Added compatibility to Java 17+

.github/workflows/check-bioc.yml

@@ -39,7 +39,7 @@ env:
   run_pkgdown: 'false'
   has_RUnit: 'false'
   cache-version: 'cache-v1'
-  run_docker: 'true'
+  run_docker: 'false'
 
 jobs:
   build-check:
@@ -52,9 +52,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.1', bioc: '3.14', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.1', bioc: '3.14'}
-          - { os: windows-latest, r: '4.1', bioc: '3.14'}
+          - { os: ubuntu-latest, r: '4.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:RELEASE_3_16", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: '4.2', bioc: '3.16'}
+          - { os: windows-latest, r: '4.2', bioc: '3.16'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -79,20 +79,20 @@ jobs:
       ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
       ## If they update their steps, we will also need to update ours.
       - name: Checkout Repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       ## R is already included in the Bioconductor docker images
       - name: Setup R from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-r@master
+        uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
 
       ## pandoc is already included in the Bioconductor docker images
       - name: Setup pandoc from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-pandoc@master
+        uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -102,19 +102,19 @@ jobs:
 
       - name: Restore R package cache
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.1-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.1-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-
 
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'
@@ -176,7 +176,7 @@ jobs:
           gha_repos <- if(
               .Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin"
           ) c(
-              "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.14/bioc",
+              "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.16/bioc",
               BiocManager::repositories()
               ) else BiocManager::repositories()
 
@@ -218,7 +218,7 @@ jobs:
       - name: Install pkgdown
         if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: |
-          remotes::install_github("r-lib/pkgdown")
+          remotes::install_cran("pkgdown")
         shell: Rscript {0}
 
       - name: Session info
@@ -236,7 +236,7 @@ jobs:
           options(crayon.enabled = TRUE)
           rcmdcheck::rcmdcheck(
               args = c("--no-manual", "--no-vignettes", "--timings"),
-              build_args = c("--no-manual", "--keep-empty-dirs", "--resave-data"),
+              build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
               error_on = "warning",
               check_dir = "check"
           )
@@ -275,31 +275,47 @@ jobs:
         if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: R CMD INSTALL .
 
-      - name: Build and deploy pkgdown site
+      - name: Build pkgdown site
         if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
-        run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "[email protected]"
-          Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
-        shell: bash {0}
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
         ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
         ## at least one locally before this will work. This creates the gh-pages
         ## branch (erasing anything you haven't version controlled!) and
         ## makes the git history recognizable by pkgdown.
 
+      - name: Install deploy dependencies
+        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        run: |
+          apt-get update && apt-get -y install rsync
+
+      - name: Deploy pkgdown site to GitHub pages 🚀
+        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        uses: JamesIves/github-pages-deploy-action@releases/v4
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
+
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-devel-r-4.1-results
+          name: ${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-results
           path: check
 
-      - name: Build & push Docker image v5
-        if: runner.os == 'Linux'
-        uses: mr-smithers-excellent/docker-build-push@v5   
+        ## Note that DOCKER_PASSWORD is really a token for your dockerhub
+        ## account, not your actual dockerhub account password.
+        ## This comes from
+        ## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html#6-add-secrets-to-github-repo
+        ## Check https://github.com/docker/build-push-action/tree/releases/v1
+        ## for more details.
+      - uses: docker/build-push-action@v1
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' "
         with:
-          image: shraddhapai/netdx_devenv          
-          tags: latest
-          registry: docker.io
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
+          repository: realpailab/netdx
+          tag_with_ref: true
+          tag_with_sha: true
+          tags: latest

.github/workflows/push-docker.yml

@@ -0,0 +1,24 @@
+name: Docker Build
+
+on:
+  push:
+    branches: [ master ]
+
+jobs: 
+  build: 
+
+    runs-on: ubuntu-latest
+
+    steps: 
+    - uses: actions/checkout@v2
+      name: Check out code
+
+    - uses: mr-smithers-excellent/docker-build-push@v5
+      name: Build and push Docker image
+      with:
+        image: realpailab/netdx 
+        registry: docker.io
+        addLatest: 'true'
+        addTimestamp: 'true'        
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}

.gitignore

@@ -4,3 +4,4 @@
 .Ruserdata
 doc
 Meta
+inst/doc

CITATION.cff

@@ -0,0 +1,30 @@
+# YAML 1.2
+---
+authors: 
+  -
+    family-names: Pai
+    given-names: Shraddha
+  -
+    family-names: Shah
+    given-names: Ahmad
+  -
+    family-names: Hui
+    given-names: Shirley
+  -
+    family-names: Isserlin
+    given-names: Ruth
+  -
+    family-names: Kaka
+    given-names: Hussam
+  -
+    family-names: Bader
+    given-names: Gary
+cff-version: "1.1.0"
+date-released: 2019
+doi: "10.15252/msb.20188497"
+license: MIT
+message: "If you use this software, please cite it using these metadata."
+repository-code: "https://github.com/RealPaiLab/netDx"
+title: "netDx: Network-based patient classifier"
+version: "1.5.5"
+...

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: netDx
 Title: Network-based patient classifier
-Version: 1.5.3
+Version: 1.7.1
 Authors@R: c(person("Shraddha", "Pai", 
 		email = "[email protected]", 
 		role = c("aut", "cre"),
@@ -9,6 +9,8 @@ Authors@R: c(person("Shraddha", "Pai",
 	person("Ahmad","Shah", role="aut"),
 	person("Luca","Giudice",role="aut"),
 	person("Shirley","Hui",role="aut"),
+	person("Anne","Nøhr",role="ctb"),
+	person("Indy","Ng",role="ctb"),
 	person("Ruth","Isserlin",role="aut"),
 	person("Hussam","Kaka", role="aut"),
 	person("Gary","Bader",role="aut"))
@@ -17,15 +19,11 @@ Depends:
     R (>= 3.6)
 Suggests: 
   curatedTCGAData,
-	TCGAutils,
 	rmarkdown,
 	testthat,
 	knitr,
 	BiocStyle,
-	RCy3,
-	clusterExperiment,
-	netSmooth,
-	scater
+	RCy3
 Imports: ROCR,pracma,ggplot2,glmnet,igraph,reshape2,
 	parallel,stats,utils,MultiAssayExperiment,graphics,grDevices,
 	methods,BiocFileCache,GenomicRanges,

NAMESPACE

@@ -12,9 +12,12 @@ export(compileFeatureScores)
 export(compileFeatures)
 export(confusionMatrix)
 export(convertProfileToNetworks)
+export(convertToMAE)
 export(countIntType)
 export(countIntType_batch)
 export(countPatientsInNet)
+export(createInputForFeatureNetworkView)
+export(createNetFuncFromSimList)
 export(createPSN_MultiData)
 export(dataList2List)
 export(enrichLabelNets)
@@ -34,15 +37,13 @@ export(getPerformance)
 export(getRegionOL)
 export(getResults)
 export(getSimilarity)
-export(makeInputForEnrichmentMap)
 export(makePSN_NamedMatrix)
 export(makePSN_RangeSets)
 export(makeQueries)
 export(makeSymmetric)
 export(mapNamedRangesToSets)
 export(normDiff)
 export(perfCalc)
-export(plotEmap)
 export(plotIntegratedPatientNetwork)
 export(plotPerf)
 export(plotPerf_multi)
@@ -59,14 +60,14 @@ export(setupFeatureDB)
 export(sim.eucscale)
 export(sim.pearscale)
 export(simpleCap)
-export(smoothMutations_LabelProp)
 export(sparsify2)
 export(sparsify3)
 export(splitTestTrain)
 export(splitTestTrain_resampling)
+export(subsampleValidationData)
 export(tSNEPlotter)
-export(thresholdSmoothedMutations)
 export(updateNets)
+export(viewSelectedFeaturesAsNetworks)
 export(writeNetsSIF)
 export(writeQueryBatchFile)
 export(writeQueryFile)

NEWS

@@ -1,10 +1,32 @@
-netDx 1.5.3
+3.14 RELEASE 
+==================
+
+netDx 1.7.1
+==================
+* Added vignette showing how to view top features as connected networks in Cytoscape (Enrichment Map). 
+* Improved Java support. Includes:
+  * Prompt to users to install Java if not installed, and requirement check for Java 16 or lower.
+  * Feature selection with Java 12+ resulted in an "illegal access" error due to a change in how Java handles reflection. netDx sidesteps
+  the error for Java 9-16 but cannot do so for Java 17. Java 12-16 should now work with feature selection.
+* plotPerf() now provides the option to not plot the ROC and PR curves with a drawPlot parameter.
+
+netDx 1.5.10
+==================
+* Functions to create network visualizations of top-scoring functions renamed to better reflect function.
+  * plotEMap() -> viewSelectedFeaturesAsNetworks 
+  * makeInputForEnrichmentMap() -> createInputForFeatureNetworkView()
+
+netDx 1.5.9
+==================
+* Ability to smooth somatic mutations over an interaction network via (smoothMutations_LabelProp) has been temporarily removed. This function made software install challenging on machines without C++ compilers as it relies on clusterExperiment. The latter can only be compiled from source. This functionality will be added back when doing so does not complicate the install. It is unclear whether users want to routinely use this functionality.
+
+netDx 1.5.8
 ==================
 * Moved RCy3, scater, clusterExperiment and netSmooth to "Suggests" to reduce dependency burden
 * Sped up vignettes by limiting all to binary classification and limiting number of layers
 * Removed TL;DR from vignettes as usefulness in question but maintainance high.
 
-Developers notes:
+Developer notes:
 -------------------
 * Added Dockerfile and Github Actions for automated testing
 * GHA auto-generates a Docker image with netDx which gets pushed to shraddhapai/netdx_devenv