Unverified Commit 81f1305b authored by Kamil Slowikowski's avatar Kamil Slowikowski Committed by GitHub
Browse files

Merge pull request #19 from AustinHartman/presto 

Passes `R CMD check --as-cran`
parents 052085db 91161a98

.Rbuildignore

+2 −1
Original line number Diff line number Diff line
@@ -2,3 +2,4 @@ 
^cran-comments.md$

^CRAN-RELEASE$

^LICENSE$

^.github$
 
 No newline at end of file

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

+8 −7
Original line number Diff line number Diff line
@@ -18,12 +18,11 @@ jobs: 
      fail-fast: false

      matrix:

        config:

          - {os: windows-latest, r: '4.0'}

          - {os: macOS-latest, r: '3.6'}

          - {os: macOS-latest, r: '4.0'}

          - {os: windows-latest, r: '4.1'}

          - {os: macOS-latest, r: '4.1'}

          - {os: macOS-latest, r: 'devel'}

          - {os: ubuntu-16.04, r: '3.6', rspm: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}

          - {os: ubuntu-16.04, r: '4.0', rspm: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}

          - {os: ubuntu-22.04, r: '4.1'}

          - {os: ubuntu-20.04, r: '4.1'}



    env:

      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -33,11 +32,12 @@ jobs: 
    steps:

      - uses: actions/checkout@v2



      - uses: r-lib/actions/setup-r@master

      - uses: r-lib/actions/setup-r@v2.3.0

        with:

          r-version: ${{ matrix.config.r }}

          use-public-rspm: true



      - uses: r-lib/actions/setup-pandoc@master

      - uses: r-lib/actions/setup-pandoc@v2.3.0



      - name: Query dependencies

        run: |
@@ -61,6 +61,7 @@ jobs: 
          Rscript -e "remotes::install_github('r-hub/sysreqs')"

          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")

          sudo -s eval "$sysreqs"



      - name: Install dependencies

        run: |

          remotes::install_deps(dependencies = TRUE)

.gitignore

+0 −1
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@@ -4,6 +4,5 @@ inst/doc 
.RData

src/*.so

src/*.o

**/*.html

.ipynb_checkpoints

**/.ipynb_checkpoints

DESCRIPTION

+7 −5
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@@ -13,6 +13,7 @@ Authors@R: c( 
    )

Description: Scalable implementation of the Wilcoxon rank sum test and auROC statistic. Interfaces to dense and sparse matrices, as well as genomics analysis frameworks Seurat and SingleCellExperiment. 

License: GPL-3

LazyData: true

Encoding: UTF-8

Depends: R (>= 3.4.0), Rcpp, data.table

LinkingTo: Rcpp, RcppArmadillo
@@ -21,13 +22,13 @@ Imports: 
    dplyr, 

    methods,

    tidyr, 

    reshape2,

    purrr,

    tibble,

    Matrix,

    rlang,

    stats, 

    utils,

    DESeq2

RoxygenNote: 6.1.1

    utils

RoxygenNote: 7.2.1

Suggests: 

    knitr,

    rmarkdown,
@@ -36,6 +37,7 @@ Suggests: 
    SingleCellExperiment, 

    SummarizedExperiment,

    broom,

    BiocStyle

    BiocStyle,

    DESeq2

NeedsCompilation: yes

VignetteBuilder: knitr

NAMESPACE

+8 −0
Original line number Diff line number Diff line
@@ -17,6 +17,7 @@ export(nnzeroGroups) 
export(pseudobulk_deseq2)

export(pseudobulk_one_vs_all)

export(pseudobulk_pairwise)

export(pseudobulk_within)

export(rank_matrix)

export(sumGroups)

export(summarize_dge_pairs)
@@ -32,12 +33,19 @@ importFrom(Matrix,Matrix) 
importFrom(Rcpp,evalCpp)

importFrom(Rcpp,loadModule)

importFrom(Rcpp,sourceCpp)

importFrom(data.table,data.table)

importFrom(dplyr,"%>%")

importFrom(dplyr,arrange)

importFrom(dplyr,mutate)

importFrom(dplyr,select)

importFrom(methods,as)

importFrom(methods,is)

importFrom(purrr,reduce)

importFrom(rlang,.data)

importFrom(stats,as.formula)

importFrom(stats,p.adjust)

importFrom(stats,pnorm)

importFrom(stats,wilcox.test)

importFrom(tibble,rownames_to_column)

importFrom(utils,head)

useDynLib(presto)

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