From 9978d4014722472d8fa24b7d3510440ef8eefe6d Mon Sep 17 00:00:00 2001 From: Ning Liu Date: Fri, 28 Apr 2023 11:35:21 +1000 Subject: [PATCH 01/14] Update R-CMD-check.yaml --- .github/workflows/R-CMD-check.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 6cab126..2dc9eb6 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -52,7 +52,7 @@ jobs: fail-fast: false matrix: config: - - { os: ubuntu-latest, r: '4.2', bioc: '3.15', cont: "bioconductor/bioconductor_docker:RELEASE_3_15", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } + - { os: ubuntu-latest, r: 'devel', bioc: '3.17', cont: "bioconductor/bioconductor_docker:RELEASE_3_17", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } #- { os: macOS-latest, r: 'devel', bioc: '3.15'} #- { os: windows-latest, r: 'devel', bioc: '3.15'} # - { os: ubuntu-latest, r: '4.1', bioc: '3.14', cont: "bioconductor/bioconductor_docker:RELEASE_3_14", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } @@ -239,17 +239,17 @@ jobs: shell: Rscript {0} - name: Test coverage - if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux' && matrix.config.r == 'devel' + if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux' && matrix.config.r == 'devel' run: | covr::codecov(type="all", commentDontrun=FALSE) shell: Rscript {0} - name: Install package - if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' && matrix.config.r == 'devel' + if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' && matrix.config.r == 'devel' run: R CMD INSTALL . - name: Deploy package - if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' && matrix.config.r == 'devel' + if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' && matrix.config.r == 'devel' run: | git config --local user.name "$GITHUB_ACTOR" git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" From 4a255e314576841b4013aae357f383679a5ea47e Mon Sep 17 00:00:00 2001 From: Ning Liu Date: Fri, 28 Apr 2023 12:32:09 +1000 Subject: [PATCH 02/14] Update R-CMD-check.yaml --- .github/workflows/R-CMD-check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 2dc9eb6..90f7640 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -239,7 +239,7 @@ jobs: shell: Rscript {0} - name: Test coverage - if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux' && matrix.config.r == 'devel' + if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux' && matrix.config.r == 'devel' run: | covr::codecov(type="all", commentDontrun=FALSE) shell: Rscript {0} From 042046c0b7335a4a4993e9540f73c6b8c4608820 Mon Sep 17 00:00:00 2001 From: Ning Liu Date: Fri, 28 Apr 2023 14:00:34 +1000 Subject: [PATCH 03/14] Update R-CMD-check.yaml --- .github/workflows/R-CMD-check.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 90f7640..46f145d 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -253,6 +253,7 @@ jobs: run: | git config --local user.name "$GITHUB_ACTOR" git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" + git config --global --add safe.directory /__w/standR/standR Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)" shell: bash {0} ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE) From d86a0a7d416c41f4da5163754a86ce9393e89c89 Mon Sep 17 00:00:00 2001 From: Ning Liu Date: Fri, 28 Apr 2023 15:49:01 +1000 Subject: [PATCH 04/14] Update R-CMD-check.yaml --- .github/workflows/R-CMD-check.yaml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 46f145d..4d627b7 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -185,13 +185,13 @@ jobs: shell: Rscript {0} - name: Install covr - if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux' && matrix.config.r == 'devel' + if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux' && matrix.config.r == 'devel' run: | remotes::install_cran("covr") shell: Rscript {0} - name: Install pkgdown and deps - if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' && matrix.config.r == 'devel' + if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' && matrix.config.r == 'devel' run: | remotes::install_cran("pkgdown") shell: Rscript {0} @@ -239,7 +239,7 @@ jobs: shell: Rscript {0} - name: Test coverage - if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux' && matrix.config.r == 'devel' + if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux' && matrix.config.r == 'devel' run: | covr::codecov(type="all", commentDontrun=FALSE) shell: Rscript {0} @@ -253,7 +253,6 @@ jobs: run: | git config --local user.name "$GITHUB_ACTOR" git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" - git config --global --add safe.directory /__w/standR/standR Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)" shell: bash {0} ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE) @@ -263,7 +262,7 @@ jobs: - name: Upload check results if: failure() - uses: actions/upload-artifact@master + uses: actions/upload-artifact@devel with: name: ${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-results path: check From f8ea5000ad87453782a096b3a57b7b06b194a614 Mon Sep 17 00:00:00 2001 From: Ning Liu Date: Fri, 28 Apr 2023 15:50:46 +1000 Subject: [PATCH 05/14] Update R-CMD-check.yaml --- .github/workflows/R-CMD-check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 4d627b7..c18e23f 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -262,7 +262,7 @@ jobs: - name: Upload check results if: failure() - uses: actions/upload-artifact@devel + uses: actions/upload-artifact@master with: name: ${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-results path: check From 9b84736412a1c253588a6c221ab2a844da9667cf Mon Sep 17 00:00:00 2001 From: Ning Liu Date: Fri, 28 Apr 2023 16:36:17 +1000 Subject: [PATCH 06/14] Update R-CMD-check.yaml --- .github/workflows/R-CMD-check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index c18e23f..e36deaa 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -249,7 +249,7 @@ jobs: run: R CMD INSTALL . - name: Deploy package - if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' && matrix.config.r == 'devel' + if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' && matrix.config.r == 'devel' run: | git config --local user.name "$GITHUB_ACTOR" git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" From 3f5045fdc68932edd3f269d5de423f94cf93cff2 Mon Sep 17 00:00:00 2001 From: ningbioinfostruggling Date: Mon, 1 May 2023 15:09:38 +1000 Subject: [PATCH 07/14] fix a bug of preparedecon --- .github/workflows/{R-CMD-check.yaml => R-CMD-check.yaml } | 2 +- R/prepareDecon.R | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename .github/workflows/{R-CMD-check.yaml => R-CMD-check.yaml } (99%) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml similarity index 99% rename from .github/workflows/R-CMD-check.yaml rename to .github/workflows/R-CMD-check.yaml index e36deaa..56947cc 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -170,7 +170,7 @@ jobs: ## Pass #2 at installing dependencies 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) - + ## For running the checks message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) remotes::install_cran("rcmdcheck") diff --git a/R/prepareDecon.R b/R/prepareDecon.R index cbbc593..85bb75a 100644 --- a/R/prepareDecon.R +++ b/R/prepareDecon.R @@ -30,7 +30,7 @@ prepareSpatialDecon <- function(spe, assay2use = "logcounts", negProbeName = "Ne } if (length(negProbeName) == 1){ - bg <- sweep(norm*0, 2, norm[negProbeName,], "+") + bg <- sweep(norm*0, 2, unlist(norm[negProbeName,]), "+") } else { if (nrow(norm) != length(pool)){ stop("length(pool) should be equal to nrow(spe).") From bf977f9f7185d846f23c0072c3faff58301d56e4 Mon Sep 17 00:00:00 2001 From: Ning Liu Date: Mon, 1 May 2023 20:34:22 +1000 Subject: [PATCH 08/14] Update R-CMD-check.yaml --- .github/workflows/{R-CMD-check.yaml => R-CMD-check.yaml} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename .github/workflows/{R-CMD-check.yaml => R-CMD-check.yaml} (99%) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml similarity index 99% rename from .github/workflows/R-CMD-check.yaml rename to .github/workflows/R-CMD-check.yaml index 56947cc..e36deaa 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -170,7 +170,7 @@ jobs: ## Pass #2 at installing dependencies 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) - + ## For running the checks message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) remotes::install_cran("rcmdcheck") From bbd6c6997142e3235dffb06d1ee9399f17a30e4a Mon Sep 17 00:00:00 2001 From: ningbioinfostruggling Date: Mon, 1 May 2023 21:56:12 +1000 Subject: [PATCH 09/14] version bump --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0c0aab6..1a544ed 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: standR Title: Spatial transcriptome analyses of Nanostring's DSP data in R -Version: 1.3.10 +Version: 1.4.1 Authors@R: c(person(given = "Ning", family = "Liu", From f9349c873869822ea6a512da129fc5c07071edcb Mon Sep 17 00:00:00 2001 From: ningbioinfostruggling Date: Wed, 10 May 2023 16:32:50 +1000 Subject: [PATCH 10/14] set devel version to 1.5 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 1a544ed..9138a1c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: standR Title: Spatial transcriptome analyses of Nanostring's DSP data in R -Version: 1.4.1 +Version: 1.5.0 Authors@R: c(person(given = "Ning", family = "Liu", From 577a9919b3f41f2f1a4cceca5abbef80639bd08f Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Tue, 25 Apr 2023 11:37:16 -0400 Subject: [PATCH 11/14] bump x.y.z version to even y prior to creation of RELEASE_3_17 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 9138a1c..7105e01 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: standR Title: Spatial transcriptome analyses of Nanostring's DSP data in R -Version: 1.5.0 +Version: 1.5.1 Authors@R: c(person(given = "Ning", family = "Liu", From 434575a67e07c934da7d66604a2826d05e18f604 Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Tue, 25 Apr 2023 11:37:16 -0400 Subject: [PATCH 12/14] bump x.y.z version to odd y following creation of RELEASE_3_17 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 7105e01..9138a1c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: standR Title: Spatial transcriptome analyses of Nanostring's DSP data in R -Version: 1.5.1 +Version: 1.5.0 Authors@R: c(person(given = "Ning", family = "Liu", From 550686ce17fcad11d8326718d3a023b376db141c Mon Sep 17 00:00:00 2001 From: ningbioinfostruggling Date: Mon, 1 May 2023 22:00:57 +1000 Subject: [PATCH 13/14] version correct --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 9138a1c..7105e01 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: standR Title: Spatial transcriptome analyses of Nanostring's DSP data in R -Version: 1.5.0 +Version: 1.5.1 Authors@R: c(person(given = "Ning", family = "Liu", From 8e0533838a315639d30826da4461552f4b84ba01 Mon Sep 17 00:00:00 2001 From: ningbioinfostruggling Date: Wed, 10 May 2023 16:28:53 +1000 Subject: [PATCH 14/14] fix a bug in plotting pca --- R/plotDR.R | 1 - 1 file changed, 1 deletion(-) diff --git a/R/plotDR.R b/R/plotDR.R index 68ec75d..2e178ea 100644 --- a/R/plotDR.R +++ b/R/plotDR.R @@ -374,7 +374,6 @@ plotDR_intl <- function(drdf, sdata, textScale, ...) { # tidystyle recommends no explicit return statements at end of functions ggplot2::ggplot(plotdf, ggplot2::aes(!!x, !!y, !!!aesmap)) + - ggplot2::geom_point() + do.call(ggplot2::geom_point,defaultmap) + bhuvad_theme(textScale) }