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Bioinformatics template copyright notice #425
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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 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 ? The template folder can be downloaded from there, and the 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 We can't remove this from with Maybe there is a need for a 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 |
I am not familiar with LaTex. If you think it would work and will not take much time, you could take a try :). |
It's been a week. I did not see any response from bioinformatics editorial board. However, the 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.
>To access an article PDF available in pay-per-view, on the article page either register to purchase access or sign in via your institution.
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@stephenturner a quick workaround I think is:
|
Thanks for all your help! |
Thanks @ShixiangWang ! I'll look closer. Regarding the workaround, there is no need to fork the package. The |
I may not know enough about LaTeX but I did not manage to remove it using a document preamble. That may not be possible.
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 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 Otherwise, the workaround from above should work:
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 I am not sure that this is a good advice to modify a I seems also to me this is quite specific for now with bioRxiv where We did not have any such request for now from other template. Also, I am fine to have a Did I miss anything ? |
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:
Looks like the culprit is around here:
rticles/inst/rmarkdown/templates/bioinformatics/skeleton/bioinfo.cls
Lines 259 to 268 in fe36003
Would be nice if this were a user-controlled variable, or possible to turn off completely.
See also #424
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xfun::session_info('rticles')
. I have upgraded all my packages to their latest versions (e.g., R, RStudio, and R packages), and also tried the development version:remotes::install_github('rstudio/rticles')
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