[Bioc-devel] CITATION error

[Shraddha Pai]

Hi Hervé,
Thank you for catching the discrepancy between release and dev builds!
How strange - I usually change dev and release build in sync, so wonder how
that happened.
I updated the file and committed -hopefully it fixes the issue.

Best,Shraddha

On Mon, Aug 16, 2021 at 10:27 PM Hervé Pagès <hpages.on.github using gmail.com>
wrote:

> 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 confidentia...{{dropped:11}}
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using gmail.com
>

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