From 7529469e6e2a46b5cef7d14c597261ab8bae1624 Mon Sep 17 00:00:00 2001 From: jack89roberts Date: Tue, 17 May 2022 13:52:28 +0100 Subject: [PATCH 01/20] touch to check if travis is working --- tmp_travis_trigger | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 tmp_travis_trigger diff --git a/tmp_travis_trigger b/tmp_travis_trigger new file mode 100644 index 00000000..e69de29b From d6f384ffd1f4b5a9c5934818a65454100d0c997b Mon Sep 17 00:00:00 2001 From: Jack Roberts Date: Tue, 17 May 2022 15:14:39 +0100 Subject: [PATCH 02/20] switch Travis bad to travis-ci.com --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 43b3164f..d977d62a 100755 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ Until this package hits release 1.0 anything can change with no notice. [![Project Status: WIP - Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](http://www.repostatus.org/badges/latest/wip.svg)](http://www.repostatus.org/#wip) [![GitHub release](https://img.shields.io/github/release/alan-turing-institute/network-comparison.svg)](https://github.com/alan-turing-institute/network-comparison/releases/latest) -[![Travis](https://img.shields.io/travis/alan-turing-institute/network-comparison/master.svg)](https://travis-ci.org/alan-turing-institute/network-comparison/branches) +[![Travis](https://app.travis-ci.com/alan-turing-institute/network-comparison.svg?branch=master)](https://app.travis-ci.com/alan-turing-institute/network-comparison) [![Appveyor](https://ci.appveyor.com/api/projects/status/jn1a36c22vjw1l4d/branch/master?svg=true)](https://ci.appveyor.com/project/alan-turing-institute/network-comparison/branch/master) [![Codecov](https://img.shields.io/codecov/c/github/alan-turing-institute/network-comparison/master.svg)](https://codecov.io/gh/alan-turing-institute/network-comparison?branch=master) From ebf59b37674949e4d59eb07c8360e14c43d0c371 Mon Sep 17 00:00:00 2001 From: jack89roberts Date: Wed, 1 Jun 2022 10:25:53 +0100 Subject: [PATCH 03/20] run on R oldrel, release, and devel versions --- .travis.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.travis.yml b/.travis.yml index f8b09bb0..b5dd399f 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,4 +1,8 @@ language: r +r: + - oldrel + - release + - devel cache: packages sudo: false warnings_are_errors: false From 6d34b9f2971c253fbf88b971387e5b8617bbb6f3 Mon Sep 17 00:00:00 2001 From: jack89roberts Date: Wed, 1 Jun 2022 10:51:13 +0100 Subject: [PATCH 04/20] see if Travis will use R v4.1 and 4.2 if harcoded --- .travis.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index b5dd399f..66916a5e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,8 +1,7 @@ language: r r: - - oldrel - - release - - devel + - 4.1 + - 4.2 cache: packages sudo: false warnings_are_errors: false From e141bc3ac6a8896f61fa4d05f4c38f451d2e2b31 Mon Sep 17 00:00:00 2001 From: jack89roberts Date: Wed, 1 Jun 2022 15:28:25 +0100 Subject: [PATCH 05/20] try gh actions --- .github/workflows/main.yml | 42 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 .github/workflows/main.yml diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml new file mode 100644 index 00000000..9c2bf510 --- /dev/null +++ b/.github/workflows/main.yml @@ -0,0 +1,42 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [main, master] + pull_request: + branches: [main, master] + +name: test-coverage + +jobs: + R-CMD-check: + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + config: + - {os: ubuntu-latest, r: 'release'} + + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + + steps: + - uses: actions/checkout@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::covr + needs: coverage + + - name: Test coverage + run: covr::codecov(quiet = FALSE) + shell: Rscript {0} From 587b4c374ed0a923aff03bc46cbeab7009e3aff1 Mon Sep 17 00:00:00 2001 From: jack89roberts Date: Wed, 1 Jun 2022 15:49:32 +0100 Subject: [PATCH 06/20] add rcmdcheck --- .github/workflows/main.yml | 6 +++++- .travis.yml | 3 +-- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 9c2bf510..54bf057c 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -6,7 +6,7 @@ on: pull_request: branches: [main, master] -name: test-coverage +name: Package checks and coverage jobs: R-CMD-check: @@ -37,6 +37,10 @@ jobs: extra-packages: any::covr needs: coverage + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true + - name: Test coverage run: covr::codecov(quiet = FALSE) shell: Rscript {0} diff --git a/.travis.yml b/.travis.yml index 66916a5e..94cbf1f3 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,7 +1,6 @@ language: r r: - - 4.1 - - 4.2 + - release cache: packages sudo: false warnings_are_errors: false From 2c368c40ebd162546cb8bb4d4c9b99e6ce146619 Mon Sep 17 00:00:00 2001 From: jack89roberts Date: Wed, 1 Jun 2022 15:54:28 +0100 Subject: [PATCH 07/20] add rcmdcheck to setup dependencies --- .github/workflows/main.yml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 54bf057c..90b8b008 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -34,8 +34,12 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::covr - needs: coverage + extra-packages: | + any::rcmdcheck + any::covr + needs: | + check + coverage - uses: r-lib/actions/check-r-package@v2 with: From 5c26bbf58a8398fb05c3f7e2b5b128a3645b441e Mon Sep 17 00:00:00 2001 From: jack89roberts Date: Wed, 1 Jun 2022 16:50:12 +0100 Subject: [PATCH 08/20] placeholders for running on schedule and other versions --- .github/workflows/main.yml | 8 ++++-- .travis.yml | 24 ------------------ appveyor.yml | 50 -------------------------------------- tmp_travis_trigger | 0 4 files changed, 6 insertions(+), 76 deletions(-) delete mode 100644 .travis.yml delete mode 100644 appveyor.yml delete mode 100644 tmp_travis_trigger diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 90b8b008..8dfe5c33 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -5,6 +5,8 @@ on: branches: [main, master] pull_request: branches: [main, master] +# schedule: +# - cron: "6 6 * * 6" # run at 6:06 every Saturday name: Package checks and coverage @@ -19,7 +21,10 @@ jobs: matrix: config: - {os: ubuntu-latest, r: 'release'} - + #- {os: ubuntu-latest, r: 'oldrel'} + #- {os: ubuntu-latest, r: 'devel'} + #- {os: macOS-latest, r: 'release'} + #- {os: windows-latest, r: 'release'} env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} @@ -29,7 +34,6 @@ jobs: - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} - http-user-agent: ${{ matrix.config.http-user-agent }} use-public-rspm: true - uses: r-lib/actions/setup-r-dependencies@v2 diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 94cbf1f3..00000000 --- a/.travis.yml +++ /dev/null @@ -1,24 +0,0 @@ -language: r -r: - - release -cache: packages -sudo: false -warnings_are_errors: false - -r_packages: -- covr - -os: -- linux - -after_success: -- Rscript -e 'library(covr); codecov()' - -notifications: - slack: - on_success: change - on_failure: change - rooms: - secure: 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 - template: - - "Build <%{build_url}|#%{build_number}> (<%{compare_url}|%{commit}>) of %{repository}@%{branch} by %{author} %{result} in %{duration}. %{message}" \ No newline at end of file diff --git a/appveyor.yml b/appveyor.yml deleted file mode 100644 index 0232e911..00000000 --- a/appveyor.yml +++ /dev/null @@ -1,50 +0,0 @@ -# DO NOT CHANGE the "init" and "install" sections below - -# Download script file from GitHub -init: - ps: | - $ErrorActionPreference = "Stop" - Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1" - Import-Module '..\appveyor-tool.ps1' - -install: - ps: Bootstrap - -# Adapt as necessary starting from here - -build_script: - - travis-tool.sh install_deps - -test_script: - - travis-tool.sh run_tests - -on_failure: - - 7z a failure.zip *.Rcheck\* - - appveyor PushArtifact failure.zip - -artifacts: - - path: '*.Rcheck\**\*.log' - name: Logs - - - path: '*.Rcheck\**\*.out' - name: Logs - - - path: '*.Rcheck\**\*.fail' - name: Logs - - - path: '*.Rcheck\**\*.Rout' - name: Logs - - - path: '\*_*.tar.gz' - name: Bits - - - path: '\*_*.zip' - name: Bits - -notifications: - - provider: Slack - on_build_success: false - on_build_failure: false - on_build_status_changed: true - incoming_webhook: - secure: k56hsY5K++kvpU/bhF5r2YmgwSeTdGJVY8qnT8z9qRug/zgo50Ev8lB9kN4FT3vNJQpfmkDBOOlXe6XURHzaJPeTtDKKciAsXQe48IVkFVw= diff --git a/tmp_travis_trigger b/tmp_travis_trigger deleted file mode 100644 index e69de29b..00000000 From ba1410ce1d412b238063d9af971899cc4a957cc9 Mon Sep 17 00:00:00 2001 From: jack89roberts Date: Wed, 1 Jun 2022 17:20:32 +0100 Subject: [PATCH 09/20] move dplyr and phangorn to suggested dependencies --- .github/workflows/main.yml | 12 ++++++------ DESCRIPTION | 4 ++-- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 8dfe5c33..864c6781 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -5,8 +5,8 @@ on: branches: [main, master] pull_request: branches: [main, master] -# schedule: -# - cron: "6 6 * * 6" # run at 6:06 every Saturday + schedule: + - cron: "5 5 5 * *" # run at 05:05 on 5th day of each month name: Package checks and coverage @@ -21,10 +21,10 @@ jobs: matrix: config: - {os: ubuntu-latest, r: 'release'} - #- {os: ubuntu-latest, r: 'oldrel'} - #- {os: ubuntu-latest, r: 'devel'} - #- {os: macOS-latest, r: 'release'} - #- {os: windows-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel'} + - {os: ubuntu-latest, r: 'devel'} + - {os: macOS-latest, r: 'release'} + - {os: windows-latest, r: 'release'} env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} diff --git a/DESCRIPTION b/DESCRIPTION index 547cf8ef..98f92f88 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -20,11 +20,11 @@ Imports: purrr, lpSolve, plyr, - dplyr, pheatmap, Rcpp, - phangorn Suggests: + dplyr, + phangorn, testthat, knitr, rmarkdown, From d22565cfeaadcf1943f04631a84c0b802f74ba2b Mon Sep 17 00:00:00 2001 From: jack89roberts Date: Mon, 6 Jun 2022 09:58:17 +0100 Subject: [PATCH 10/20] setup pandoc and latex in actions --- .github/workflows/main.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 864c6781..298d9a50 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -36,6 +36,9 @@ jobs: r-version: ${{ matrix.config.r }} use-public-rspm: true + - uses: r-lib/actions/setup-pandoc@v2 + - uses: r-lib/actions/setup-tinytex@v2 + - uses: r-lib/actions/setup-r-dependencies@v2 with: extra-packages: | From 9bbd7394327d8bfcd6b08a2a2274efb3961e36d0 Mon Sep 17 00:00:00 2001 From: jack89roberts Date: Mon, 6 Jun 2022 10:41:00 +0100 Subject: [PATCH 11/20] remove space in docstring --- R/measures_net_dis.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/measures_net_dis.R b/R/measures_net_dis.R index f32e85a5..55931c09 100644 --- a/R/measures_net_dis.R +++ b/R/measures_net_dis.R @@ -395,7 +395,7 @@ netdis_one_to_many <- function(graph_1 = NULL, #' @param min_ego_edges Filter ego networks which have fewer #' than min_ego_edges edges (default 1). #' -#' @param binning_fn Function used to bin ego network densities. Takes edge \code{densities} +#' @param binning_fn Function used to bin ego network densities. Takes edge \code{densities} #' as its single argument, and returns a named list including, the input \code{densities}, the resulting bin \code{breaks} (vector of density bin limits), and the vector \code{interval_indexes} which states to what bin each of the individual elements in \code{densities} belongs to. #' ego network). If \code{NULL}, then the method \code{binned_densities_adaptive} with #' \code{min_counts_per_interval = 5} and \code{num_intervals = 100} is used From 2b6d48e791508018e79fd15c0332887ee31967b7 Mon Sep 17 00:00:00 2001 From: jack89roberts Date: Mon, 6 Jun 2022 11:24:00 +0100 Subject: [PATCH 12/20] [#140] remove += syntax fro, PKG_CPPFLAGS --- src/Makevars | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Makevars b/src/Makevars index 25761e11..1b86740a 100644 --- a/src/Makevars +++ b/src/Makevars @@ -1,2 +1,2 @@ CXX_STD = CXX11 -PKG_CPPFLAGS += -fno-fast-math -msse2 -mfpmath=sse -mstackrealign +PKG_CPPFLAGS = -fno-fast-math -msse2 -mfpmath=sse -mstackrealign From b2d31c04415c77ceb41ae1aed0344e118ff83087 Mon Sep 17 00:00:00 2001 From: jack89roberts Date: Mon, 6 Jun 2022 11:24:15 +0100 Subject: [PATCH 13/20] fix docstring spacing in netdis_many_to_many --- R/measures_net_dis.R | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/R/measures_net_dis.R b/R/measures_net_dis.R index 55931c09..d1120d03 100644 --- a/R/measures_net_dis.R +++ b/R/measures_net_dis.R @@ -380,7 +380,6 @@ netdis_one_to_many <- function(graph_1 = NULL, #' 3) NULL (default) - Expected counts will be calculated based on the properties of the #' query graphs themselves. (Geometric-Poisson approximation). #' -#' #' @param comparisons Which comparisons to perform between graphs. #' Can be "many-to-many" (all pairwise combinations) or "one-to-many" #' (compare first graph in graphs to all other graphs.) @@ -394,18 +393,17 @@ netdis_one_to_many <- function(graph_1 = NULL, #' #' @param min_ego_edges Filter ego networks which have fewer #' than min_ego_edges edges (default 1). -#' +#' #' @param binning_fn Function used to bin ego network densities. Takes edge \code{densities} #' as its single argument, and returns a named list including, the input \code{densities}, the resulting bin \code{breaks} (vector of density bin limits), and the vector \code{interval_indexes} which states to what bin each of the individual elements in \code{densities} belongs to. #' ego network). If \code{NULL}, then the method \code{binned_densities_adaptive} with -#' \code{min_counts_per_interval = 5} and \code{num_intervals = 100} is used -#' (Default: NULL). +#' \code{min_counts_per_interval = 5} and \code{num_intervals = 100} is used (default: NULL). #' #' @param bin_counts_fn Function used to calculate expected graphlet counts in #' each density bin. Takes \code{graphlet_counts}, \code{interval_indexes} #' (bin indexes) and \code{max_graphlet_size} as arguments. If \code{bin_counts_fn} is \code{NULL}, (default), -#' it will apply either the approach from the original Netdis paper, or the respective Geometric-Poisson -#' approximation; depending on the values of \code{ref_graph} and \code{graphlet_counts_ref}. +#' it will apply either the approach from the original Netdis paper, or the respective Geometric-Poisson +#' approximation; depending on the values of \code{ref_graph} and \code{graphlet_counts_ref}. #' #' @param exp_counts_fn Function used to map from binned reference counts to #' expected counts for each graphlet in each ego network of the query graphs. @@ -414,7 +412,7 @@ netdis_one_to_many <- function(graph_1 = NULL, #' If \code{exp_counts_fn} is \code{NULL}, (default), it will apply #' either the approach from the original Netdis paper, or the respective Geometric-Poisson approximation; depending on the #' values of \code{ref_graph} and \code{graphlet_counts_ref}. -#' +#' #' @param graphlet_counts Pre-generated graphlet counts (default: NULL). If the #' \code{graphlet_counts} argument is defined then \code{graphs} will not be #' used. @@ -433,7 +431,7 @@ netdis_one_to_many <- function(graph_1 = NULL, #' each ego network. #' If the \code{graphlet_counts_ref} argument is defined then \code{ref_graph} will not #' be used. - +#' #' @return Netdis statistics between query graphs for graphlet sizes #' up to and including max_graphlet_size. #' From 87201793de58aae651bedf77891038b94b9119f3 Mon Sep 17 00:00:00 2001 From: jack89roberts Date: Mon, 6 Jun 2022 11:24:31 +0100 Subject: [PATCH 14/20] run devtools::check instead of rcmdcheck --- .github/workflows/main.yml | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 298d9a50..527cb93c 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -42,15 +42,12 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: extra-packages: | - any::rcmdcheck + any::devtools any::covr - needs: | - check - coverage - - uses: r-lib/actions/check-r-package@v2 - with: - upload-snapshots: true + - name: Check package + run: devtools::check() + shell: Rscript {0} - name: Test coverage run: covr::codecov(quiet = FALSE) From a0d7aa8b9fd48d23d287f1df14d3f34055bb5b46 Mon Sep 17 00:00:00 2001 From: jack89roberts Date: Mon, 6 Jun 2022 11:55:49 +0100 Subject: [PATCH 15/20] rebuild docs --- .github/workflows/main.yml | 2 +- DESCRIPTION | 2 +- man/netdis_many_to_many.Rd | 11 +++++------ man/virusppi.Rd | 4 +++- man/worldtradesub.Rd | 4 +++- src/RcppExports.cpp | 5 +++++ 6 files changed, 18 insertions(+), 10 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 527cb93c..2606a005 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -46,7 +46,7 @@ jobs: any::covr - name: Check package - run: devtools::check() + run: devtools::document();devtools::check() shell: Rscript {0} - name: Test coverage diff --git a/DESCRIPTION b/DESCRIPTION index 98f92f88..015e7215 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -29,6 +29,6 @@ Suggests: knitr, rmarkdown, roxygen2 -RoxygenNote: 7.1.0 +RoxygenNote: 7.2.0 VignetteBuilder: knitr Encoding: UTF-8 diff --git a/man/netdis_many_to_many.Rd b/man/netdis_many_to_many.Rd index 26869a29..ef60e0f6 100644 --- a/man/netdis_many_to_many.Rd +++ b/man/netdis_many_to_many.Rd @@ -44,19 +44,18 @@ Can be "many-to-many" (all pairwise combinations) or "one-to-many" than min_ego_nodes nodes (default 3).} \item{min_ego_edges}{Filter ego networks which have fewer -than min_ego_edges edges (default 1). +than min_ego_edges edges (default 1).} - @param binning_fn Function used to bin ego network densities. Takes edge \code{densities} +\item{binning_fn}{Function used to bin ego network densities. Takes edge \code{densities} as its single argument, and returns a named list including, the input \code{densities}, the resulting bin \code{breaks} (vector of density bin limits), and the vector \code{interval_indexes} which states to what bin each of the individual elements in \code{densities} belongs to. ego network). If \code{NULL}, then the method \code{binned_densities_adaptive} with -\code{min_counts_per_interval = 5} and \code{num_intervals = 100} is used -(Default: NULL).} +\code{min_counts_per_interval = 5} and \code{num_intervals = 100} is used (default: NULL).} \item{bin_counts_fn}{Function used to calculate expected graphlet counts in each density bin. Takes \code{graphlet_counts}, \code{interval_indexes} (bin indexes) and \code{max_graphlet_size} as arguments. If \code{bin_counts_fn} is \code{NULL}, (default), - it will apply either the approach from the original Netdis paper, or the respective Geometric-Poisson - approximation; depending on the values of \code{ref_graph} and \code{graphlet_counts_ref}.} +it will apply either the approach from the original Netdis paper, or the respective Geometric-Poisson +approximation; depending on the values of \code{ref_graph} and \code{graphlet_counts_ref}.} \item{exp_counts_fn}{Function used to map from binned reference counts to expected counts for each graphlet in each ego network of the query graphs. diff --git a/man/virusppi.Rd b/man/virusppi.Rd index ddbb8eb2..6c905b2c 100644 --- a/man/virusppi.Rd +++ b/man/virusppi.Rd @@ -5,7 +5,9 @@ \name{virusppi} \alias{virusppi} \title{Protein-protein interaction (PPI) networks for 5 microorganisms} -\format{A list of \code{igraph} objects.} +\format{ +A list of \code{igraph} objects. +} \source{ \strong{PPI data (EBV, HSV-1, KSHV, VZV):} Fossum E, Friedel CC, Rajagopala SV, Titz B, Baiker A, Schmidt T, et al. (2009) Evolutionarily Conserved Herpesviral Protein Interaction Networks. PLoS Pathog 5(9): e1000570. \url{https://doi.org/10.1371/journal.ppat.1000570}. Data from Table S2 in the supporting information. diff --git a/man/worldtradesub.Rd b/man/worldtradesub.Rd index 1cdcf890..aa537cac 100644 --- a/man/worldtradesub.Rd +++ b/man/worldtradesub.Rd @@ -5,7 +5,9 @@ \name{worldtradesub} \alias{worldtradesub} \title{World trade networks from 1985–2014} -\format{A list of two elements. The first element, 'wtnets', is a list of \code{igraph} objects providing a small sample of world trade networks from 2001–2014. The second element, 'Counts', is a list of pre-computed subgraph counts of world trade networks in the years 1985-2014.} +\format{ +A list of two elements. The first element, 'wtnets', is a list of \code{igraph} objects providing a small sample of world trade networks from 2001–2014. The second element, 'Counts', is a list of pre-computed subgraph counts of world trade networks in the years 1985-2014. +} \source{ \strong{World trade networks:}. United nations commodity trade statistics database (UN comtrade). http://comtrade.un.org/, 2015. diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp index a1fe416b..d47fea91 100644 --- a/src/RcppExports.cpp +++ b/src/RcppExports.cpp @@ -5,6 +5,11 @@ using namespace Rcpp; +#ifdef RCPP_USE_GLOBAL_ROSTREAM +Rcpp::Rostream& Rcpp::Rcout = Rcpp::Rcpp_cout_get(); +Rcpp::Rostream& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get(); +#endif + // counts_from_observations NumericMatrix counts_from_observations(NumericMatrix features); RcppExport SEXP _netdist_counts_from_observations(SEXP featuresSEXP) { From c1c219dea1e0a4ef5df8c6f708e53598febeabc5 Mon Sep 17 00:00:00 2001 From: jack89roberts Date: Mon, 6 Jun 2022 12:23:08 +0100 Subject: [PATCH 16/20] change badges to GitHub actions --- .github/workflows/main.yml | 2 +- README.md | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 2606a005..7eeda1f7 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -49,6 +49,6 @@ jobs: run: devtools::document();devtools::check() shell: Rscript {0} - - name: Test coverage + - name: Check coverage run: covr::codecov(quiet = FALSE) shell: Rscript {0} diff --git a/README.md b/README.md index d977d62a..380c78b6 100755 --- a/README.md +++ b/README.md @@ -6,8 +6,7 @@ Until this package hits release 1.0 anything can change with no notice. [![Project Status: WIP - Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](http://www.repostatus.org/badges/latest/wip.svg)](http://www.repostatus.org/#wip) [![GitHub release](https://img.shields.io/github/release/alan-turing-institute/network-comparison.svg)](https://github.com/alan-turing-institute/network-comparison/releases/latest) -[![Travis](https://app.travis-ci.com/alan-turing-institute/network-comparison.svg?branch=master)](https://app.travis-ci.com/alan-turing-institute/network-comparison) -[![Appveyor](https://ci.appveyor.com/api/projects/status/jn1a36c22vjw1l4d/branch/master?svg=true)](https://ci.appveyor.com/project/alan-turing-institute/network-comparison/branch/master) +[![Build](https://github.com/alan-turing-institute/network-comparison/actions/workflows/main.yml/badge.svg)](https://github.com/alan-turing-institute/network-comparison/actions/workflows/main.yml) [![Codecov](https://img.shields.io/codecov/c/github/alan-turing-institute/network-comparison/master.svg)](https://codecov.io/gh/alan-turing-institute/network-comparison?branch=master) [![license](https://img.shields.io/github/license/alan-turing-institute/network-comparison.svg)](https://github.com/alan-turing-institute/network-comparison/edit/master/LICENSE) From 619c546a3e4220ccc0716b86b3b5024e484720e6 Mon Sep 17 00:00:00 2001 From: andeElliott Date: Wed, 18 May 2022 10:26:56 +0100 Subject: [PATCH 17/20] removed the flag for sse to test if this will work on M1 --- src/Makevars | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Makevars b/src/Makevars index 1b86740a..56211606 100644 --- a/src/Makevars +++ b/src/Makevars @@ -1,2 +1,2 @@ CXX_STD = CXX11 -PKG_CPPFLAGS = -fno-fast-math -msse2 -mfpmath=sse -mstackrealign +PKG_CPPFLAGS = -fno-fast-math -msse2 -mstackrealign From 36cfa85c0d44af1f5c3b0c1a48ef3dd659eb39f8 Mon Sep 17 00:00:00 2001 From: jack89roberts Date: Mon, 6 Jun 2022 13:24:00 +0100 Subject: [PATCH 18/20] rename build action --- .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 7eeda1f7..37827033 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -8,7 +8,7 @@ on: schedule: - cron: "5 5 5 * *" # run at 05:05 on 5th day of each month -name: Package checks and coverage +name: Build jobs: R-CMD-check: From d576f894a64654621833269c441d73c126b10077 Mon Sep 17 00:00:00 2001 From: jack89roberts Date: Mon, 6 Jun 2022 13:24:38 +0100 Subject: [PATCH 19/20] minor version bump --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 015e7215..98c333f1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: netdist Title: An implementation of the NetEMD alignment-free network distance measure -Version: 0.4.9000 +Version: 0.4.9100 Authors@R: person("Martin", "O'Reilly",email = "developer@mtspace.net", role = c("aut", "cre")) Description: An implementation of the NetEMD alignment-free network From 1f4d833395be1d67c2e6b900738a5d487272dbde Mon Sep 17 00:00:00 2001 From: jack89roberts Date: Mon, 6 Jun 2022 16:45:09 +0100 Subject: [PATCH 20/20] undo Makevars changes pending decision re #138 --- src/Makevars | 2 +- src/RcppExports.cpp | 5 ----- 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/src/Makevars b/src/Makevars index 56211606..25761e11 100644 --- a/src/Makevars +++ b/src/Makevars @@ -1,2 +1,2 @@ CXX_STD = CXX11 -PKG_CPPFLAGS = -fno-fast-math -msse2 -mstackrealign +PKG_CPPFLAGS += -fno-fast-math -msse2 -mfpmath=sse -mstackrealign diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp index d47fea91..a1fe416b 100644 --- a/src/RcppExports.cpp +++ b/src/RcppExports.cpp @@ -5,11 +5,6 @@ using namespace Rcpp; -#ifdef RCPP_USE_GLOBAL_ROSTREAM -Rcpp::Rostream& Rcpp::Rcout = Rcpp::Rcpp_cout_get(); -Rcpp::Rostream& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get(); -#endif - // counts_from_observations NumericMatrix counts_from_observations(NumericMatrix features); RcppExport SEXP _netdist_counts_from_observations(SEXP featuresSEXP) {