在正在运行的 docker 容器上一一执行许多 R 命令

Question

I have a running container with RStudio image and my own preinstalled package. My task is to call different functions from the package one by one - an output from one function is the input to other functions. I don't want to do it this way: fun1(x) %>% fun2(x) %>%... %>% funN(x) . I want it to work like this:

out1 <- fun1(x)
out2 <- fun2(out1)
...
funN(outN-1)

The reason I'd it like to be done this way is that I'd like to call these functions as separate docker exec commands against the running container. I'm planning to convert these commands into separate Jenkins jobs.

I tried docker exec... commands but failed on the second step. In the first step, the fun1 function creates an R object out1 . But the out1 is not available for the second docker exec call, ie this does not work:

docker run --name=my_container -d my_image (ok)
docker exec -it my_container Rscript main.R (ok)
docker exec -it my_container R "-e my_package::fun2(out1)" (not ok - object out1 not found)

where main.R is something like this:

library(my_package)
out1 <- my_package::fun1()

In other words, the next docker exec is a continuation of the previous one - all the objects living in the R workspace after the previous step is finished should be available for functions in the next step. Is it possible? I'd like to avoid putting all the functions (steps) into one R script. Any help would be very appreciated.

Answer 1

You can try this:

    docker run -it rocker/rstudio-stable:3.5.1 echo 'set.seed(123); 
    out1 <- base::sample(1:100, 3);
    print(out1);
    out2 <- out1 * 3;
    print(out2)'  | R --no-save 

Output:

> set.seed(123);
                 >     out1 <- base::sample(1:100, 3);
                                                      >     print(out1);
                                                                        [1] 29 79 41
                                                                                    >     out2 <- out1 * 3;
                                                                                                           >     print(out2)
                                                                                                                            [1]  87 237 123
                                                                                                                                           >