From e2d4dfb8994e70b343917deae0531bf31e0a6c18 Mon Sep 17 00:00:00 2001 From: Nicole Gay Date: Wed, 8 Nov 2023 19:07:52 -0800 Subject: [PATCH 01/11] update message --- vignettes/MotrpacRatTraining6mo.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/MotrpacRatTraining6mo.Rmd b/vignettes/MotrpacRatTraining6mo.Rmd index f4309a9..4e39395 100644 --- a/vignettes/MotrpacRatTraining6mo.Rmd +++ b/vignettes/MotrpacRatTraining6mo.Rmd @@ -64,7 +64,7 @@ div.yellow {
-This vignette is under construction. If something is unclear or obviously missing, +If you run into problems, please submit an issue [here](https://github.com/MoTrPAC/MotrpacRatTraining6mo/issues).
From 556d3b2b97c12b335b7fb3e22597219bdd824fc7 Mon Sep 17 00:00:00 2001 From: Nicole Gay Date: Wed, 8 Nov 2023 19:40:36 -0800 Subject: [PATCH 02/11] add CODEOWNERS --- CODEOWNERS | 1 + DESCRIPTION | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) create mode 100644 CODEOWNERS diff --git a/CODEOWNERS b/CODEOWNERS new file mode 100644 index 0000000..80ea2af --- /dev/null +++ b/CODEOWNERS @@ -0,0 +1 @@ +* @nicolerg \ No newline at end of file diff --git a/DESCRIPTION b/DESCRIPTION index 323334f..86cf97a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -66,7 +66,7 @@ Suggests: MotrpacBicQC (>= 0.6.9), multcomp, parallel, - RCy3, + RCy3 (>= 2.23.2), repfdr, RMariaDB, rmarkdown, From bf6ef90d5ab07d173d51d9e66000e0e8dc0d3630 Mon Sep 17 00:00:00 2001 From: Nicole Gay Date: Wed, 8 Nov 2023 19:49:53 -0800 Subject: [PATCH 03/11] change RCy3 version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 86cf97a..44eaf0e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -66,7 +66,7 @@ Suggests: MotrpacBicQC (>= 0.6.9), multcomp, parallel, - RCy3 (>= 2.23.2), + RCy3 (>= 2.22.1), repfdr, RMariaDB, rmarkdown, From a11554cabd1b7ad665864233d526e0560c850d8b Mon Sep 17 00:00:00 2001 From: Nicole Gay Date: Wed, 8 Nov 2023 20:00:18 -0800 Subject: [PATCH 04/11] add step to check --- .github/workflows/R-CMD-check.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 84b587c..d8a3d2d 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -21,6 +21,10 @@ jobs: - uses: r-lib/actions/setup-r@v2 with: use-public-rspm: true + + - name: install specific version of RCy3 + run: | + BiocManager::install("RCy3", version = "3.18") - uses: r-lib/actions/setup-r-dependencies@v2 with: From ec5236ce08eda7f070a135c1438e11d286e5c940 Mon Sep 17 00:00:00 2001 From: Nicole Gay Date: Wed, 8 Nov 2023 20:03:01 -0800 Subject: [PATCH 05/11] use bash --- .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 d8a3d2d..7d2a39c 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -24,7 +24,7 @@ jobs: - name: install specific version of RCy3 run: | - BiocManager::install("RCy3", version = "3.18") + Rscript -e "BiocManager::install('RCy3', version = '3.18')" - uses: r-lib/actions/setup-r-dependencies@v2 with: From 5dec0fc20bd6c9b706fb621957cbef2efb618672 Mon Sep 17 00:00:00 2001 From: Nicole Gay Date: Wed, 8 Nov 2023 20:05:41 -0800 Subject: [PATCH 06/11] install BiocManager --- .github/workflows/R-CMD-check.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 7d2a39c..833b914 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -22,6 +22,10 @@ jobs: with: use-public-rspm: true + - name: install BiocManager + run: | + Rscript -e "install.packages('BiocManager')" + - name: install specific version of RCy3 run: | Rscript -e "BiocManager::install('RCy3', version = '3.18')" From 773dcbe5fd1051ead179af2b6e14cb32f40fc123 Mon Sep 17 00:00:00 2001 From: Nicole Gay Date: Wed, 8 Nov 2023 20:12:02 -0800 Subject: [PATCH 07/11] download RCy3 from remote --- .github/workflows/R-CMD-check.yaml | 8 -------- DESCRIPTION | 5 +++-- 2 files changed, 3 insertions(+), 10 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 833b914..84b587c 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -21,14 +21,6 @@ jobs: - uses: r-lib/actions/setup-r@v2 with: use-public-rspm: true - - - name: install BiocManager - run: | - Rscript -e "install.packages('BiocManager')" - - - name: install specific version of RCy3 - run: | - Rscript -e "BiocManager::install('RCy3', version = '3.18')" - uses: r-lib/actions/setup-r-dependencies@v2 with: diff --git a/DESCRIPTION b/DESCRIPTION index 44eaf0e..e015f04 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -66,7 +66,7 @@ Suggests: MotrpacBicQC (>= 0.6.9), multcomp, parallel, - RCy3 (>= 2.22.1), + RCy3 (>= 2.23.2), repfdr, RMariaDB, rmarkdown, @@ -89,7 +89,8 @@ Remotes: MoTrPAC/MotrpacRatTraining6moData, MoTrPAC/MotrpacBicQC, YuLab-SMU/ggtree, - nicolerg/ssGSEA2 + nicolerg/ssGSEA2, + cytoscape/RCy3 Config/testthat/edition: 3 Encoding: UTF-8 Roxygen: list(markdown = TRUE) From 9e4bc3fef9b30e8441b19b5bf50e2edf8fc43e45 Mon Sep 17 00:00:00 2001 From: Nicole Gay Date: Wed, 8 Nov 2023 21:37:09 -0800 Subject: [PATCH 08/11] download plotrix from GitHub to avoid R-CMD-check warning --- .Rbuildignore | 1 + DESCRIPTION | 4 +++- vignettes/key_metabolites.Rmd | 2 +- 3 files changed, 5 insertions(+), 2 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index 55e25d7..897a22b 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -11,3 +11,4 @@ devnotes.md ^workshops$ ^\.github$ ^reports$ +CODEOWNERS diff --git a/DESCRIPTION b/DESCRIPTION index e015f04..83d5985 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -36,6 +36,7 @@ Imports: magrittr, metap, methods, + plotrix, purrr, r2r, RColorBrewer, @@ -90,7 +91,8 @@ Remotes: MoTrPAC/MotrpacBicQC, YuLab-SMU/ggtree, nicolerg/ssGSEA2, - cytoscape/RCy3 + cytoscape/RCy3, + plotrix/plotrix Config/testthat/edition: 3 Encoding: UTF-8 Roxygen: list(markdown = TRUE) diff --git a/vignettes/key_metabolites.Rmd b/vignettes/key_metabolites.Rmd index 7447ed3..99c0164 100644 --- a/vignettes/key_metabolites.Rmd +++ b/vignettes/key_metabolites.Rmd @@ -11,7 +11,7 @@ output: highlight: tango vignette: > - %\VignetteIndexEntry{Tutorial for MotrpacRatTraining6mo R package} + %\VignetteIndexEntry{Key metabolites} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} %\usepackage[utf8]{inputenc} From d6074b7417ffc16b69fc5344af0336e3273e4bc0 Mon Sep 17 00:00:00 2001 From: Nicole Gay Date: Wed, 8 Nov 2023 21:56:48 -0800 Subject: [PATCH 09/11] bump version and update NEWS --- DESCRIPTION | 2 +- NEWS.md | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 83d5985..1a295a2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Type: Package Package: MotrpacRatTraining6mo Title: Analysis of the MoTrPAC endurance exercise training data in 6-month-old rats -Version: 1.6.4 +Version: 1.6.5 Authors@R: c( person("Nicole", "Gay", , "nicole.r.gay@gmail.com", role = c("cre", "aut")), person("David", "Amar", , "ddam.am@gmail.com", role = "aut"), diff --git a/NEWS.md b/NEWS.md index 276526e..0ac4aec 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,9 @@ +# MotrpacRatTraining6mo 1.6.5 (2023-11-08) + +* Point to development version of `RCy3` from GitHub to avoid `R-CMD check` error `RCy3: Can't install dependency uchardet`. +* Install `plotrix` from GitHub instead of CRAN to avoid `R-CMD check` warning `Requires (indirectly) orphaned package: ‘plotrix’`. + CRAN has marked `plotrix` as orphaned. `plotrix` is a dependency for `mutoss`, which is a dependency for `metap`. + # MotrpacRatTraining6mo 1.6.4 (2023-06-02) * Bug fix in `transcript_timewise_da()` to run with limited contrasts when `tissue="VENACV"`. From 1638ef0680818f42482ce8b54419ebdf54e3f9aa Mon Sep 17 00:00:00 2001 From: Nicole Gay Date: Thu, 9 Nov 2023 21:39:57 -0800 Subject: [PATCH 10/11] move plotrix from imports to suggests --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 1a295a2..acc6767 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -36,7 +36,6 @@ Imports: magrittr, metap, methods, - plotrix, purrr, r2r, RColorBrewer, @@ -67,6 +66,7 @@ Suggests: MotrpacBicQC (>= 0.6.9), multcomp, parallel, + plotrix, RCy3 (>= 2.23.2), repfdr, RMariaDB, From c59598dac8b433bbc4f5017924f67e673bbe2882 Mon Sep 17 00:00:00 2001 From: Nicole Gay Date: Thu, 9 Nov 2023 21:41:17 -0800 Subject: [PATCH 11/11] increment data package version --- DESCRIPTION | 2 +- NEWS.md | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index acc6767..61d620a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -98,6 +98,6 @@ Encoding: UTF-8 Roxygen: list(markdown = TRUE) RoxygenNote: 7.2.3 Depends: - MotrpacRatTraining6moData (>= 1.8.0), + MotrpacRatTraining6moData (>= 2.0.0), R (>= 2.10) LazyData: true diff --git a/NEWS.md b/NEWS.md index 0ac4aec..5b83a45 100644 --- a/NEWS.md +++ b/NEWS.md @@ -3,6 +3,7 @@ * Point to development version of `RCy3` from GitHub to avoid `R-CMD check` error `RCy3: Can't install dependency uchardet`. * Install `plotrix` from GitHub instead of CRAN to avoid `R-CMD check` warning `Requires (indirectly) orphaned package: ‘plotrix’`. CRAN has marked `plotrix` as orphaned. `plotrix` is a dependency for `mutoss`, which is a dependency for `metap`. +* Increment required `MotrpacRatTraining6moData` version. # MotrpacRatTraining6mo 1.6.4 (2023-06-02)