No date being picked by CITATION #42

annakrystalli · 2022-09-16T09:09:59Z

I'm trying recreate here:

Lines 1 to 12 in 691bb86

    
           year <- sub("-.*", "", meta$Date) 
        
           note <- paste0(sprintf("R package version %s", meta$Version), ". Integrated data products created under the European Marine Observation Data Network (EMODnet) Biology project (EASME/EMFF/2017/1.3.1.2/02/SI2.789013), funded by the European Union under Regulation (EU) No 508/2014 of the European Parliament and of the Council of 15 May 2014 on the European Maritime and Fisheries Fund") 
        
           bibentry(bibtype = "Manual", 
        
                    title = "{EMODnetWCS}: Access EMODnet Web Coverage Service data through R", 
        
                    author = c( 
        
                    person("Anna", "Krystalli") 
        
                    ), 
        
                    year = year, 
        
                    note = note, 
        
                    url = "https://github.com/EMODnet/EMODnetWCS")

the citation generating approach in EMODnetWFS by @maelle:

https://github.com/EMODnet/EMODnetWFS/blob/c1ac54a25d91537bb57a94438fa6e9a41528bd9e/inst/CITATION#L1-L13

However, it's not picking up a Date:

citation(package = "EMODnetWCS")
#> Warning in citation(package = "EMODnetWCS"): no date field in DESCRIPTION file
#> of package 'EMODnetWCS'
#> Warning in citation(package = "EMODnetWCS"): could not determine year for
#> 'EMODnetWCS' from package DESCRIPTION file
#> 
#> To cite package 'EMODnetWCS' in publications use:
#> 
#>   Anna Krystalli (NA). EMODnetWCS: Access EMODnet Web Coverage Service
#>   data through R. https://github.com/EMODnet/EMODnetWCS,
#>   https://emodnet.github.io/EMODnetWCS/.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {EMODnetWCS: Access EMODnet Web Coverage Service data through R},
#>     author = {Anna Krystalli},
#>     note = {https://github.com/EMODnet/EMODnetWCS,
#> https://emodnet.github.io/EMODnetWCS/},
#>   }

which makes sense in this case as it's not included in the EMODnetWCS DESCRIPTION file:

EMODnetWCS/DESCRIPTION

Lines 1 to 49 in 691bb86

    
           Package: EMODnetWCS 
        
           Title: Access EMODnet Web Coverage Service data through R 
        
           Version: 0.0.0.9010 
        
           Authors@R: c( 
        
               person("Anna", "Krystalli", , "annakrystalli@googlemail.com", role = "aut", 
        
                      comment = c(ORCID = "0000-0002-2378-4915")), 
        
               person("Salvador", "Fernández-Bejarano", , "salvador.fernandez@vliz.be", role = "cre", 
        
                      comment = c(ORCID = "0000-0003-0535-7677")), 
        
               person("European Marine Observation Data Network (EMODnet) Biology project", "European Commission's Directorate - General for Maritime Affairs and Fisheries (DG MARE)", , "bio@emodnet.eu", role = "cph"), 
        
               person("VLIZ (VLAAMS INSTITUUT VOOR DE ZEE)", , , "info@vliz.be", role = "fnd") 
        
             ) 
        
           Description: Access and interrogate EMODnet Web Coverage Service data 
        
               through R. 
        
           License: MIT + file LICENSE 
        
           Imports:  
        
               checkmate, 
        
               cli, 
        
               curl, 
        
               glue, 
        
               httr, 
        
               memoise, 
        
               purrr, 
        
               rlang, 
        
               sf, 
        
               tibble 
        
           Suggests:  
        
               covr, 
        
               fs, 
        
               httptest, 
        
               huxtable, 
        
               knitr, 
        
               rmarkdown, 
        
               terra, 
        
               testthat (>= 3.0.0), 
        
               webmockr, 
        
               withr 
        
           Config/testthat/edition: 3 
        
           Remotes:  
        
               eblondel/ows4R 
        
           Encoding: UTF-8 
        
           Roxygen: list(markdown = TRUE) 
        
           RoxygenNote: 7.2.0 
        
           URL: https://github.com/EMODnet/EMODnetWCS, 
        
               https://emodnet.github.io/EMODnetWCS/ 
        
           BugReports: https://github.com/EMODnet/EMODnetWCS/issues 
        
           Depends:  
        
               R (>= 4.1), ows4R (>= 0.3-1) 
        
           LazyData: true 
        
           VignetteBuilder: knitr

A datePublished field hasn't ended up in the codemate.json file either.

EMODnetWCS/codemeta.json

Lines 305 to 320 in 691bb86

    
             "citation": [ 
        
               { 
        
                 "@type": "SoftwareSourceCode", 
        
                 "author": [ 
        
                   { 
        
                     "@type": "Person", 
        
                     "givenName": "Anna", 
        
                     "familyName": "Krystalli" 
        
                   } 
        
                 ], 
        
                 "name": "{EMODnetWCS}: Access EMODnet Web Coverage Service data through R", 
        
                 "url": "https://github.com/EMODnet/EMODnetWCS", 
        
                 "description": "R package version 0.0.0.9010. Integrated data products created under the European Marine Observation Data Network (EMODnet) Biology project (EASME/EMFF/2017/1.3.1.2/02/SI2.789013), funded by the European Union under Regulation (EU) No 508/2014 of the European Parliament and of the Council of 15 May 2014 on the European Maritime and Fisheries Fund" 
        
               } 
        
             ] 
        
           }

The odd thing is that is IS being picked up in EMODnetWFS

citation(package = "EMODnetWFS")
#> 
#> Krystalli A (2020). _EMODnetWFS: Access EMODnet Web Feature Service
#> data through R_. R package version 2.0.1.9001. Integrated data products
#> created under the European Marine Observation Data Network (EMODnet)
#> Biology project (EASME/EMFF/2017/1.3.1.2/02/SI2.789013), funded by the
#> by the European Union under Regulation (EU) No 508/2014 of the European
#> Parliament and of the Council of 15 May 2014 on the European Maritime
#> and Fisheries Fund, <URL: https://github.com/EMODnet/EMODnetWFS>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {{EMODnetWFS}: Access EMODnet Web Feature Service data through R},
#>     author = {Anna Krystalli},
#>     year = {2020},
#>     note = {R package version 2.0.1.9001. Integrated data products created under the European Marine Observation Data Network (EMODnet) Biology project (EASME/EMFF/2017/1.3.1.2/02/SI2.789013), funded by the by the European Union under Regulation (EU) No 508/2014 of the European Parliament and of the Council of 15 May 2014 on the European Maritime and Fisheries Fund},
#>     url = {https://github.com/EMODnet/EMODnetWFS},
#>   }

^{Created on 2022-09-16 by the reprex package (v2.0.1)}

even though there is no Date field in it's DESCRIPTION file: https://github.com/EMODnet/EMODnetWFS/blob/c1ac54a25d91537bb57a94438fa6e9a41528bd9e/DESCRIPTION#L1-L61

There is however a datePublished field in the EMODnetWFS codemeta.json!
https://github.com/EMODnet/EMODnetWFS/blob/c1ac54a25d91537bb57a94438fa6e9a41528bd9e/codemeta.json#L392-L413

I'm trying to figure out where meta$Date data is coming from in inst/CITATION script: https://github.com/EMODnet/EMODnetWFS/blob/c1ac54a25d91537bb57a94438fa6e9a41528bd9e/inst/CITATION#L1

and how a datePublished field ended up in the EMODnetWFS codemeta.json. Any ideas @maelle ?

The text was updated successfully, but these errors were encountered:

maelle · 2022-09-16T10:15:29Z

Have you installed EMODnetWCS?

annakrystalli · 2022-09-16T10:23:12Z

yup. It's picking up the rest of the details. Just no date 🤔

maelle · 2022-09-16T10:36:28Z

I'll try

maelle · 2022-09-16T10:37:47Z

> pak::pak("EMODnet/EMODnetWCS")
✓ Updated metadata database: 3.32 MB in 7 files.                           
✓ Updating metadata database ... done                                      
                                                                             
→ Will install 1 package.
→ Will download 1 package with unknown size.
+ EMODnetWCS   0.0.0.9010 [bld][cmp][dl] (GitHub: 88c8afc)
ℹ Getting 1 pkg with unknown size
✓ Got EMODnetWCS 0.0.0.9010 (source) (214.73 kB)              
✓ Downloaded 1 package (214.73 kB)in 1.4s                     
ℹ Packaging EMODnetWCS 0.0.0.9010
✓ Packaged EMODnetWCS 0.0.0.9010 (634ms)                              
ℹ Building EMODnetWCS 0.0.0.9010                                      
✓ Built EMODnetWCS 0.0.0.9010 (15.6s)                                 
✓ Installed EMODnetWCS 0.0.0.9010 (github::EMODnet/EMODnetWCS@88c8afc) (25ms)
✓ 1 pkg + 58 deps: kept 55, added 1, dld 1 (NA B) [32.8s]               
> citation(package = "EMODnetWCS")

To cite package ‘EMODnetWCS’ in publications
use:

  Krystalli A (2022). _EMODnetWCS: Access
  EMODnet Web Coverage Service data through R_.
  https://github.com/EMODnet/EMODnetWCS,
  https://emodnet.github.io/EMODnetWCS/.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {EMODnetWCS: Access EMODnet Web Coverage Service data through R},
    author = {Anna Krystalli},
    year = {2022},
    note = {https://github.com/EMODnet/EMODnetWCS,
https://emodnet.github.io/EMODnetWCS/},
  }



Warning message:
In citation(package = "EMODnetWCS") :
  no date field in DESCRIPTION file of package ‘EMODnetWCS’

annakrystalli · 2022-09-16T10:39:44Z

Oh, I didn't realise I needed to install it from GitHub to work. I had installed it locally from source

annakrystalli · 2022-09-16T10:39:59Z

Thank you!

maelle · 2022-09-16T10:40:54Z

Let me try cloning! I was lazy 😜

maelle · 2022-09-16T10:42:23Z

I get the same as you with the local installation.

 citation(package = "EMODnetWCS")

To cite package ‘EMODnetWCS’ in publications use:

  Krystalli A (????). _EMODnetWCS: Access EMODnet Web
  Coverage Service data through R_.
  https://github.com/EMODnet/EMODnetWCS,
  https://emodnet.github.io/EMODnetWCS/.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {EMODnetWCS: Access EMODnet Web Coverage Service data through R},
    author = {Anna Krystalli},
    note = {https://github.com/EMODnet/EMODnetWCS,
https://emodnet.github.io/EMODnetWCS/},
  }



Warning messages:
1: In citation(package = "EMODnetWCS") :
  no date field in DESCRIPTION file of package ‘EMODnetWCS’
2: In citation(package = "EMODnetWCS") :
  could not determine year for ‘EMODnetWCS’ from package DESCRIPTION file

annakrystalli · 2022-09-16T10:43:27Z

Interesting! Where is that meta$Date coming from??

maelle · 2022-09-16T11:51:28Z

sorry for the delay!
it comes from the DESCRIPTION file that is in find.package("EMODnetWCS").

For instance for a package I installed from CRAN there is a date file.path(find.package("anytime"), "DESCRIPTION") |> file.edit()

annakrystalli · 2022-09-30T08:58:24Z

Solved manually for now by installing from GitHub using pak and then rendering README but needs a longer term approach.

I also tried adding a date into DESCRIPTION but, while that is being picked up by codemeta.json, it still doesn't work in citation() when package is installed locally through source

annakrystalli added the bug Something isn't working label Sep 16, 2022

annakrystalli added this to the D4: Conduct full testing suite for package functionality including continuous integration for continuous testing milestone Sep 16, 2022

annakrystalli modified the milestones: D4: Conduct full testing suite for package functionality including continuous integration for continuous testing, D5: Provide full documentation of functionality, including long form demonstration of package usage and online documentation website Sep 30, 2022

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No date being picked by CITATION #42

No date being picked by CITATION #42

annakrystalli commented Sep 16, 2022

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annakrystalli commented Sep 30, 2022

No date being picked by CITATION #42

No date being picked by CITATION #42

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annakrystalli commented Sep 16, 2022

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