roxytest cannot work

[ShixiangWang]

I upgrade my R to v4.0 and find that this package cannot work anymore.

Loading sigminer
sigminer version 1.0.3, run hello() to see usage and citation.
Warning: [/Users/wsx/Documents/GitHub/sigminer/R/add_labels.R:46] @testexamples unknown tag
Warning: [/Users/wsx/Documents/GitHub/sigminer/R/get_adj_p.R:66] @testexamples unknown tag
Warning: [/Users/wsx/Documents/GitHub/sigminer/R/get_bayesian_result.R:22] @testexamples unknown tag
Warning: [/Users/wsx/Documents/GitHub/sigminer/R/get_cn_ploidy.R:16] @testexamples unknown tag
Warning: [/Users/wsx/Documents/GitHub/sigminer/R/get_genome_annotation.R:27] @testexamples unknown tag
Warning: [/Users/wsx/Documents/GitHub/sigminer/R/get_sig_exposure.R:25] @testexamples unknown tag
Warning: [/Users/wsx/Documents/GitHub/sigminer/R/get_sig_similarity.R:51] @testexamples unknown tag

Could you take a look at this problem?

[pdiakumis]

I'm having the same issue - happy to provide more info or take a look at the code if you give me some pointers, @mikldk

CODE

``` $ R R version 4.0.0 (2020-04-24) -- "Arbor Day" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) > sessionInfo() R version 4.0.0 (2020-04-24) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Mojave 10.14.6 > packageVersion("roxytest") [1] ‘0.0.0.9102’ > packageVersion("roxygen2") [1] ‘7.1.0’ > packageVersion("testthat") [1] ‘2.3.2’ > require(roxytest) Loading required package: roxytest > require(roxygen2) Loading required package: roxygen2 > roxygen2::roxygenise() Loading gpgr Warning: [/Users/pdiakumis/Desktop/projects/umccr/gpgr/R/purple.R:17] @testexamples unknown tag Warning: [/Users/pdiakumis/Desktop/projects/umccr/gpgr/R/purple.R:79] @testexamples unknown tag Warning: [/Users/pdiakumis/Desktop/projects/umccr/gpgr/R/purple.R:151] @testexamples unknown tag Warning: [/Users/pdiakumis/Desktop/projects/umccr/gpgr/R/purple.R:203] @testexamples unknown tag Warning: [/Users/pdiakumis/Desktop/projects/umccr/gpgr/R/purple.R:266] @testexamples unknown tag Warning: [/Users/pdiakumis/Desktop/projects/umccr/gpgr/R/purple.R:292] @testexamples unknown tag Warning: [/Users/pdiakumis/Desktop/projects/umccr/gpgr/R/purple.R:318] @testexamples unknown tag Warning: [/Users/pdiakumis/Desktop/projects/umccr/gpgr/R/purple.R:346] @testexamples unknown tag Warning: [/Users/pdiakumis/Desktop/projects/umccr/gpgr/R/purple.R:373] @testexamples unknown tag Warning: [/Users/pdiakumis/Desktop/projects/umccr/gpgr/R/sv.R:16] @testexamples unknown tag Warning: [/Users/pdiakumis/Desktop/projects/umccr/gpgr/R/sv.R:58] @testexamples unknown tag Writing NAMESPACE Writing NAMESPACE ```

[rubak]

I will have a quick look at this later this week, but we might need help from @mikldk to get anywhere. I was just trying to define the tag functions, roclets etc. in a live R session by copy/pasting from roxytest source code. Then the tags @tests and @testexamples appear to be working OK. Maybe it is a scoping thing about finding the functions in the roxytest package and not in the global environment. I have no idea why this problem should be introduced in R 4.0.

[mikldk]

Thanks for reporting this. I will look into it.

[mikldk]

This was caused by faulty entries in NAMESPACE and should be fixed by 0fbba62a20c7dc44026002643796d82e217ef1d8. Can you please try with the newest commit and report back if it now works? I apologise for the long waiting time. Hopefully, that shouldn't happen again.

[ShixiangWang]

thanks I will try

[ShixiangWang]

It works @mikldk, thanks.