[WIP] Reader for new logging format

.Rbuildignore

@@ -1,11 +1,11 @@
-^\.travis\.yml$
-^.*\.Rproj$
-^\.Rproj\.user$
-^cran-comments\.md$
-^NEWS\.md$
-^\.vscode$
-^\.vs*$
-^_config\.yml$
-^LICENSE\.md$
-^misc*$
-^\.github$
+^\.travis\.yml$
+^.*\.Rproj$
+^\.Rproj\.user$
+^cran-comments\.md$
+^NEWS\.md$
+^\.vscode$
+^\.vs*$
+^_config\.yml$
+^LICENSE\.md$
+^misc*$
+^\.github$

.github/workflows/R-CMD-check.yaml

@@ -1,91 +1,91 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
-on:
-  push:
-    branches:
-      - main
-      - master
-  pull_request:
-    branches:
-      - main
-      - master
-
-name: R-CMD-check
-
-jobs:
-  R-CMD-check:
-    runs-on: ${{ matrix.config.os }}
-
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
-    strategy:
-      fail-fast: false
-      matrix:
-        config:
-          - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-
-    env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
-    steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-r@v1
-        with:
-          r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Restore R package cache
-        uses: actions/cache@v2
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install X11 dependencies on MacOS
-        if: runner.os == 'macOS'
-        run: |
-          brew install xquartz --cask
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_bioc('ComplexHeatmap')
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - name: Install X11 dependencies on MacOS
+        if: runner.os == 'macOS'
+        run: |
+          brew install xquartz --cask
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_bioc('ComplexHeatmap')
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.gitignore

@@ -1,26 +1,26 @@
-*.csv
-*.o
-*.so
-*.dll
-*.log
-*.RData
-*.Rhistory
-*.Rbuildignore
-*.bk
-*.pdf
-*.html
-.*
-
-!/.Rbuildignore
-!/.gitignore
-__pycache__
-rawdata/
-test/
-rsconnect/
-tmp/
-tmp2/
-rawdata/
-extract_data.R
-.Rproj.user
-*.Rproj
-.Rhistory
+*.csv
+*.o
+*.so
+*.dll
+*.log
+*.RData
+*.Rhistory
+*.Rbuildignore
+*.bk
+*.pdf
+*.html
+.*
+
+!/.Rbuildignore
+!/.gitignore
+__pycache__
+rawdata/
+test/
+rsconnect/
+tmp/
+tmp2/
+rawdata/
+extract_data.R
+.Rproj.user
+*.Rproj
+.Rhistory

DESCRIPTION

@@ -1,57 +1,59 @@
-Package: IOHanalyzer
-Type: Package
-Title: Data Analysis Part of 'IOHprofiler'
-Version: 0.1.5.2
-Author: Hao Wang [cre, aut], Diederick Vermetten [aut], Carola Doerr [aut], Thomas Bäck [aut]
-Maintainer: Hao Wang <h.wang@liacs.leidenuniv.nl>
-Authors@R: c(
-    person("Hao", "Wang", email = "h.wang@liacs.leidenuniv.nl", role = c("cre","aut")),
-    person("Diederick", "Vermetten", email="d.vermetten@gmail.com", role = "aut"),
-    person("Carola", "Doerr", email = "Carola.Doerr@mpi-inf.mpg.de", role = "aut"),
-    person("Thomas", "Bäck", email="t.h.w.baeck@liacs.leidenuniv.nl", role = "aut"))
-Description: The data analysis module for the Iterative Optimization Heuristics
-    Profiler ('IOHprofiler'). This module provides statistical analysis methods for the 
-    benchmark data generated by optimization heuristics, which can be visualized through a 
-    web-based interface. The benchmark data is usually generated by the 
-    experimentation module, called 'IOHexperimenter'. 'IOHanalyzer' also supports
-    the widely used 'COCO' (Comparing Continuous Optimisers) data format for benchmarking.
-License: BSD_3_clause + file LICENSE
-Encoding: UTF-8
-LazyData: true
-URL: http://iohprofiler.liacs.nl, https://github.com/IOHprofiler/IOHAnalyzer
-BugReports: https://github.com/IOHprofiler/IOHAnalyzer/issues
-Imports: 
-  magrittr,
-  dplyr,
-  data.table,
-  ggplot2,
-  plotly,
-  colorspace,
-  colorRamps,
-  RColorBrewer,
-  shiny,
-  markdown,
-  reshape2,
-  shinyjs,
-  colourpicker,
-  bsplus,
-  DT,
-  kableExtra,
-  stringi,
-  httr,
-  knitr
-LinkingTo: Rcpp
-SystemRequirements: C++11
-RoxygenNote: 7.0.0
-Suggests: 
-  Rcpp,
-  testthat,
-  withr,
-  shinydashboard,
-  ComplexHeatmap,
-  grid,
-  keyring,
-  PlayerRatings,
-  xtable,
-  igraph
-Depends: R (>= 2.10)
+Package: IOHanalyzer
+Type: Package
+Title: Data Analysis Part of 'IOHprofiler'
+Version: 0.1.6.0
+Author: Hao Wang [cre, aut], Diederick Vermetten [aut], Carola Doerr [aut], Thomas Bäck [aut]
+Maintainer: Hao Wang <h.wang@liacs.leidenuniv.nl>
+Authors@R: c(
+    person("Hao", "Wang", email = "h.wang@liacs.leidenuniv.nl", role = c("cre","aut")),
+    person("Diederick", "Vermetten", email="d.vermetten@gmail.com", role = "aut"),
+    person("Carola", "Doerr", email = "Carola.Doerr@mpi-inf.mpg.de", role = "aut"),
+    person("Thomas", "Bäck", email="t.h.w.baeck@liacs.leidenuniv.nl", role = "aut"))
+Description: The data analysis module for the Iterative Optimization Heuristics
+    Profiler ('IOHprofiler'). This module provides statistical analysis methods for the 
+    benchmark data generated by optimization heuristics, which can be visualized through a 
+    web-based interface. The benchmark data is usually generated by the 
+    experimentation module, called 'IOHexperimenter'. 'IOHanalyzer' also supports
+    the widely used 'COCO' (Comparing Continuous Optimisers) data format for benchmarking.
+License: BSD_3_clause + file LICENSE
+Encoding: UTF-8
+LazyData: true
+URL: http://iohprofiler.liacs.nl, https://github.com/IOHprofiler/IOHAnalyzer
+BugReports: https://github.com/IOHprofiler/IOHAnalyzer/issues
+Imports: 
+  magrittr,
+  dplyr,
+  data.table,
+  ggplot2,
+  plotly,
+  colorspace,
+  colorRamps,
+  RColorBrewer,
+  shiny,
+  markdown,
+  reshape2,
+  shinyjs,
+  colourpicker,
+  bsplus,
+  DT,
+  kableExtra,
+  stringi,
+  httr,
+  knitr,
+  methods,
+  rjson
+LinkingTo: Rcpp
+SystemRequirements: C++11
+RoxygenNote: 7.0.0
+Suggests: 
+  Rcpp,
+  testthat,
+  withr,
+  shinydashboard,
+  ComplexHeatmap,
+  grid,
+  keyring,
+  PlayerRatings,
+  xtable,
+  igraph
+Depends: R (>= 2.10)

LICENSE

@@ -1,3 +1,3 @@
-YEAR: 2019
-COPYRIGHT HOLDER: Hao Wang
+YEAR: 2019
+COPYRIGHT HOLDER: Hao Wang
 ORGANIZATION: Leiden University