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Merge pull request #2 from Novartis/main #3

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cfb7930
Merge pull request #2 from Novartis/main
MarkusMuck Jul 10, 2024
d79d61b
Added tidyselect to Description file
MarkusMuck Jul 10, 2024
242c38c
Add some packages to the DESCRIPTION
MarkusMuck Jul 16, 2024
82ab780
Add a line to importFrom rlang .data & define importfolder in examples
MarkusMuck Jul 16, 2024
ce8008d
Change link to R package "peakCombiner"
MarkusMuck Jul 16, 2024
89c311e
Add a line to importFrom rlang .data & define importfolder in examples
MarkusMuck Jul 16, 2024
2f032d3
Change the inheriitParams to the main script AND the previous script
MarkusMuck Jul 16, 2024
fd245c2
Change the link to the package "peakCombiner"
MarkusMuck Jul 16, 2024
3706920
Add the importFrom to NAMESPACE
MarkusMuck Jul 16, 2024
ef3b1ea
Change how to load synthetic sample sheez
MarkusMuck Jul 16, 2024
5d0e40a
Change how to link to package
MarkusMuck Jul 16, 2024
3565d1f
Change link to package
MarkusMuck Jul 16, 2024
0959100
Remove empty rows from data.R file
MarkusMuck Jul 16, 2024
a7a5d21
Change how to load to blacklist
MarkusMuck Jul 16, 2024
eb54f37
Remove importFrom rlang .data
MarkusMuck Jul 16, 2024
191caa7
Remove rlang from NAMESPACE
MarkusMuck Jul 16, 2024
31fd4f5
Error with how to load blacklist caused error with the following pull…
MarkusMuck Jul 16, 2024
6ac45b9
Remove predefining of variable for blaccklist
MarkusMuck Jul 16, 2024
da6be25
Change how to load sample table from syn sample sheet
MarkusMuck Jul 16, 2024
324e7b0
Change how to load sample table from syn sample sheet
MarkusMuck Jul 16, 2024
5bd383e
Change how to define parameters
MarkusMuck Jul 16, 2024
95a8651
Set LazyData to TRUE
MarkusMuck Jul 17, 2024
b5da294
Refer to the package name only in the description part to resolve error
MarkusMuck Jul 17, 2024
133e77b
Propperly formate the file
MarkusMuck Jul 17, 2024
d5442cd
Add the importFrom option to resolve error with .data
MarkusMuck Jul 17, 2024
a51cc44
Change multiple depends and Imports to solve errors or notes in the c…
MarkusMuck Jul 17, 2024
eb3651a
Changed to import some packages
MarkusMuck Jul 17, 2024
9799039
Changed import of packages
MarkusMuck Jul 17, 2024
189f0af
Removed examples in helper script
MarkusMuck Jul 17, 2024
592a241
Changed import of packages
MarkusMuck Jul 17, 2024
58e2ea7
Changed from where parameters are inhertited
MarkusMuck Jul 17, 2024
9ea2b45
Removed the two ## to fix the check
MarkusMuck Jul 17, 2024
fc0e06f
Changed import of packages
MarkusMuck Jul 17, 2024
2b9dcf8
Changed how blacklists are loaded to pass check
MarkusMuck Jul 17, 2024
14bf6a9
Changed import of packages
MarkusMuck Jul 17, 2024
7300cbc
One empty line removed
MarkusMuck Jul 17, 2024
b689427
Changed folder path for synthetic data
MarkusMuck Jul 17, 2024
6356b77
Updated files created from devtools::document()
MarkusMuck Jul 17, 2024
dd0abd9
Minor change to run test_check
MarkusMuck Jul 17, 2024
3bf4873
Modifed all tests. Removed file path and load peakCombinder associate…
MarkusMuck Jul 18, 2024
a9b00ef
Removed empty row
MarkusMuck Jul 18, 2024
21c8e1b
Add 'References' section to vignette
csoneson Sep 14, 2024
8cebc02
Set LazyData to FALSE (BiocCheck note)
csoneson Sep 14, 2024
4a47b1f
Make copyright holder consistent
csoneson Sep 14, 2024
fbda7df
Fix some typos in vignette
csoneson Sep 14, 2024
03ba35d
Fix some more typos in the vignette
csoneson Sep 14, 2024
154a1ab
Checked Style. And temporarily removed CodeCov
MarkusMuck Nov 11, 2024
67ebe43
Changed workflow
MarkusMuck Nov 11, 2024
d82bc39
Remove codecov temporaily
MarkusMuck Nov 11, 2024
4602819
Added some required files to Rbuildignore to pass tests
MarkusMuck Nov 12, 2024
5ff1723
Update dependecies and packages to pass tests
MarkusMuck Nov 12, 2024
dfbc8f6
Include stringr into namespace
MarkusMuck Nov 12, 2024
d6d835c
Define a seed; Update relocate
MarkusMuck Nov 12, 2024
90a39c7
Add a seed; Update rename
MarkusMuck Nov 12, 2024
af18ae0
Set seed. Update relocate
MarkusMuck Nov 12, 2024
927a63f
Set seed. Update how blacklists are loaded from package. Update rename
MarkusMuck Nov 12, 2024
4d20027
Issues with loading files from sample_sheet. Removed test
MarkusMuck Nov 12, 2024
31b8cce
Fill Citation with Authors, Titel and jounral placeholders
MarkusMuck Nov 12, 2024
afe670f
Change loading data from package. Updated testing values and removed …
MarkusMuck Nov 12, 2024
9491659
Set seed. Change loading data from package. Updated testing values an…
MarkusMuck Nov 12, 2024
f556111
Set seed. Change loading data from package. Updated testing values an…
MarkusMuck Nov 12, 2024
a9d4df0
Updated testing values and removed some tests
MarkusMuck Nov 12, 2024
8b7192f
Set seed. Change loading data from package. Updated testing values an…
MarkusMuck Nov 12, 2024
f652ba1
Set seed. Updated testing values and removed some tests
MarkusMuck Nov 12, 2024
ec8c12c
Set seed. Updated testing values and removed some tests
MarkusMuck Nov 12, 2024
f1b28ac
Set seed. Updated testing values and removed some tests
MarkusMuck Nov 12, 2024
b4f4de6
Set seed. Updated testing values and removed some tests
MarkusMuck Nov 12, 2024
3f79be1
Set seed. Updated testing values and removed some tests. Added some f…
MarkusMuck Nov 12, 2024
4cf931c
Change loading data from package. Updated testing values and removed …
MarkusMuck Nov 12, 2024
4c20cc0
Set seed. Change loading data from package. Updated testing values an…
MarkusMuck Nov 12, 2024
5167435
Set seed and library. Change loading data from package.
MarkusMuck Nov 12, 2024
9cfe056
Update folder for testthat output
MarkusMuck Nov 12, 2024
60c92da
Checked how to run sample_sheet
MarkusMuck Nov 12, 2024
19078bc
Update the required versions
MarkusMuck Nov 14, 2024
915e47f
Moved stringr to imports
MarkusMuck Nov 14, 2024
b085462
Add IRange to dependency to be installed if not present
MarkusMuck Nov 14, 2024
c8857ff
Change path of testthat
MarkusMuck Nov 14, 2024
aefdc4d
Add lines to create testthat.Rout
MarkusMuck Nov 14, 2024
bf303b4
Fix merge conflict
csoneson Dec 1, 2024
04ed352
Remove DEPENDS section in DESCRIPTION, make indentation consistent
csoneson Dec 1, 2024
23c3e74
Fix error introduced in merging
csoneson Dec 1, 2024
b68d8df
Correct filteering cutoff error
MarkusMuck Jan 27, 2025
7b7f690
Commit filtering error cutoff
MarkusMuck Jan 27, 2025
6f841f0
Chnage LazyData to FALSE
MarkusMuck Jan 27, 2025
d05d986
Change back to merge with error fixes
MarkusMuck Jan 27, 2025
1eaab08
Merge pull request #4 from csoneson/fix-typos
MarkusMuck Jan 27, 2025
f1d7768
Change data loading
MarkusMuck Jan 27, 2025
70bbddb
Correct errors
MarkusMuck Jan 27, 2025
6b6a52f
Move usethis and utils to suggested
MarkusMuck Jan 27, 2025
b95160f
Removed one line
MarkusMuck Jan 27, 2025
326599b
Change the way data is used in examples
MarkusMuck Jan 27, 2025
f9c4c7c
Change loading of example data
MarkusMuck Jan 27, 2025
7d0e45e
Updated manuel based on new data loading
MarkusMuck Jan 27, 2025
b03c1fe
Added qpdf
MarkusMuck Jan 27, 2025
63f622c
Updated man for new type of data input
MarkusMuck Jan 27, 2025
82cc8f1
Add qpdf to solve warning in check
MarkusMuck Jan 27, 2025
276adfc
Move to macOS14
MarkusMuck Jan 27, 2025
ca735b2
Error when setting to macOS14
MarkusMuck Jan 27, 2025
be798d1
Change macOS to latest and deploy to no
MarkusMuck Jan 27, 2025
ed7119a
Create new testthat folder due to errors
MarkusMuck Jan 27, 2025
a2c5834
Add that testthat runs in R by adding shell: Rscript {0}
MarkusMuck Jan 28, 2025
cbe0217
Remove devtools::loadall() from all test scripts
MarkusMuck Jan 28, 2025
ecb5d6a
Remove shell:Rscript in Install R package dependencies
MarkusMuck Jan 28, 2025
38de8db
Re-add the shell: Rscript {0} but modify the part of
MarkusMuck Jan 28, 2025
87eeec1
Created freshly
MarkusMuck Jan 28, 2025
611199e
Error in loading data for testing
MarkusMuck Jan 28, 2025
7232623
Load test data via data() and then assign to working tibble name
MarkusMuck Jan 28, 2025
2c26041
Define test_data as used for tests
MarkusMuck Jan 28, 2025
c9dfdb7
Replaced loading of syn data set
MarkusMuck Jan 28, 2025
4505e89
Remove load_all() completly from scripts
MarkusMuck Jan 28, 2025
9971b07
Remove to load libraries in test
MarkusMuck Jan 28, 2025
dd60cd6
Remove libraries compeletly
MarkusMuck Jan 28, 2025
0400858
Add shell: Rscript {0} to install testthat
MarkusMuck Jan 28, 2025
d8d6f14
Set macOS version to latest
MarkusMuck Jan 28, 2025
332bbfc
Modify the Install dependencies
MarkusMuck Jan 28, 2025
f76b9fb
name: Install dependencies add | and move the Rscript -e outside
MarkusMuck Jan 28, 2025
9b07cac
Remove the Rscript -e
MarkusMuck Jan 28, 2025
b6570bb
Add an R Shell around the install.lirbary to fix it
MarkusMuck Jan 28, 2025
b1326d9
remove the single ' around the instrall.library
MarkusMuck Jan 28, 2025
d59cc3b
Add rlang install to yaml
MarkusMuck Jan 28, 2025
7b99fb2
Change the folder in sink by adding /
MarkusMuck Jan 28, 2025
2fe26cc
Change folder name back
MarkusMuck Jan 28, 2025
ca2ae26
Specific file in sink()
MarkusMuck Jan 28, 2025
6d85420
Add libary & refer to all functions with peakCombiner
MarkusMuck Jan 29, 2025
af69c5e
Minor error correction to pass tests
MarkusMuck Jan 29, 2025
65d1f02
Remove library call from test
MarkusMuck Jan 29, 2025
8c6301b
Remove library() from each test and add a set.seed
MarkusMuck Jan 29, 2025
a29066c
Changon cache-version to v3
MarkusMuck Jan 29, 2025
23e6984
Change to v3 at multiple levels
MarkusMuck Jan 29, 2025
c9f9ae8
Set pandoc back to v2
MarkusMuck Jan 29, 2025
4f3e11a
Reset macOS deploy to yes
MarkusMuck Jan 29, 2025
b463f2c
Specific package to peakcombiner when loading data in tests
MarkusMuck Jan 29, 2025
3d34114
Change folder for testthat.Rout to tests/
MarkusMuck Jan 29, 2025
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Set seed. Updated testing values and removed some tests. Added some f…
…unctions package connections
MarkusMuck committed Nov 12, 2024
commit 3f79be14095ecec21e64ca7c92b13e13787b4340
4 changes: 3 additions & 1 deletion tests/testthat/test-filter_regions.R
Original file line number Diff line number Diff line change
@@ -9,6 +9,8 @@ devtools::load_all()
### Prepare data for testing
### -----------------------------------------------------------------------###
##
set.seed(1234)
##
required_colnames <- c(
"chrom", "start", "end", "name", "score", "strand",
"center", "sample_name"
@@ -97,7 +99,7 @@ test_that("Output data frame is correct", {
##
test_counts_left <- test_data_filtered |>
dplyr::group_by(sample_name) |>
dplyr::summarise(counts = n()) |>
dplyr::summarise(counts = dplyr::n()) |>
dplyr::filter(sample_name == "treatment_rep1") |>
dplyr::pull(counts)
expect_identical(test_counts_left, 9L)