\textit does not work in a caption in bioinfo.cls

[diekhans]

As described in this posting https://tex.stackexchange.com/questions/453542/unable-to-use-texit-in-caption

bioinfo.cls defines an invalid font:

\renewcommand{\sfdefault}{phb}

resulting in \textit not working in figure captions

xfun::session_info('rticles')

R version 4.2.0 Patched (2022-04-28 r82285)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur/Monterey 10.16

Locale: en_US.UTF-8 / en_US.UTF-8 / en_US.UTF-8 / C / en_US.UTF-8 / en_US.UTF-8

Package version:
  base64enc_0.1.3   bslib_0.4.2       cachem_1.0.8      cli_3.6.1        
  digest_0.6.31     ellipsis_0.3.2    evaluate_0.21     fastmap_1.1.1    
  fontawesome_0.5.1 fs_1.6.2          glue_1.6.2        graphics_4.2.0   
  grDevices_4.2.0   highr_0.10        htmltools_0.5.5   jquerylib_0.1.4  
  jsonlite_1.8.5    knitr_1.43        lifecycle_1.0.3   magrittr_2.0.3   
  memoise_2.0.1     methods_4.2.0     mime_0.12         R6_2.5.1         
  rappdirs_0.3.3    rlang_1.1.1       rmarkdown_2.22    rticles_0.25     
  sass_0.4.6        stats_4.2.0       stringi_1.7.12    stringr_1.5.0    
  tinytex_0.45      tools_4.2.0       utils_4.2.0       vctrs_0.6.2      
  xfun_0.39         yaml_2.3.7       

bioinfo-cap-it.Rmd.gz

[cderv]

Thanks for the feedback. I can surely do a patch for our cls file we have included.

However, I am wondering if this template function is still relevant as it seems Bioinformatics Journal (https://academic.oup.com/bioinformatics) is no more using this CLS class

From https://academic.oup.com/bioinformatics/pages/submission_online, I see

Alternatively, you may prepare your manuscript in LaTeX, and then submit the source files directly as part of your submission. Please note that initial submissions are not required to follow the Word or LaTex template. However, because manuscripts are published online following acceptance , it is important that any revised version of the manuscript supplied by the author follow the provided templates. The Word and LaTex templates can be found here.

And the LaTeX template now points to generic OUP page (https://academic.oup.com/pages/authoring/journals/preparing_your_manuscript?login=true). We have a OUP template too so maybe this new one should be use ?

I did not try it. This relates also to https://github.com/rstudio/rticles/issues/425 It seems overleaf add a bioinfo template but not more as this link now redirect to OUP : https://www.overleaf.com/latex/templates/template-for-oxford-bioinformatics-journal-new-version/zjrmbrmtrytg

Otherwise, do you know if bioinfo.cls is maintained somewhere ?