Added R packages gap, grain, pcalg, xref #12586

bioconda · Dec 20, 2018 · 37ee57e · 37ee57e
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diff --git a/recipes/r-gap/build.sh b/recipes/r-gap/build.sh
@@ -0,0 +1,9 @@
+if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then
+  export DISABLE_AUTOBREW=1
+  mv DESCRIPTION DESCRIPTION.old
+  grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
+  $R CMD INSTALL --build .
+else
+  mkdir -p $PREFIX/lib/R/library/gap
+  mv * $PREFIX/lib/R/library/gap
+fi
diff --git a/recipes/r-gap/meta.yaml b/recipes/r-gap/meta.yaml
@@ -0,0 +1,81 @@
+{% set version = '1.1-22' %}
+
+{% set posix = 'm2-' if win else '' %}
+{% set native = 'm2w64-' if win else '' %}
+
+package:
+  name: r-gap
+  version: {{ version|replace("-", "_") }}
+
+source:
+
+  url:
+    - {{ cran_mirror }}/src/contrib/gap_{{ version }}.tar.gz
+    - {{ cran_mirror }}/src/contrib/Archive/gap/gap_{{ version }}.tar.gz
+  sha256: 71a691aac9ce29bfcf1159eacba1866c8571b781f68fb32a3e52fb8584f03ef7
+
+build:
+  merge_build_host: True  # [win]
+
+  number: 0
+  skip: true  # [win32]
+
+  rpaths:
+    - lib/R/lib/
+    - lib/
+
+requirements:
+  build:
+    - {{ compiler('c') }}        # [not win]
+    - {{ compiler('fortran') }}  # [not win]
+    - {{native}}toolchain        # [win]
+    - {{posix}}filesystem        # [win]
+    - {{posix}}make
+    - {{posix}}sed               # [win]
+    - {{posix}}coreutils         # [win]
+    - {{posix}}zip               # [win]
+
+  host:
+    - r-base
+
+  run:
+    - r-base
+    - {{native}}gcc-libs         # [win]
+
+test:
+  commands:
+    - $R -e "library('gap')"           # [not win]
+    - "\"%R%\" -e \"library('gap')\""  # [win]
+
+about:
+  home: https://jinghuazhao.github.io
+  license: GPL (>= 2)
+  summary: It is designed as an integrated package for genetic data analysis of both population
+    and family data. Currently, it contains functions for sample size calculations of
+    both population-based and family-based designs, probability of familial disease
+    aggregation, kinship calculation, statistics in linkage analysis, and association
+    analysis involving genetic markers including haplotype analysis with or without
+    environmental covariates.
+  license_family: GPL3
+  license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3'  # [unix]
+  license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3'  # [win]
+  license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3'  # [unix]
+  license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3'  # [win]
+extra:
+  recipe-maintainers:
+    - MathiasHaudgaard
+    - FrodePedersen
+    - ArneKr
+    - johanneskoester
+    - bgruening
+    - daler
+    - jdblischak
+extra:
+  recipe-maintainers:
+    - MathiasHaudgaard
+    - FrodePedersen
+    - ArneKr
+    - johanneskoester
+    - bgruening
+    - daler
+    - jdblischak
diff --git a/recipes/r-grain/build.sh b/recipes/r-grain/build.sh
@@ -0,0 +1,9 @@
+if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then
+  export DISABLE_AUTOBREW=1
+  mv DESCRIPTION DESCRIPTION.old
+  grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
+  $R CMD INSTALL --build .
+else
+  mkdir -p $PREFIX/lib/R/library/gRain
+  mv * $PREFIX/lib/R/library/gRain
+fi
diff --git a/recipes/r-grain/meta.yaml b/recipes/r-grain/meta.yaml
@@ -0,0 +1,93 @@
+{% set version = '1.3-0' %}
+
+{% set posix = 'm2-' if win else '' %}
+{% set native = 'm2w64-' if win else '' %}
+
+package:
+  name: r-grain
+  version: {{ version|replace("-", "_") }}
+
+source:
+
+  url:
+    - {{ cran_mirror }}/src/contrib/gRain_{{ version }}.tar.gz
+    - {{ cran_mirror }}/src/contrib/Archive/gRain/gRain_{{ version }}.tar.gz
+  sha256: 5e1acec4fec41079242fb4e08619c8bd74ea5620ff7c8b54e06822e8af216775
+
+build:
+  merge_build_host: True  # [win]
+
+  number: 0
+  skip: true  # [win32]
+
+  rpaths:
+    - lib/R/lib/
+    - lib/
+
+requirements:
+  build:
+    - {{ compiler('c') }}        # [not win]
+    - {{ compiler('cxx') }}      # [not win]
+    - {{native}}toolchain        # [win]
+    - {{posix}}filesystem        # [win]
+    - {{posix}}make
+    - {{posix}}sed               # [win]
+    - {{posix}}coreutils         # [win]
+    - {{posix}}zip               # [win]
+
+  host:
+    - r-base
+    - r-rcpp >=0.11.1
+    - r-rcpparmadillo
+    - r-rcppeigen
+    - r-functional
+    - r-grbase >=1.7_2
+    - r-graph
+    - r-igraph
+    - r-magrittr
+
+  run:
+    - r-base
+    - {{native}}gcc-libs         # [win]
+    - r-rcpp >=0.11.1
+    - r-rcpparmadillo
+    - r-rcppeigen
+    - r-functional
+    - r-grbase >=1.7_2
+    - r-graph
+    - r-igraph
+    - r-magrittr
+
+test:
+  commands:
+    - $R -e "library('gRain')"           # [not win]
+    - "\"%R%\" -e \"library('gRain')\""  # [win]
+
+about:
+  home: http://people.math.aau.dk/~sorenh/software/gR/
+  license: GPL (>= 2)
+  summary: Probability propagation in graphical independence networks, also known as Bayesian
+    networks or probabilistic expert systems.
+  license_family: GPL3
+  license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3'  # [unix]
+  license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3'  # [win]
+  license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3'  # [unix]
+  license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3'  # [win]
+extra:
+  recipe-maintainers:
+    - MathiasHaudgaard
+    - FrodePedersen
+    - ArneKr
+    - johanneskoester
+    - bgruening
+    - daler
+    - jdblischak
+extra:
+  recipe-maintainers:
+    - MathiasHaudgaard
+    - FrodePedersen
+    - ArneKr
+    - johanneskoester
+    - bgruening
+    - daler
+    - jdblischak
diff --git a/recipes/r-pcalg/build.sh b/recipes/r-pcalg/build.sh
@@ -0,0 +1,9 @@
+if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then
+  export DISABLE_AUTOBREW=1
+  mv DESCRIPTION DESCRIPTION.old
+  grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
+  $R CMD INSTALL --build .
+else
+  mkdir -p $PREFIX/lib/R/library/pcalg
+  mv * $PREFIX/lib/R/library/pcalg
+fi
diff --git a/recipes/r-pcalg/meta.yaml b/recipes/r-pcalg/meta.yaml
@@ -0,0 +1,114 @@
+{% set version = '2.6-0' %}
+
+{% set posix = 'm2-' if win else '' %}
+{% set native = 'm2w64-' if win else '' %}
+
+package:
+  name: r-pcalg
+  version: {{ version|replace("-", "_") }}
+
+source:
+
+  url:
+    - {{ cran_mirror }}/src/contrib/pcalg_{{ version }}.tar.gz
+    - {{ cran_mirror }}/src/contrib/Archive/pcalg/pcalg_{{ version }}.tar.gz
+  sha256: 2ed97698a0c5bdee7fa499504eb774b589067e03b27bb4ec18b49baf607cacf5
+
+build:
+  merge_build_host: True  # [win]
+  number: 0
+  skip: true  # [win32]
+
+  rpaths:
+    - lib/R/lib/
+    - lib/
+
+requirements:
+  build:
+    - {{ compiler('c') }}        # [not win]
+    - {{ compiler('cxx') }}      # [not win]
+    - {{native}}toolchain        # [win]
+    - {{posix}}filesystem        # [win]
+    - {{posix}}make
+    - {{posix}}sed               # [win]
+    - {{posix}}coreutils         # [win]
+    - {{posix}}zip               # [win]
+
+  host:
+    - r-base
+    - r-bh
+    - r-rbgl
+    - r-rcpp
+    - r-rcpparmadillo
+    - r-abind
+    - r-bdsmatrix
+    - r-clue
+    - r-corpcor
+    - r-dagitty
+    - r-fastica
+    - r-ggm
+    - r-graph
+    - r-igraph
+    - r-robustbase
+    - r-sfsmisc >=1.0_26
+    - r-vcd
+
+  run:
+    - r-base
+    - {{native}}gcc-libs         # [win]
+    - r-bh
+    - r-rbgl
+    - r-rcpp
+    - r-rcpparmadillo
+    - r-abind
+    - r-bdsmatrix
+    - r-clue
+    - r-corpcor
+    - r-dagitty
+    - r-fastica
+    - r-ggm
+    - r-graph
+    - r-igraph
+    - r-robustbase
+    - r-sfsmisc >=1.0_26
+    - r-vcd
+
+test:
+  commands:
+    - $R -e "library('pcalg')"           # [not win]
+    - "\"%R%\" -e \"library('pcalg')\""  # [win]
+
+about:
+  home: http://pcalg.r-forge.r-project.org/
+  license: GPL (>= 2)
+  summary: Functions for causal structure learning and causal inference using graphical models.
+    The main algorithms for causal structure learning are PC (for observational data
+    without hidden variables), FCI and RFCI (for observational data with hidden variables),
+    and GIES (for a mix of data from observational studies (i.e. observational data)
+    and data from experiments involving interventions (i.e. interventional data) without
+    hidden variables). For causal inference the IDA algorithm, the Generalized Backdoor
+    Criterion (GBC), the Generalized Adjustment Criterion (GAC) and some related functions
+    are implemented. Functions for incorporating background knowledge are provided.
+  license_family: GPL3
+  license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3'  # [unix]
+  license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3'  # [win]
+  license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3'  # [unix]
+  license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3'  # [win]
+extra:
+  recipe-maintainers:
+    - MathiasHaudgaard
+    - FrodePedersen
+    - ArneKr
+    - johanneskoester
+    - bgruening
+    - daler
+    - jdblischak
+extra:
+  recipe-maintainers:
+    - MathiasHaudgaard
+    - FrodePedersen
+    - ArneKr
+    - johanneskoester
+    - bgruening
+    - daler
+    - jdblischak