From 311b3d2395966bc12cc52946d54759a0342e68a5 Mon Sep 17 00:00:00 2001 From: marouenbg Date: Sat, 29 Jan 2022 12:09:44 -0500 Subject: [PATCH 01/10] update crane --- R/CRANE.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/CRANE.R b/R/CRANE.R index 6ddde6c4..453795aa 100644 --- a/R/CRANE.R +++ b/R/CRANE.R @@ -81,7 +81,7 @@ alpacaCrane = function(input,alp,alpha=0.1,beta=0,iteration=30,isParallel=F){ if (i %% round(iteration/5)==0){ print(paste("Computing Differential Score",(i/iteration)*100,"%")) } - dwbm = computeDWBMmat.mscale(pos.table,ctrl.memb[V(pos.graph)$name]) + dwbm = alpacaComputeDWBMmatmScale(pos.table,ctrl.memb[V(pos.graph)$name]) miss_tf=setdiff(tfcheck,rownames(dwbm)) miss_g=setdiff(gcheck,colnames(dwbm)) From 58b38e4bb7052a78d692af0930f0f5a2a2f1a51a Mon Sep 17 00:00:00 2001 From: marouenbg Date: Sat, 29 Jan 2022 16:42:11 -0500 Subject: [PATCH 02/10] update workflows --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index f73477e5..552f0bcf 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -54,7 +54,7 @@ jobs: run: | library('reticulate') py_config() - use_python("/usr/bin/python3") + use_python("/usr/local/bin/python3") virtualenv_create("r-reticulate") shell: sudo -E Rscript {0} - name: Install reticulate 3 From 0f665a3e7f06dcec0dbb5d06f7eeab8df2b226a0 Mon Sep 17 00:00:00 2001 From: marouenbg Date: Sat, 29 Jan 2022 16:55:44 -0500 Subject: [PATCH 03/10] update workflows --- .github/workflows/main.yml | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 552f0bcf..018e1e24 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -52,10 +52,16 @@ jobs: shell: Rscript {0} - name: Install reticulate 2 run: | - library('reticulate') - py_config() - use_python("/usr/local/bin/python3") - virtualenv_create("r-reticulate") + if: matrix.os == 'macos-latest' + library('reticulate') + py_config() + use_python("/usr/local/bin/python3") + virtualenv_create("r-reticulate") + if: matrix.os == 'ubuntu-latest' + library('reticulate') + py_config() + use_python("/usr/bin/python3") + virtualenv_create("r-reticulate") shell: sudo -E Rscript {0} - name: Install reticulate 3 run: | From 764c899b46cb7b025fec22404c3cecb4d1bdf707 Mon Sep 17 00:00:00 2001 From: marouenbg Date: Sat, 29 Jan 2022 17:01:49 -0500 Subject: [PATCH 04/10] update workfolw --- .github/workflows/main.yml | 21 ++++++++++----------- 1 file changed, 10 insertions(+), 11 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 018e1e24..e9a378ba 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -51,17 +51,16 @@ jobs: library('reticulate') shell: Rscript {0} - name: Install reticulate 2 - run: | - if: matrix.os == 'macos-latest' - library('reticulate') - py_config() - use_python("/usr/local/bin/python3") - virtualenv_create("r-reticulate") - if: matrix.os == 'ubuntu-latest' - library('reticulate') - py_config() - use_python("/usr/bin/python3") - virtualenv_create("r-reticulate") + if: matrix.os == 'macos-latest' + library('reticulate') + py_config() + use_python("/usr/local/bin/python3") + virtualenv_create("r-reticulate") + if: matrix.os == 'ubuntu-latest' + library('reticulate') + py_config() + use_python("/usr/bin/python3") + virtualenv_create("r-reticulate") shell: sudo -E Rscript {0} - name: Install reticulate 3 run: | From 7180ebeafd607c21c4437c316075ffc4d320e96e Mon Sep 17 00:00:00 2001 From: marouenbg Date: Sat, 29 Jan 2022 17:03:24 -0500 Subject: [PATCH 05/10] update workfolw --- .github/workflows/main.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index e9a378ba..5a390d88 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -52,11 +52,13 @@ jobs: shell: Rscript {0} - name: Install reticulate 2 if: matrix.os == 'macos-latest' + run: | library('reticulate') py_config() use_python("/usr/local/bin/python3") virtualenv_create("r-reticulate") if: matrix.os == 'ubuntu-latest' + run: | library('reticulate') py_config() use_python("/usr/bin/python3") From 5076cf796add9f7ae303a27c66f0f94ac8367276 Mon Sep 17 00:00:00 2001 From: marouenbg Date: Sat, 29 Jan 2022 17:06:26 -0500 Subject: [PATCH 06/10] update workfolw --- .github/workflows/main.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 5a390d88..cf7dda8d 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -57,6 +57,7 @@ jobs: py_config() use_python("/usr/local/bin/python3") virtualenv_create("r-reticulate") + shell: sudo -E Rscript {0} if: matrix.os == 'ubuntu-latest' run: | library('reticulate') From 18af94dd2e8ea4ab385c0d2ac0b2cc694f58c6f9 Mon Sep 17 00:00:00 2001 From: marouenbg Date: Sat, 29 Jan 2022 17:07:55 -0500 Subject: [PATCH 07/10] update workfolw --- .github/workflows/main.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index cf7dda8d..de1d8602 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -50,7 +50,7 @@ jobs: install.packages('reticulate', repos = "http://cran.us.r-project.org") library('reticulate') shell: Rscript {0} - - name: Install reticulate 2 + - name: Install reticulate 2-1 if: matrix.os == 'macos-latest' run: | library('reticulate') @@ -58,6 +58,7 @@ jobs: use_python("/usr/local/bin/python3") virtualenv_create("r-reticulate") shell: sudo -E Rscript {0} + - name: Install reticulate 2-2 if: matrix.os == 'ubuntu-latest' run: | library('reticulate') From 0f09c0d98f594c8526e62cd02e9318ed377239f5 Mon Sep 17 00:00:00 2001 From: Marouen Date: Sat, 29 Jan 2022 18:11:57 -0500 Subject: [PATCH 08/10] Update main.yml --- .github/workflows/main.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index de1d8602..c6f27b60 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -59,8 +59,8 @@ jobs: virtualenv_create("r-reticulate") shell: sudo -E Rscript {0} - name: Install reticulate 2-2 - if: matrix.os == 'ubuntu-latest' - run: | + if: matrix.os == 'ubuntu-latest' + run: | library('reticulate') py_config() use_python("/usr/bin/python3") From 7af599896ee434fc1d7de3ad6fea71c32dc9fc7f Mon Sep 17 00:00:00 2001 From: Marouen Date: Sat, 29 Jan 2022 18:30:17 -0500 Subject: [PATCH 09/10] Update main.yml --- .github/workflows/main.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index c6f27b60..8e99e7d1 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -82,7 +82,6 @@ jobs: - name: Check run: | library('reticulate') - use_condaenv("r-reticulate") py_config() rcmdcheck::rcmdcheck(args = c("--no-manual","--ignore-vignettes"), error_on = "error", build_args="--no-build-vignettes") shell: sudo -E Rscript {0} From 14e87e95d27d772969e842e1523e4b49619106e7 Mon Sep 17 00:00:00 2001 From: Marouen Date: Sat, 29 Jan 2022 18:51:13 -0500 Subject: [PATCH 10/10] Update main.yml --- .github/workflows/main.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 8e99e7d1..c8ed5506 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -88,7 +88,6 @@ jobs: - name: Report coverage run: | library('reticulate') - use_condaenv("r-reticulate") py_config() covr::codecov() shell: sudo -E Rscript {0}