priority: high
* type: enhancement
* status: open
* keywords: database, gemma, reaper, rqtl2

# Description

R/qtl2 handles multi-parent populations, such as DO, HS rat and the collaborative cross (CC). It also comes with an LMM implementation. Here we describe using and embedding R/qtl2 in GN2.

# Tasks


## R/qtl2

R/qtl2 is packaged in guix and can be run in a shell with


```
guix shell -C r r-qtl2
R
library(qtl2)
```

R/qtl2 also comes with many tests. When starting up with development tools in the R/qtl2 checked out git repo

```sh
cd qtl2
guix shell -C -D r r-qtl2 r-devtools make coreutils gcc-toolchain
make test
Warning: Your system is mis-configured: '/var/db/timezone/localtime' is not a symlink
i Testing qtl2
Error in dyn.load(dll_copy_file) :
unable to load shared object '/tmp/RtmpWaf4td/pkgload31850824d/qtl2.so': /gnu/store/hs6jjk97kzafl3qn4wkdc8l73bfqqmqh-gfortran-11.4.0-lib/lib/libstdc++.so.6: version `GLIBCXX_3.4.32' not found (required by /tmp/RtmpWaf4td/pkgload31850824d/qtl2.so)
Calls: <Anonymous> ... <Anonymous> -> load_dll -> library.dynam2 -> dyn.load
Execution halted
make: *** [Makefile:9: test] Error 1
```

not sure what the problem is yet.