如何从 Docker 容器中的一个脚本运行多个 R 脚本

Question

I've got a script called initiate.R which runs two other scripts, like so:

source("Step1_databaseConnection.R")
source("Step2_buildingDateInfoAndMainFlowInfo.R")

In my dockerfile I have defined the following:

COPY Step1_databaseConnection.R  /home/project/Step1_databaseConnection.R

COPY Step2_buildingDateInfoAndMainFlowInfo.R  /home/project/Step2_buildingDateInfoAndMainFlowInfo.R

COPY initiate.R  /home/project/initiate.R

CMD ["/usr/local/bin/Rscript", "/home/project/initiate.R"]

However, I get the following error when running the task on AWS: cannot open file 'Step1_databaseConnection.R': No such file or directory

When I change my dockerfile to run the two scripts separately it works. Here is the code that works:

COPY Step1_databaseConnection.R  /home/project/Step1_databaseConnection.R

COPY Step2_buildingDateInfoAndMainFlowInfo.R  /home/project/Step2_buildingDateInfoAndMainFlowInfo.R

COPY initiate.R  /home/project/initiate.R

CMD ["/usr/local/bin/Rscript", "/home/project/Step1_databaseConnection.R"]

CMD ["/usr/local/bin/Rscript", "/home/project/Step2_buildingDateInfoAndMainFlowInfo.R"]

Any ideas? Many thanks

Answer 1

In your second try with executing the scripts by hand, you are using absolute paths. However, the first try starts the script with the current working directory of docker es working directory of R. This is not the file location. Therefore you have first move to this location with WORKDIR filepath . afterthet you can execute the script as expected.