This patch in the sty file seems to have some incompatibility with longtable v4.17 which is distributed with TexLive 2021 and produces the error seen in #89.
I've found it pretty hard to track down specific version changes for longtable but v4.13 2020-01-07 (https://github.com/latex3/latex2e/blob/develop/required/tools/longtable-2020-01-07.sty) seems to have to have all the patch code already applied. That version ships with my Ubuntu 20.04 LTS / TexLive 2019 setup and I think makes the patch in our .sty file redundant for "current" systems
Give that, this change ensures the patch is only applied if longtable is older than v4.13. This seems to have no effect on PDFs produced with longtable v4.13 and allows documents to be successfully created when using longtable v4.17. Of course I may not have tested the specific problem scenario the original patch addressed, but I've tried various combinations of large tables, figures and text without seeing an issue.
This patch tries to address #89
I think the current code below tries to address issues where a float and a longtable on the same page would cause content to be rendered off the page. https://github.com/Bioconductor/BiocStyle/blob/0d7515b137239b784f2061425b4c1a541745b7c0/inst/resources/tex/Bioconductor.sty#L550-L595
This patch in the sty file seems to have some incompatibility with longtable v4.17 which is distributed with TexLive 2021 and produces the error seen in #89.
I've found it pretty hard to track down specific version changes for longtable but v4.13 2020-01-07 (https://github.com/latex3/latex2e/blob/develop/required/tools/longtable-2020-01-07.sty) seems to have to have all the patch code already applied. That version ships with my Ubuntu 20.04 LTS / TexLive 2019 setup and I think makes the patch in our .sty file redundant for "current" systems
Give that, this change ensures the patch is only applied if longtable is older than v4.13. This seems to have no effect on PDFs produced with longtable v4.13 and allows documents to be successfully created when using longtable v4.17. Of course I may not have tested the specific problem scenario the original patch addressed, but I've tried various combinations of large tables, figures and text without seeing an issue.