zji90/TSCAN

TSCAN broken in development branch of Bioconductor

PeteHaitch opened this issue · 4 comments

PeteHaitch commented

The version of TSCAN currently available on Bioconductor's development branch is broken: please see https://www.bioconductor.org/checkResults/3.16/bioc-LATEST/TSCAN/

Taking a look at the the git logs of the Bioconductor git-hosted version, it looks like you may have accidentally clobbered a bunch of changes that were available on the Bioconductor git-hosted version that were not mirrored to the GitHub-hosted version when you made the changes in #13.

git clone https://git.bioconductor.org/packages/TSCAN
(master)*$ git log --summary HEAD...64483787c8d53e3d2913fd0f6af22b922ab0776d | cat
commit dbb1dfdccab085ca25e45d617554fd5e26b31e1e
Author: Zhicheng Ji <zhichengji@gmail.com>
Date:   Fri Sep 23 20:25:09 2022 -0400

    commit


commit 33a83908a11468d3cd412ba02ec7c7bdf1c4691f
Author: Zhicheng Ji <zhichengji@gmail.com>
Date:   Fri Sep 23 20:23:59 2022 -0400

    commit


commit 8b680d1a5750dcd0984e7e12d221e7bd729fcf7b
Author: Zhicheng Ji <zhichengji@gmail.com>
Date:   Fri Sep 23 20:23:04 2022 -0400

    commit

 create mode 100755 R/genedynamics.R
 create mode 100755 R/guided_MST.R
 create mode 100755 R/guided_tscan.R
 delete mode 100644 R/mapCellsToEdges.R
 delete mode 100644 R/orderCells.R
 delete mode 100644 R/perCellEntropy.R
 delete mode 100644 R/quickPseudotime.R
 delete mode 100644 R/reexports.R
 delete mode 100644 R/reportEdges.R
 delete mode 100644 R/testPseudotime.R
 delete mode 100644 inst/NEWS.Rd
 create mode 100644 inst/shiny/rsconnect/shinyapps.io/zhiji/TSCAN.dcf
 create mode 100644 inst/shiny/rsconnect/shinyapps.io/zhiji/shiny.dcf
 delete mode 100644 inst/shiny/shinyapps/zhiji/TSCAN.dcf
 mode change 100755 => 100644 inst/shiny/www/ajaxloaderq.gif
 mode change 100755 => 100644 inst/shiny/www/busy.js
 mode change 100755 => 100644 inst/shiny/www/style.css
 create mode 100644 man/genedynamics.Rd
 create mode 100644 man/guided_MST.Rd
 create mode 100644 man/guided_tscan.Rd
 delete mode 100644 man/mapCellsToEdges.Rd
 delete mode 100644 man/orderCells.Rd
 delete mode 100644 man/perCellEntropy.Rd
 delete mode 100644 man/quickPseudotime.Rd
 delete mode 100644 man/reexports.Rd
 delete mode 100644 man/reportEdges.Rd
 delete mode 100644 man/testPseudotime.Rd
 delete mode 100644 tests/testthat.R
 delete mode 100644 tests/testthat/test-entropy.R
 delete mode 100644 tests/testthat/test-mapping.R
 delete mode 100644 tests/testthat/test-order.R
 delete mode 100644 tests/testthat/test-quick.R
 delete mode 100644 tests/testthat/test-report.R
 delete mode 100644 tests/testthat/test-test.R
 create mode 100644 vignettes/guided_tscan.pdf

Note the large number of changes in commit 8b680d1a5750dcd0984e7e12d221e7bd729fcf7b, including deletion of a number of files.

This has undone all the work @LTLA put into improving TSCAN for inclusion in Bioconductor (#9) and has also broken the use of TSCAN featured in 'Orchestrating Single Cell Analysis with Bioconductor' book (e.g., the material in https://bioconductor.org/books/3.16/OSCA.multisample/merged-hsc.html#combined-analyses no longer works because these changes have also removed the TSCAN::quickPseudotime() function).

Will you be able to fix this before the October 28, which is the deadline for the next release (https://bioconductor.org/developers/release-schedule/)?

zji90 commented
PeteHaitch commented

Hi Jason,

That's okay, I realise it was unintentional.
Git is not the easiest tool to use!
I suggest emailing bioc-devel@r-project.org to ask for advice on how to fix this and roll-back to the previous version.

Cheers,
Pete

zji90 commented
PeteHaitch commented

Hi Jason,

Thank you promptly taking care of this.
TSCAN is now building again on BioC 3.16 (https://www.bioconductor.org/checkResults/3.16/bioc-LATEST/TSCAN/)!
And this enables OSCA to build again.

Thanks,
Pete