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Fixed drop parameter #62

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merged 32 commits into from
Feb 11, 2024
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266409b
update subset.FRASER drop argument
drewjbeh Jan 24, 2024
e6fc2ef
Update RoxyGen documentation to 7.3.0
Jan 24, 2024
47cc161
correctly pass on 'drop' argument in subset call
c-mertes Jan 24, 2024
2f95016
move to GHA bioconductor (#47)
c-mertes Nov 25, 2022
fecfbbe
hardcode drop parameter for subset to FALSE
Feb 1, 2024
9a51b49
update github actions R and bioc versions
Feb 1, 2024
a795fca
remove vignette building
Feb 2, 2024
cbfaa57
remove vignettes from build
Feb 2, 2024
e650af9
remove drop from actually subsetting commands
Feb 2, 2024
4a15970
add drop=FALSE to all FraserDataSet subsetting in countRNA
Feb 5, 2024
49f25f9
additional argument before drop to subset
Feb 5, 2024
e67e86d
drop parameter for subsetting in tests and results function
Feb 6, 2024
18a5dee
more drop parameters for tests
Feb 6, 2024
0adbb1e
missing comma before drop
Feb 6, 2024
c70ed19
update subsetting in example commands
Feb 6, 2024
5e2a322
update drop parameter in mapSeqlevels generic and example calls
Feb 6, 2024
fa5ce9c
drop in mapSeqlevels and update docs to match code
Feb 7, 2024
2811236
documenation matching to functions and reinstate vignette building
Feb 7, 2024
a1489c8
remove vignette building
Feb 7, 2024
c74deda
add magick to Suggetss to avoid vignette knitr error
Feb 9, 2024
5c37a73
more drop parameter fixes and documentation
Feb 9, 2024
aacb2e1
vignette building
Feb 9, 2024
9263c5a
change generic subset.FRASER drop, and formal argument matching in se…
Feb 10, 2024
9b2bad3
document ... parameter
Feb 10, 2024
e17ad2b
rebuild documentation
Feb 10, 2024
2e46996
Correct documentation for and in subset.FRASER
c-mertes Feb 11, 2024
087935f
add tests for setting the generic '[' function
c-mertes Feb 11, 2024
e311f5a
remove CCX11 flags from Makevars
c-mertes Feb 11, 2024
622d5cf
add OCID IDs and Karoline Lutz to DESCRIPTION
c-mertes Feb 11, 2024
5d25711
fix bugreport typo
c-mertes Feb 11, 2024
535939c
bump version 1.15 -> 1.15.1
c-mertes Feb 11, 2024
e68992a
fix typo in DESCRIPTION
c-mertes Feb 11, 2024
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remove vignette building
Drew Behrens committed Feb 7, 2024
commit a1489c88a1ad56ffbfbe4e612e2dd2b4cae00291
4 changes: 2 additions & 2 deletions .github/workflows/check-bioc.yml
Original file line number Diff line number Diff line change
@@ -211,7 +211,7 @@ jobs:
## This pass does not use AnVIL and will thus update any packages
## that have seen been updated in Bioconductor
message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE, force = TRUE)
shell: Rscript {0}

- name: Install BiocGenerics
@@ -248,7 +248,7 @@ jobs:
options(crayon.enabled = TRUE)
rcmdcheck::rcmdcheck(
args = c("--no-manual", "--no-vignettes", "--timings"),
build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
build_args = c("--no-build-vignettes", "--no-manual", "--keep-empty-dirs", "--no-resave-data"),
error_on = "warning",
check_dir = "check"
)