[Bioc-devel] Vignette build fail on Windows: cannot open connection

Michael Morgan M|ch@e|@Morg@n @end|ng |rom cruk@c@m@@c@uk
Fri Mar 12 18:57:21 CET 2021

Dear Bioc-devel,
We currently have an open package submission for Bioconductor that fails (on Windows) due to an error in the vignette building: http://bioconductor.org/spb_reports/miloR_buildreport_20210308174731.html#tokay2_buildsrc_anchor

The same error occurs on our GitHub Actions testing: https://github.com/MarioniLab/miloR/runs/2089115229?check_suite_focus=true

This error is specific to Windows, as the vignettes build fine on both ubuntu and macOS on our GitHub Actions setup. The (un)informative error is: “cannot open connection” for both Rmd files that contain the package vignettes. The offending lines are:

embryo_milo <- Milo(embryo_data)

In milo_gastrulation.Rmd, and for milo_demo.Rmd:

traj_milo <- Milo(traj_sce)
reducedDim(traj_milo, "UMAP") <- reducedDim(traj_sce, "UMAP")


The only thing that these two code blocks have in common are that they are access package data from either  the MouseGastrulationAtlas package (embryo_data) or from our package. However, this is not the first time these data are accessed in either vignette.

Has this issue occurred before, and if so, what were the solutions? I’ve spent some time googling around but with no luck, and we don’t have access to a Windows box to test this out interactively.

Many thanks in advance

Senior Research Associate
Marioni Group
CRUK-Cambridge Institute, Cambridge University

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