Write to a temporary directory rather than user's home directory

[jwokaty]

I run the Bioconductor builds and noticed tripr is writing to the user's home directory on both devel and release during R CMD check. This isn't allowed (see BioC Packages - Other Data). We recommend that it instead write to a temporary directory using BiocFileCache or R's default caching directory tools::R_user_dir("tripr", which="cache").

On the Linux builder, I see the following, which I've truncated:

biocbuild@nebbiolo1:~$ tree Documents
Documents
└── my_output
    ├── output_124745
    │   ├── Analysis
    │   │   ├── clonotypes_bar_plot_with_threshold0.1.png
    │   │   ├── hist3D-nucleotides_top_20clonotypes__BcellA_BcellB.png
    │   │   ├── image2D-nucleotides_top_20clonotypes__BcellA_BcellB.png
    │   │   └── persp3D-nucleotides_top_20clonotypes__BcellA_BcellB.png
    │   └── output_tables
    │       ├── Clonotypes_Summary.V.GENE+Summary.AA.JUNCTIONAll_Data.txt
    │       ├── Clonotypes_Summary.V.GENE+Summary.AA.JUNCTION_BcellA.txt
    │       ├── Clonotypes_Summary.V.GENE+Summary.AA.JUNCTION_BcellB.txt
    │       ├── filterin_clono_All_Data.txt
    │       ├── filterin_clono_BcellA.txt
    │       └── filterin_clono_BcellB.txt

We appreciate your attention to this matter as well as your contribution to Bioconductor.

[aspaor]

Dear @jwokaty,
Thank you for raising this issue. We are currently looking into it and we plan to have an updated version within the next ~10 days.

With kind regards,
Aspa

[aspaor]

Hi @jwokaty,

In its current version, tripr allows the user to save all datasets that are produced by its functionalities into an output directory, or to save specific tables that she/he chooses.

At the moment we are working to optimize the package and make it more robust. During the workflow of the package a lot of useful outputs are being produced and therefore it would be necessary for a user to have all generated outputs into the working directory (Analysis and output_tables from your example above).

Looking forward to your feedback. Thank you in advance for your time.

With regards,
Aspa

[jwokaty]

Hi @aspaor,

The examples and code in the vignettes should save to a temporary directory when not run interactively--e.g., R CMD check--so it doesn't pollute the current working directory. So I would set the default output path to the temporary directory and make it clear that the user should set the output path for persistence.

[aspaor]

Dear @jwokaty ,
Thank you for your comment. We are planning to do some modifications to the output storage part as you suggested. Thank you again for your help.

All the best,
Aspa