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I used the Bioinformatics template to format a submission to a preprint server (biorXiv). The PDF was rejected because there's a copyright notice in the footer. Here's the email I got from the biorXiv rejection:

Dear ;

We are returning this submission so that you can remove the following text from the pg. 1 footer:

"Published by Oxford University Press. All rights reserved. For permissions, please e-mail: <OUP email address>"

We believe this is part of a document submission template and recommend that it be removed so as to avoid confusing readers. Please resupply your manuscript PDF when you are ready to the above MS ID #000000 so that screening can proceed. Please do not create a new submission, as this will create a duplicate entry in our system.

Please contact us should you have any questions, and thank you for your interest in using the bioRxiv preprint service.

The bioRxiv team

Looks like the culprit is around here:

https://github.com/rstudio/rticles/blob/fe36003858246a045212ac069310edcee698a4a1/inst/rmarkdown/templates/bioinformatics/skeleton/bioinfo.cls#L259-L268

Would be nice if this were a user-controlled variable, or possible to turn off completely.

See also #424

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If this is the culprit, then this is part of the cls file.

We should check if the cls file is up to date. If so, it will be hard to had a switch in the cls file has we do not touch that.

What could probably be done if we have no other solution is to add a post processor function in bioinformatic_article() to "patch" the resulting tex file and remove this part if asked by the user.

Also pinging @ShixiangWang here as he is the contributor of this template.

We welcome any contribution to help maintain those community contributed template. Feel free to look around and submit a PR. I'll have look when possible on my side.

Thanks!

@stefanocoretta Sorry for the convenience.

I downloaded the template files from Bioinformatics submission site, it should be the latest version when I submitted the PR.

Is it necessary to contact the journal? I know little about cls format, how about directly moving the copyright notice to R function/code which uses the template?

Template is from there right ? https://academic.oup.com/bioinformatics/pages/submission_online

The template folder can be downloaded from there, and the bioinfo.cls files contains these lines.

So I don't know if we can take the liberty to remove them from the CLS class maintain by "bioinformatics" journal.

@stephenturner which is biorXiv position regarding this CLS file ?

@stephenturner I am not sure what to do about this in rticles. The copyright line are added by the bioinfo.cls document class which is from academic.oup.com/bioinformatics/pages/submission_online

We can't remove this from with bioinformatics_article() format. It is possible that bioinformatics_article() must not be used to published to bioRxiv. 🤷

Maybe there is a need for a biorxiv_article same as there is a arxiv_article() ?

Do you know about bioRXiv template ? do they accept any format in PDF or Word file ?

biorxiv has no template, no required format. I'd used this for formatting the biorxiv submission because I'd planned to immediately submit the same PDF to bioinformatics.

I will email the journal and see if there is a solution for this.

Oh thanks @ShixiangWang !

Otherwise if anyone know a LaTeX trick to not include those footers. Maybe redefining in the Rmd file the command oddfoot and evenfoot that are defined in the bioinfo.cls ? Would that work in your opinion ? I did not try.

I am not familiar with LaTex. If you think it would work and will not take much time, you could take a try :).

@cderv

It's been a week. I did not see any response from bioinformatics editorial board. However, the [email protected] auto-reply me many messages about commercial use. I checked the link https://academic.oup.com/journals/pages/access_purchase/rights_and_permissions/publication_rights. Nothing mentions the template reuse. I also checked the template available at https://www.overleaf.com/latex/templates/template-for-oxford-bioinformatics-journal-new-version/zjrmbrmtrytg, they used the same template:

In summary, if your workaround mentioned above works, that's fine. If not, I suggest removing the copyright notice and mention it in the comment part of calling function or header of RMarkdown template to make this template is acceptable for bioRxiv.

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@stephenturner a quick workaround I think is:

1. fork this repo
2. remove the copyright notice in the cls file (you can also modify pubyear)
3. install it with remotes package
4. recompile your manuscript for biorxiv and bioinformatics

Thanks for all your help!

Thanks @ShixiangWang ! I'll look closer.

Regarding the workaround, there is no need to fork the package. The bioinfo.cls file should be copied into the project directory when creating the article. You can then modify the local copy of the cls. It is stored by convenience in the package to make it available easily. So it should be easy to remove the unwanted part from the cls if desired. Only the .tex template is not copied locally for now.

In summary, if your workaround mentioned above works, that's fine.

I may not know enough about LaTeX but I did not manage to remove it using a document preamble. That may not be possible.

If not, I suggest removing the copyright notice and mention it in the comment part of calling function or header of RMarkdown template to make this template is acceptable for bioRxiv.

I don't want to change the template for oup which contains the copyright, only so that it can be used with biorxiv. This copyright may be needed and also it is not the only thing in the CLS - there is also the oxford logo. SO it feels not right remove a part of the CLS file, and it will make future updates more complicated.

Excuse my inexperience with publishing but, if BioRXiv has not specific template, why not use another template different than bioinfo.cls ?

Seems like arXiv and BioRxiv are not too constraint. I found this one: https://www.overleaf.com/latex/templates/arxiv-slash-biorxiv-template/phncddwqtxpc.

Could we adapt arxiv_article() or create a new biorxiv_article() with a default template based on this ? What do you all think ?

Otherwise, the workaround from above should work:

• Create a new bioinformatic_article() template
• Open the bioinfo.cls file
• Remove the part you don't want

Something like this

diff --git a/Untitled/bioinfo.cls b/Untitled/bioinfo.cls
index b42e50b2..aa939e96 100644
--- a/Untitled/bioinfo.cls
+++ b/Untitled/bioinfo.cls
@@ -258,13 +258,10 @@
 \def\ps@opening
   {%
   \def\@oddfoot{{
-        \hbox to \textwidth{\helvetica
-        \fontsize{7}{9}\fontshape{n}\selectfont \copyright\space The Author \@copyrightyear. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: [email protected]%
-          \hfill\small\helveticabold\thepage}%
+        \hbox to \textwidth{\hfill\small\helveticabold\thepage}%
         }}%
   \def\@evenfoot{{
-        \hbox to \textwidth{\helvetica\thepage\hfill
-          \fontsize{7}{9}\fontshape{n}\selectfont The Author \@copyrightyear. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: [email protected]}%
+        \hbox to \textwidth{\helvetica\thepage\hfill}
         }}%
   \let\@evenhead\relax
   \let\@oddhead\relax}

@cderv Thanks for your adjustment. Suddenly I realize the case is not specific to Bioinformatics. Instead of creating a modified journal template, my idea is describing such situation with the workaround in a QA section in README or somewhere.

I am not sure I am following here anymore.

format *_article() most often use a specific CLS file that is provided by a journal or an editor. In the better case, this file is provided through a CTAN package that will be installed using LaTeX. The .cls file won't be local but stored with other CTAN package locally. When this is not the case, the file is often provided directly with a Journal's template and we include this .cls file in the package so that it is available. Putting locally to the .tex file make its findable by LaTeX as with a CTAN package.

I am not sure that this is a good advice to modify a .cls file provided by a Journal with a template. It seems to me that if the .cls file must be modified then this means it may not be the right one to use with the article. Am I wrong about this ?

I seems also to me this is quite specific for now with bioRxiv where bioinfo.cls from OUP is used but it is not required to be followed.

We did not have any such request for now from other template.

Also, I am fine to have a biorxiv_article() if there is a template to follow to publish on bioRxiv.

Did I miss anything ?