[Bioc-devel] CITATION error

[Hervé Pagès]

Hi Shraddha,

Note that we only see this error for the release version of netDx:

   https://bioconductor.org/packages/3.13/netDx

The devel version does not have it:

   https://bioconductor.org/packages/3.14/netDx

With the release version, I get:

   > library(netDx)



   Attaching package: ‘netDx’



   The following object is masked from ‘package:stats’:



     predict


   > packageVersion("netDx")

   [1] ‘1.4.2’



   > citation("netDx")

   Error in parse(con) : 18:60: unexpected ','

   17:            pubmed = "30872331",

   18:            header = "The netDx algorithm is described in:"),

                                                                ^

This confirms that the CITATION file is broken in netDx 1.4.2.

FWIW the diff between the release CITATION and the devel CITATION is:

   hpages using spectre:~/$ diff CITATION-release CITATION-devel

   1c1

   < bibentry(bibtype = "Article",

   ---

   > c(bibentry(bibtype = "Article",

   43c43

   < )

   ---

   > )

   \ No newline at end of file


So it looks like you've managed to get the file right in devel (netDx 
1.5.2) but not in release (netDx 1.4.2).

Cheers,
H.


On 16/08/2021 15:48, Shraddha Pai wrote:
> Hello BioC community,
> 
> I've recently added a CITATION file for our package "netDx".
> The package description page on bioconductor.org shows an error
> message: Important
> note to the maintainer of the netDx package: An error occured while trying
> to generate the citation from the CITATION file. This typically occurs when
> the file contains R code that relies on the package to be installed e.g. it
> contains calls to things like packageVersion() or packageDate() instead of
> using meta$Version or meta$Date. See R documentation
> <https://cran.r-project.org/doc/manuals/r-release/R-exts.html#CITATION-files>
> for
> more information.
> 
> However, when I install the package locally and run citation("netDx"), I
> get the expected output (see below e-mail).
> 
> The CITATION file does not make function calls. Here are the contents:
> c(bibentry(bibtype = "Article",
>             key = "netDx-methods",
>             title = "{netDx: interpretable patient classification using
> integrated patient similarity networks}",
>             author = c(
>                 person("Shraddha", "Pai"),
>                 person("Shirley", "Hui"),
>                 person("Ruth", "Isserlin"),
>                 person(c("Muhammad","A"), "Shah"),
>                 person("Hussam","Kaka"),
>                 person(c("Gary", "D."), "Bader")
>             ),
>             year = 2019,
>             journal = "Molecular Systems Biology",
>             volume = "15",
>             pages = "e8497",
>             doi = "10.15252/msb.20188497",
>             pubmed = "30872331",
>             header = "The netDx algorithm is described in:"),
> bibentry(bibtype = "Article",
>             key = "netDx-software",
>             title = "{netDx: Software for building interpretable patient
> classifiers by multi-'omic data integration using patient similarity
> networks}",
>             author = c(
>                 person("Shraddha", "Pai"),
>                 person("Philipp", "Weber"),
>                 person("Ruth", "Isserlin"),
>                 person("Hussam","Kaka"),
>                 person("Shirley", "Hui"),
>                 person(c("Muhammad","A"), "Shah"),
>                 person("Luca", "Giudice"),
>                 person("Rosalba", "Giugno"),
>                 person(c("Anne","Krogh"), "Nøhr"),"
>                 person("Jan", "Baumbach"),
>                 person(c("Gary", "D."), "Bader")
>             ),
>             year = 2021,
>             journal = "F1000Research",
>             volume = "9",
>             pages = "1239",
>             doi = "10.12688/f1000research.26429.2",
>             pubmed = "33628435",
>             header = "The netDx package is described in:")
> 
> )
> 
> What can I change to fix the error on the bioconductor page?
> 
> Thank you,
> Shraddha
> 
> Output from running citation("netDx") on a local installation:
>> citation("netDx")
> 
> The netDx algorithm is described in:
> 
> Pai S, Hui S, Isserlin R, Shah MA, Kaka H, Bader GD (2019). “netDx:
> interpretable patient classification using integrated patient
> similarity networks.” _Molecular Systems Biology_, *15*, e8497. doi:
> 10.15252/msb.20188497 (URL: https://doi.org/10.15252/msb.20188497).
> 
> The netDx package is described in:
> 
> Pai S, Weber P, Isserlin R, Kaka H, Hui S, Shah MA, Giudice L, Giugno
> R, Nøhr AK, Baumbach J, Bader GD (2021). “netDx: Software for building
> interpretable patient classifiers by multi-'omic data integration using
> patient similarity networks.” _F1000Research_, *9*, 1239. doi:
> 10.12688/f1000research.26429.2 (URL:
> https://doi.org/10.12688/f1000research.26429.2).
> 
> To see these entries in BibTeX format, use 'print(<citation>,
> bibtex=TRUE)', 'toBibtex(.)', or set
> 'options(citation.bibtex.max=999)'.
> 
> 
> --
> 
> *Shraddha Pai, PhD*
> Principal Investigator, OICR
> Assistant Professor, Department of Molecular Biophysics, University of
> Toronto
> shraddhapai.com; @spaiglass on Twitter
> https://pailab.oicr.on.ca
> 
> 
> *Ontario Institute for Cancer Research*
> MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G
> 0A3
> *@OICR_news* <https://twitter.com/oicr_news> | *www.oicr.on.ca*
> <http://www.oicr.on.ca/>
> 
> 
> 
> *Collaborate. Translate. Change lives.*
> 
> 
> 
> This message and any attachments may contain confident...{{dropped:13}}