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.git...@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@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@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > -- > Hervé Pagès > > Bioconductor Core Team > hpages.on.git...@gmail.com > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
