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Add CI #192

Merged
merged 20 commits into from
Jun 5, 2024
Merged

Add CI #192

merged 20 commits into from
Jun 5, 2024

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ghar1821
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First iteration of CI using R-lib actions to install dependencies and the package itself.

@ghar1821 ghar1821 requested a review from tomashhurst May 25, 2024 13:53
@ghar1821 ghar1821 added the enhancement New feature or request label May 28, 2024
@tomashhurst
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@ghar1821 are these are failing because the branch does not yet have the full r-libs setup?

image

@ghar1821
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@tomashhurst More I don't think I set it up correctly. Those commits were pretty much trial and error to troubleshoot what caused the error. Github log wasn't clear what the error was, it only said

❯ checking whether package ‘Spectre’ can be installed ... [13s/14s] ERROR
  See below...

But then there was no indication as to what the error was, just a bunch of warnings. So then I tweaked the r-libs settings a bit and removed some of the manual test scripts in testthat folder (these are not automated unit tests). Only after then the error message popped out saying it has issues compiling the function documentations. Turns out, a comment in the example of run.pca was missing # which caused R CMD check to give out error when compiling examples.

So at the end, the numerous commits were my way of troubleshooting what has gone wrong. Once I managed to finalise the r-libs setting, I then did a test run and fix the errors locally before doing a commit.

@tomashhurst tomashhurst merged commit 336c2ca into v1.2.0-beta Jun 5, 2024
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ghar1821 added a commit that referenced this pull request Jul 11, 2024
commit 0e914ef
Author: Givanna Putri <[email protected]>
Date:   Mon Jul 8 11:05:26 2024 +1000

    small updates

commit 666b03a
Author: Givanna Putri <[email protected]>
Date:   Mon Jul 8 10:53:11 2024 +1000

    small updates to examples

commit 94362de
Author: Thomas Ashhurst <[email protected]>
Date:   Wed Jun 5 11:10:25 2024 +0100

    Update Segmentation - process TIFFs.R

commit c5768e8
Author: Thomas Ashhurst <[email protected]>
Date:   Wed Jun 5 11:09:59 2024 +0100

    Update ChronoClust.R

commit 291330c
Author: Thomas Ashhurst <[email protected]>
Date:   Wed Jun 5 11:09:28 2024 +0100

    Update Simple spatial 1 - add masks.R

commit 44b7021
Author: Thomas Ashhurst <[email protected]>
Date:   Wed Jun 5 11:08:35 2024 +0100

    Update Adv spatial 1 - add masks.R

commit 4885a97
Author: Thomas Ashhurst <[email protected]>
Date:   Wed Jun 5 11:08:05 2024 +0100

    Update TIFF to FCS.R

commit acef1db
Author: Thomas Ashhurst <[email protected]>
Date:   Wed Jun 5 11:04:44 2024 +0100

    Update Spectre rPCA.R

commit 61ab9e8
Author: Thomas Ashhurst <[email protected]>
Date:   Wed Jun 5 11:04:29 2024 +0100

    Update CytoNorm workflow.R

commit 7483277
Author: Thomas Ashhurst <[email protected]>
Date:   Wed Jun 5 11:03:45 2024 +0100

    Update Spectre simple discovery workflow.R

commit 336c2ca
Merge: 1275c87 e5572ca
Author: Thomas Ashhurst <[email protected]>
Date:   Wed Jun 5 11:00:22 2024 +0100

    Merge pull request #192 from ImmuneDynamics/introduce_ci

    Add CI

commit e5572ca
Author: Givanna Putri <[email protected]>
Date:   Sat May 25 23:46:32 2024 +1000

    Update check-standard.yaml

commit 6cb82a3
Author: Givanna Putri <[email protected]>
Date:   Sat May 25 23:38:33 2024 +1000

    Update check-standard.yaml

commit c567b87
Author: Givanna Putri <[email protected]>
Date:   Sat May 25 23:31:25 2024 +1000

    attempt to fix examples..

commit 3b6ff93
Author: Givanna Putri <[email protected]>
Date:   Sat May 25 18:19:20 2024 +1000

    Update do.add.cols.Rd

commit ddacced
Author: Givanna Putri <[email protected]>
Date:   Sat May 25 18:15:17 2024 +1000

    Update do.add.cols.R

commit 700a68e
Author: Givanna Putri <[email protected]>
Date:   Sat May 25 08:28:27 2024 +1000

    Update check-standard.yaml

commit 41369c8
Merge: da1c026 1275c87
Author: Givanna Putri <[email protected]>
Date:   Sat May 25 08:24:41 2024 +1000

    Merge remote-tracking branch 'origin/v1.2.0-beta' into introduce_ci

commit da1c026
Author: Givanna Putri <[email protected]>
Date:   Sat May 25 08:24:30 2024 +1000

    redo docs

commit 91d79dc
Author: Givanna Putri <[email protected]>
Date:   Sat May 25 08:03:01 2024 +1000

    Update check-standard.yaml

commit 4f48141
Author: Givanna Putri <[email protected]>
Date:   Fri May 24 12:26:28 2024 +1000

    Update run.pca.R

commit 62d0b90
Author: Givanna Putri <[email protected]>
Date:   Fri May 24 12:19:54 2024 +1000

    Update check-standard.yaml

commit 2ca8a22
Author: Givanna Putri <[email protected]>
Date:   Fri May 24 12:17:44 2024 +1000

    Update check-standard.yaml

commit 25eb1ef
Author: Givanna Putri <[email protected]>
Date:   Fri May 24 12:13:16 2024 +1000

    Update check-standard.yaml

commit 8aa8085
Author: Givanna Putri <[email protected]>
Date:   Fri May 24 12:08:37 2024 +1000

    Update check-standard.yaml

commit f7ba966
Merge: 68201f3 de3848e
Author: Givanna Putri <[email protected]>
Date:   Fri May 24 11:51:12 2024 +1000

    Merge branch 'updates' into introduce_ci

commit 68201f3
Author: Givanna Putri <[email protected]>
Date:   Thu Feb 29 16:30:19 2024 +1100

    still errorring god..

commit ff5a8bb
Author: Givanna Putri <[email protected]>
Date:   Thu Feb 29 11:57:05 2024 +1100

    remove test for now

commit 993f7f9
Author: Givanna Putri <[email protected]>
Date:   Thu Feb 29 11:13:57 2024 +1100

    Update check-standard.yaml

commit eab4a1d
Author: Givanna Putri <[email protected]>
Date:   Thu Feb 29 11:13:00 2024 +1100

    Update check-standard.yaml

    have to switch the push on just to test.

commit b6718f8
Author: Givanna Putri <[email protected]>
Date:   Thu Feb 29 11:08:50 2024 +1100

    test ci
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2 participants