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.*
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