diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index af644e3f0..2af93fe23 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -19,73 +19,66 @@ jobs: fail-fast: false matrix: config: - - { os: macOS-latest, r: 'devel' } - - { os: windows-latest, r: 'devel' } - - { os: macOS-latest, r: 'release' } - - { os: windows-latest, r: 'release' } - - { os: ubuntu-16.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest" } - - { os: macOS-latest, r: 'oldrel' } - - { os: windows-latest, r: 'oldrel' } - - { os: ubuntu-16.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest" } + # - { os: macOS-latest, r: 'devel', force_suggests: "0" } + - { os: windows-latest, r: 'devel', force_suggests: "1" } + + - { os: macOS-latest, r: 'release', force_suggests: "1" } + - { os: windows-latest, r: 'release', force_suggests: "1" } + - { os: ubuntu-16.04, r: 'release', force_suggests: "1", rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest" } + + - { os: macOS-latest, r: 'oldrel', force_suggests: "1" } + - { os: windows-latest, r: 'oldrel', force_suggests: "1" } + - { os: ubuntu-16.04, r: 'oldrel', force_suggests: "1" , rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest" } env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true RSPM: ${{ matrix.config.rspm }} GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - _R_CHECK_FORCE_SUGGESTS_: 0 + _R_CHECK_FORCE_SUGGESTS_: ${{ matrix.config.force_suggests }} steps: - uses: actions/checkout@v2 - uses: r-lib/actions/setup-r@master + id: install-r with: r-version: ${{ matrix.config.r }} - uses: r-lib/actions/setup-pandoc@master - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") + - name: Install pak and query dependencies shell: Rscript {0} + run: | + install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/") + saveRDS(pak::pkg_deps_tree("local::.", dependencies = TRUE), ".github/r-depends.rds") - name: Cache R packages - if: runner.os != 'Windows' - uses: actions/cache@v1 + 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- + key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }} + restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1- - name: Install system dependencies if: runner.os == 'Linux' - env: - RHUB_PLATFORM: linux-x86_64-ubuntu-gcc + shell: Rscript {0} run: | - Rscript -e "remotes::install_github('r-hub/sysreqs')" - sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") - sudo -s eval "$sysreqs" + pak::local_system_requirements(execute = TRUE) + pak::pkg_system_requirements("rcmdcheck", execute = TRUE) + pak::pkg_system_requirements("sessioninfo", execute = TRUE) - name: Install dependencies - if: runner.os != 'Windows' || matrix.config.r == 'devel' - run: | - remotes::install_deps(dependencies = TRUE) - remotes::install_cran("rcmdcheck") shell: Rscript {0} - - name: Install dependencies (Windows binary) - if: runner.os == 'Windows' && matrix.config.r != 'devel' run: | - remotes::install_deps(dependencies = TRUE, type = "binary") - remotes::install_cran("rcmdcheck", type = "binary") - shell: Rscript {0} + pak::local_install_dev_deps(upgrade = TRUE) + pak::pkg_install(c("rcmdcheck", "sessioninfo")) - name: Session info + shell: Rscript {0} run: | options(width = 100) pkgs <- installed.packages()[, "Package"] sessioninfo::session_info(pkgs, include_base = TRUE) - shell: Rscript {0} - name: Check with printing env: diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index de3620e74..a3e19413a 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -13,36 +13,54 @@ name: pkgdown jobs: pkgdown: - runs-on: macOS-latest + runs-on: ${{ matrix.config.os }} + + strategy: + fail-fast: false + matrix: + config: + - { os: ubuntu-16.04, r: 'release', force_suggests: "1", rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest" } + env: + RSPM: ${{ matrix.config.rspm }} GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - uses: actions/checkout@v2 - uses: r-lib/actions/setup-r@master + id: install-r + with: + r-version: ${{ matrix.config.r }} - uses: r-lib/actions/setup-pandoc@master - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") + - name: Install pak and query dependencies shell: Rscript {0} + run: | + install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/") + saveRDS(pak::pkg_deps_tree("local::.", dependencies = TRUE), ".github/r-depends.rds") - name: Cache R packages - uses: actions/cache@v1 + 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- + key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-pkgdown-${{ hashFiles('.github/r-depends.rds') }} + restore-keys: | + ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-pkgdown- + ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1- - - name: Install dependencies + - name: Install system dependencies + if: runner.os == 'Linux' + shell: Rscript {0} run: | - install.packages("remotes") - remotes::install_deps(dependencies = TRUE) - remotes::install_dev("pkgdown") + pak::local_system_requirements(execute = TRUE) + pak::pkg_system_requirements("pkgdown", execute = TRUE) + + - name: Install dependencies shell: Rscript {0} + run: | + pak::local_install_dev_deps(upgrade = TRUE) + pak::pkg_install("pkgdown") - name: Install package run: R CMD INSTALL . diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 03e9c34b4..bcb04ea1a 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -11,36 +11,53 @@ name: test-coverage jobs: test-coverage: - runs-on: macOS-latest + runs-on: ${{ matrix.config.os }} + + strategy: + fail-fast: false + matrix: + config: + - { os: ubuntu-16.04, r: 'release', force_suggests: "1", rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest" } env: + RSPM: ${{ matrix.config.rspm }} GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - uses: actions/checkout@v2 - uses: r-lib/actions/setup-r@master + id: install-r + with: + r-version: ${{ matrix.config.r }} - uses: r-lib/actions/setup-pandoc@master - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") + - name: Install pak and query dependencies shell: Rscript {0} + run: | + install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/") + saveRDS(pak::pkg_deps_tree("local::.", dependencies = TRUE), ".github/r-depends.rds") - name: Cache R packages - uses: actions/cache@v1 + 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- + key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-testing-${{ hashFiles('.github/r-depends.rds') }} + restore-keys: | + ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-testing- + ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1- - - name: Install dependencies + - name: Install system dependencies + if: runner.os == 'Linux' + shell: Rscript {0} run: | - install.packages(c("remotes")) - remotes::install_deps(dependencies = TRUE) - remotes::install_cran("covr") + pak::local_system_requirements(execute = TRUE) + pak::pkg_system_requirements("covr", execute = TRUE) + + - name: Install dependencies shell: Rscript {0} + run: | + pak::local_install_dev_deps(upgrade = TRUE) + pak::pkg_install("covr") - name: Test coverage env: diff --git a/.gitignore b/.gitignore index cf799b752..e3d5d486f 100644 --- a/.gitignore +++ b/.gitignore @@ -2,7 +2,6 @@ .Rhistory ..Rcheck *ggmapTemp.png -inst/* tests/testthat/Rplots.pdf vignettes/figure vignettes/docs.html diff --git a/DESCRIPTION b/DESCRIPTION index 1a16a6656..e30c3f0e1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: GGally -Version: 2.1.0 +Version: 2.1.1 License: GPL (>= 2.0) Title: Extension to 'ggplot2' Type: Package diff --git a/NEWS.md b/NEWS.md index 377a5dfc5..90a267a26 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,12 @@ +# GGally 2.1.1 + +### Bug fixes + +* Ignore `colour` aesthetic if all values are `NA`. (@larmarange, #404) +* Avoid all duplicates within `stat_cross()`. (@larmarange, #402) +* Avoid an error when tidiers do not return p-values. (@larmarange, #400) +* Suggest `emmeans` to allow `ggcoef()` example to execute. (#407) + # GGally 2.1.0 ### Breaking changes diff --git a/cran-comments.md b/cran-comments.md index f5b76bc21..a0db25934 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,42 +1,38 @@ ## Comments +#### 2021-03-07 -#### 2021-01-04 +Have addressed the missing `emmeans` package error. -New features added. Time to share them to CRAN. - -Please let me know if there is anything I can provide! +Have also included other small bug fixes. No new features / functions. Thank you, Barret +#### 2021-02-24 -#### 2020-12-28 - -Sorry for the delay but would you please give me 2 more days to check the package? - -- Mingmei +Dear maintainer, -#### 2020-12-16 +Please see the problems shown on +. -Reached out to {bootclust} maintainer Mingmei Tian about not importing `sets::%>%` to avoid conflict with (possibly) many packages. +Please correct before 2021-03-10 to safely retain your package on CRAN. -Waiting until >= 2020-12-29 to submit. +Best, +-k ## Test environments and R CMD check results -* local macOS install 10.15.7 +* local macOS install 11.2.2 * R 4.0 -* GitHub Actions - https://github.com/ggobi/ggally/pull/397/checks - * macOS, windows - R devel - * macOS, windows, ubuntu 16 - R 4.0 - * macOS, windows, ubuntu 16 - R 3.6 +* GitHub Actions - https://github.com/ggobi/ggally/pull/408/checks + * windows - R devel + * macOS, windows, ubuntu 16 - R release + * macOS, windows, ubuntu 16 - R oldrelease * win-builder - * oldrelease - * release * devel #### R CMD check results @@ -46,24 +42,13 @@ Waiting until >= 2020-12-29 to submit. ## revdepcheck results -We checked 113 reverse dependencies (88 from CRAN + 25 from BioConductor), comparing R CMD check results across CRAN and dev versions of this package. +We checked 116 reverse dependencies (91 from CRAN + 25 from BioConductor), comparing R CMD check results across CRAN and dev versions of this package. - * We saw 1 new problems + * We saw 0 new problems * We failed to check 1 packages Issues with CRAN packages are summarised below. -### New problems -(This reports the first line of each new failure) - -* bootcluster - checking whether package ‘bootcluster’ can be installed ... WARNING - - - Maintainer (Mingmei Tian ) was contacted on Dec 16th about an upcoming release of GGally. - * A possible patch was provided over email. - * Mingmei replied to the email and asked for time until Jan 1st. - * I have not heard an update since. - -### Failed to check +### Failed to install * loon.ggplot (NA) diff --git a/inst/WORDLIST b/inst/WORDLIST new file mode 100644 index 000000000..fbf40b4b5 --- /dev/null +++ b/inst/WORDLIST @@ -0,0 +1,170 @@ +aede +aedeagus +aes +Aes +anova +api +axisLabels +axisVars +barDiag +bb +behaviour +Biometrics +blankDiag +Broomify +broomify'ed +cardinality +centerObs +ci +cityServiceFirms +cloudhigh +cloudlow +cloudmid +cmu +codebook +codecov +ColorBrewer +colour +colours +columnsY +concinna +corMethod +covr +dae +densityDiag +df +dfc +diag +directedness +DOI +edu +Environmetrics +exponentiate +facet'ed +fe +finrela +formatter +Fruchterman +Gb +geocoded +geoms +ggally +ggbivariate +ggcoef +ggcorr +ggduo +ggfluctuation +gglegend +gglyph +ggmap +ggmatrix +ggnet +ggnetworkmap +ggnostic +ggpairs +ggparcoord +ggplot +ggscatmat +ggsurv +ggtable +github +glyphmap +glyphplot +glyphs +gplot +grayscale +grey +gridlines +GSS +heikertingeri +Heptapot +heptapotamica +herdsz +Herzberg +hjust +Hout +http +ide +idre +igraph +ing +intergraph +io +Jibum +jitter +Jordano +JSM +Kaplan +Kutner +larmarange +labelled +labeller +labellers +linetype +lintr +Liu +lm +loess +lon +lowertriangle +lt +Lubischew +Marsden +McGraw +Mengjia +Murrell +na +Nachtsheim +naDiag +NaN +Neter +newpage +NORC +num +Opsahl +param +parcoord +plotmath +preallocates +Programme +PV +quartiles +RColorBrewer +rdocumentation +Reingold +rescale +Rescaling +resid +RStudio +scagnostic +scagnostics +scaler +SCIE +se +SENWGT +shadebox +shadeBox +spambots +Springer +Statlib +stdres +Storrs +stratums +Su's +Summarise +surftemp +th +Tian +travis +truthy +ucla +univariately +uppertriangle +vjust +Wickham's +wtsall +www +Yau +Yu +Zheng +tidiers diff --git a/revdep/README.md b/revdep/README.md index ad62a0e19..14d52c531 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -3,20 +3,20 @@ |field |value | |:--------|:----------------------------| |version |R version 4.0.2 (2020-06-22) | -|os |macOS Catalina 10.15.7 | +|os |macOS 10.16 | |system |x86_64, darwin17.0 | |ui |X11 | |language |(EN) | |collate |en_US.UTF-8 | |ctype |en_US.UTF-8 | |tz |America/New_York | -|date |2021-01-04 | +|date |2021-03-07 | # Dependencies |package |old |new |Δ | |:-------|:-----|:-----|:--| -|GGally |2.0.0 |2.1.0 |* | +|GGally |2.1.0 |2.1.1 |* | # Revdeps @@ -26,127 +26,124 @@ |:-------------------------------------|:-------|:-----|:-------|:----| |[loon.ggplot](failures.md#loonggplot) |1.0.1 |1 | | | -## New problems (1) +## All (116) -|package |version |error |warning |note | -|:--------------------------------------|:-------|:-----|:-------|:----| -|[bootcluster](problems.md#bootcluster) |0.2.0 | |__+1__ | | - -## All (113) - -|package |version |error |warning |note | -|:----------------------------------------------------------------|:-------|:-----|:-------|:----| -|[adventr](problems.md#adventr) |0.1.8 | | |2 | -|[AirSensor](problems.md#airsensor) |1.0.2 | | |1 | -|[alevinQC](problems.md#alevinqc) |1.6.0 | | |1 | -|[ALPS](problems.md#alps) |1.4.0 | | |1 | -|[AlpsNMR](problems.md#alpsnmr) |3.0.4 | |1 |1 | -|BAS |1.5.5 | | | | -|[BasketballAnalyzeR](problems.md#basketballanalyzer) |0.5.0 | | |1 | -|bayestestR |0.8.0 | | | | -|[BGGM](problems.md#bggm) |2.0.3 | | |1 | -|[bigPint](problems.md#bigpint) |1.6.0 | | |1 | -|[bootcluster](problems.md#bootcluster) |0.2.0 | |__+1__ | | -|brinton |0.2.1 | | | | -|CARBayes |5.2 | | | | -|CARBayesST |3.1 | | | | -|[CeTF](problems.md#cetf) |1.2.4 | | |1 | -|[CINNA](problems.md#cinna) |1.1.53 | | |1 | -|[CluMSID](problems.md#clumsid) |1.6.0 | | |1 | -|clustrd |1.3.7-2 | | | | -|[ctsem](problems.md#ctsem) |3.4.1 | | |3 | -|DescribeDisplay |0.2.7 | | | | -|discourseGT |1.1.2 | | | | -|eechidna |1.4.0 | | | | -|[egoTERGM](problems.md#egotergm) |2.1.1 | | |1 | -|EMMIXmfa |2.0.11 | | | | -|ezEDA |0.1.0 | | | | -|[fic](problems.md#fic) |1.0.0 | | |1 | -|finalfit |1.0.2 | | | | -|[fingerPro](problems.md#fingerpro) |1.1 | | |1 | -|fpp2 |2.4 | | | | -|freqparcoord |1.0.1 | | | | -|[GENESIS](problems.md#genesis) |2.20.0 | | |3 | -|gfilmm |2.0.2 | | | | -|[ggbio](problems.md#ggbio) |1.38.0 | |1 |2 | -|ggmcmc |1.5.0 | | | | -|[GGPA](problems.md#ggpa) |1.2.0 | | |2 | -|[ggPMX](problems.md#ggpmx) |1.1.2 | | |1 | -|[ggquickeda](problems.md#ggquickeda) |0.1.9 | | |1 | -|glancedata |1.0.1 | | | | -|growthPheno |1.0-30 | | | | -|gsynth |1.0.9 | | | | -|HierDpart |0.5.0 | | | | -|[httk](problems.md#httk) |2.0.3 | | |1 | -|[ICtest](problems.md#ictest) |0.3-2 | | |1 | -|imageData |0.1-60 | | | | -|[isomiRs](problems.md#isomirs) |1.18.0 | |1 |2 | -|ITNr |0.6.0 | | | | -|[jmv](problems.md#jmv) |1.2.23 | | |1 | -|[jsmodule](problems.md#jsmodule) |1.1.4 | | |1 | -|[LANDD](problems.md#landd) |1.1.0 | | |1 | -|[loon.ggplot](failures.md#loonggplot) |1.0.1 |1 | | | -|[MAINT.Data](problems.md#maintdata) |2.5.0 | | |1 | -|[MAST](problems.md#mast) |1.16.0 |1 |1 |2 | -|[MCbiclust](problems.md#mcbiclust) |1.14.0 | | |1 | -|metan |1.11.0 | | | | -|[mgcViz](problems.md#mgcviz) |0.1.6 | | |1 | -|[MissingDataGUI](problems.md#missingdatagui) |0.2-5 | |4 |4 | -|mitch |1.2.2 | | | | -|miWQS |0.2.0 | | | | -|mlergm |0.7 | | | | -|mlr3viz |0.5.0 | | | | -|mlrMBO |1.1.5 | | | | -|[MOFA](problems.md#mofa) |1.6.1 |1 |1 |5 | -|[MOFA2](problems.md#mofa2) |1.0.1 | | |7 | -|MRPC |2.2.1 | | | | -|[nanny](problems.md#nanny) |0.1.8 | | |1 | -|[NetworkChange](problems.md#networkchange) |0.7 | | |1 | -|[nzelect](problems.md#nzelect) |0.4.0 | | |2 | -|[ORFik](problems.md#orfik) |1.10.1 | |1 |3 | -|OutliersO3 |0.6.3 | | | | -|[PAFway](problems.md#pafway) |0.1.3 | | |1 | -|ParamHelpers |1.14 | | | | -|[PAsso](problems.md#passo) |0.1.8 | | |2 | -|PhosR |1.0.0 | | | | -|[Pi](problems.md#pi) |2.2.1 | |1 | | -|[plotly](problems.md#plotly) |4.9.2.2 | | |1 | -|[PopGenReport](problems.md#popgenreport) |3.0.4 | | |1 | -|PPforest |0.1.1 | | | | -|[pubh](problems.md#pubh) |1.1.19 | | |1 | -|qualvar |0.2.0 | | | | -|QuantNorm |1.0.5 | | | | -|randomForestExplainer |0.10.1 | | | | -|RHMS |1.6 | | | | -|[robCompositions](problems.md#robcompositions) |2.3.0 | | |1 | -|[robustbase](problems.md#robustbase) |0.93-6 | | |1 | -|robustSingleCell |0.1.1 | | | | -|[rrr](problems.md#rrr) |1.0.0 | | |1 | -|rwty |1.0.2 | | | | -|[scPipe](problems.md#scpipe) |1.12.0 | |1 |4 | -|[seer](problems.md#seer) |1.1.5 | | |1 | -|[SeqSQC](problems.md#seqsqc) |1.12.0 |1 |1 |1 | -|SHELF |1.7.0 | | | | -|SimBIID |0.2.0 | | | | -|simplexdesign |0.1.0 | | | | -|[SmartEDA](problems.md#smarteda) |0.3.6 | | |1 | -|[specmine](problems.md#specmine) |3.0.3 | | |3 | -|[spinifex](problems.md#spinifex) |0.2.7 |1 | |1 | -|[spup](problems.md#spup) |1.3-2 | | |1 | -|staRdom |1.1.18 | | | | -|[statVisual](problems.md#statvisual) |1.2.1 | |1 |1 | -|[tidybulk](problems.md#tidybulk) |1.2.0 | |1 |3 | -|tidyseurat |0.1.17 | | | | -|[tidySingleCellExperiment](problems.md#tidysinglecellexperiment) |1.0.0 | |1 |2 | -|[TNBC.CMS](problems.md#tnbccms) |1.6.0 | |1 | | -|tsfeatures |1.0.2 | | | | -|[TVTB](problems.md#tvtb) |1.16.0 | | |1 | -|[ubiquity](problems.md#ubiquity) |1.0.3 | | |1 | -|[ufs](problems.md#ufs) |0.4.0 | | |2 | -|userfriendlyscience |0.7.2 | | | | -|ushr |0.2.3 | | | | -|[vidger](problems.md#vidger) |1.10.0 | | |1 | -|vortexR |1.1.7 | | | | -|WRS2 |1.1-0 | | | | -|WRSS |3.0 | | | | +|package |version |error |warning |note | +|:----------------------------------------------------------------|:--------|:-----|:-------|:----| +|[adventr](problems.md#adventr) |0.1.8 | | |2 | +|airGR |1.6.10.4 | | | | +|[AirSensor](problems.md#airsensor) |1.0.2 | | |1 | +|[alevinQC](problems.md#alevinqc) |1.6.1 | | |1 | +|AlleleShift |0.9-2 | | | | +|[ALPS](problems.md#alps) |1.4.0 | | |1 | +|[AlpsNMR](problems.md#alpsnmr) |3.0.5 | |1 |1 | +|BAS |1.5.5 | | | | +|[BasketballAnalyzeR](problems.md#basketballanalyzer) |0.5.0 | | |1 | +|[bayestestR](problems.md#bayestestr) |0.8.2 | | |1 | +|[BGGM](problems.md#bggm) |2.0.3 | | |1 | +|[bigPint](problems.md#bigpint) |1.6.0 | | |1 | +|[bootcluster](problems.md#bootcluster) |0.2.0 | |1 | | +|brinton |0.2.4 | | | | +|CARBayes |5.2.3 | | | | +|CARBayesST |3.1.1 | | | | +|[CeTF](problems.md#cetf) |1.2.4 | | |1 | +|[CINNA](problems.md#cinna) |1.1.54 | | |1 | +|[CluMSID](problems.md#clumsid) |1.6.0 | | |1 | +|clustrd |1.3.7-2 | | | | +|[communication](problems.md#communication) |0.1 | | |1 | +|DescribeDisplay |0.2.7 | | | | +|[discourseGT](problems.md#discoursegt) |1.1.4 | | |1 | +|eechidna |1.4.1 | | | | +|EGAnet |0.9.8 | | | | +|[egoTERGM](problems.md#egotergm) |2.1.1 | | |1 | +|EMMIXmfa |2.0.11 | | | | +|ezEDA |0.1.0 | | | | +|[fic](problems.md#fic) |1.0.0 | | |1 | +|finalfit |1.0.2 | | | | +|[fingerPro](problems.md#fingerpro) |1.1 | | |1 | +|fpp2 |2.4 | | | | +|freqparcoord |1.0.1 | | | | +|[GENESIS](problems.md#genesis) |2.20.1 | | |3 | +|gfilmm |2.0.2 | | | | +|[ggbio](problems.md#ggbio) |1.38.0 | |1 |2 | +|ggmcmc |1.5.1.1 | | | | +|[GGPA](problems.md#ggpa) |1.2.0 | | |2 | +|[ggPMX](problems.md#ggpmx) |1.1.2 | | |1 | +|[ggquickeda](problems.md#ggquickeda) |0.2.0 | | |1 | +|glancedata |1.0.1 | | | | +|growthPheno |1.0-30 | | | | +|gsynth |1.0.9 | | | | +|HierDpart |0.5.0 | | | | +|[httk](problems.md#httk) |2.0.3 | | |1 | +|ICtest |0.3-3 | | | | +|imageData |0.1-61 | | | | +|[isomiRs](problems.md#isomirs) |1.18.1 | |1 |2 | +|ITNr |0.6.0 | | | | +|[jmv](problems.md#jmv) |1.2.23 | | |1 | +|[jsmodule](problems.md#jsmodule) |1.1.6 | | |1 | +|[LANDD](problems.md#landd) |1.1.0 | | |1 | +|[loon.ggplot](failures.md#loonggplot) |1.0.1 |1 | | | +|[MAINT.Data](problems.md#maintdata) |2.5.0 | | |1 | +|[MAST](problems.md#mast) |1.16.0 | |1 |2 | +|[MCbiclust](problems.md#mcbiclust) |1.14.0 | | |1 | +|metan |1.12.0 | | | | +|[mgcViz](problems.md#mgcviz) |0.1.6 | | |1 | +|[MissingDataGUI](problems.md#missingdatagui) |0.2-5 | |4 |4 | +|mitch |1.2.2 | | | | +|miWQS |0.4.2 | | | | +|mlergm |0.7 | | | | +|mlr3viz |0.5.1 | | | | +|mlrMBO |1.1.5 | | | | +|[MOFA](problems.md#mofa) |1.6.2 |1 |1 |5 | +|[MOFA2](problems.md#mofa2) |1.0.1 | | |7 | +|MRPC |2.2.2 | | | | +|[nanny](problems.md#nanny) |0.1.8 | | |1 | +|[NetworkChange](problems.md#networkchange) |0.7 | | |1 | +|[nzelect](problems.md#nzelect) |0.4.0 | | |2 | +|[ORFik](problems.md#orfik) |1.10.11 | |1 |3 | +|OutliersO3 |0.6.3 | | | | +|[PAFway](problems.md#pafway) |0.1.3 | | |1 | +|ParamHelpers |1.14 | | | | +|[PAsso](problems.md#passo) |0.1.8 | | |2 | +|PhosR |1.0.0 | | | | +|[Pi](problems.md#pi) |2.2.1 | |1 | | +|[plotly](problems.md#plotly) |4.9.3 | | |1 | +|[PopGenReport](problems.md#popgenreport) |3.0.4 | | |1 | +|PPforest |0.1.1 | | | | +|[pubh](problems.md#pubh) |1.1.20 | | |1 | +|qualvar |0.2.0 | | | | +|QuantNorm |1.0.5 | | | | +|randomForestExplainer |0.10.1 | | | | +|RHMS |1.6 | | | | +|[robCompositions](problems.md#robcompositions) |2.3.0 | | |1 | +|[robustbase](problems.md#robustbase) |0.93-7 | | |2 | +|robustSingleCell |0.1.1 | | | | +|[rrr](problems.md#rrr) |1.0.0 | | |1 | +|rwty |1.0.2 | | | | +|[scPipe](problems.md#scpipe) |1.12.0 | |1 |4 | +|[seer](problems.md#seer) |1.1.5 | | |1 | +|[SeqSQC](problems.md#seqsqc) |1.12.0 |1 |1 |1 | +|SHELF |1.7.0 | | | | +|SimBIID |0.2.1 | | | | +|simplexdesign |0.1.0 | | | | +|[SmartEDA](problems.md#smarteda) |0.3.6 | | |1 | +|[specmine](problems.md#specmine) |3.1.4 | | |3 | +|[spinifex](problems.md#spinifex) |0.2.7 |1 | |1 | +|[spup](problems.md#spup) |1.3-2 | | |1 | +|staRdom |1.1.18 | | | | +|[statVisual](problems.md#statvisual) |1.2.1 | |1 |1 | +|[tidybulk](problems.md#tidybulk) |1.2.0 | |1 |3 | +|tidyseurat |0.1.17 | | | | +|[tidySingleCellExperiment](problems.md#tidysinglecellexperiment) |1.0.0 | |1 |2 | +|[TNBC.CMS](problems.md#tnbccms) |1.6.0 | |1 | | +|tsfeatures |1.0.2 | | | | +|[TVTB](problems.md#tvtb) |1.16.0 | | |1 | +|[ubiquity](problems.md#ubiquity) |1.0.3 | | |1 | +|ufs |0.4.3 | | | | +|userfriendlyscience |0.7.2 | | | | +|ushr |0.2.3 | | | | +|[vidger](problems.md#vidger) |1.10.0 | | |1 | +|vortexR |1.1.7 | | | | +|WRS2 |1.1-1 | | | | +|WRSS |3.0 | | | | diff --git a/revdep/cran.md b/revdep/cran.md index 2238ee598..c6acbaeb4 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,18 +1,12 @@ ## revdepcheck results -We checked 113 reverse dependencies (88 from CRAN + 25 from BioConductor), comparing R CMD check results across CRAN and dev versions of this package. +We checked 116 reverse dependencies (91 from CRAN + 25 from BioConductor), comparing R CMD check results across CRAN and dev versions of this package. - * We saw 1 new problems + * We saw 0 new problems * We failed to check 1 packages Issues with CRAN packages are summarised below. -### New problems -(This reports the first line of each new failure) - -* bootcluster - checking whether package ‘bootcluster’ can be installed ... WARNING - ### Failed to check * loon.ggplot (NA) diff --git a/revdep/problems.md b/revdep/problems.md index 11b9111d5..0315777d0 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -6,7 +6,7 @@ * GitHub: NA * Source code: https://github.com/cran/adventr * Date/Publication: 2020-05-05 16:50:06 UTC -* Number of recursive dependencies: 169 +* Number of recursive dependencies: 162 Run `revdep_details(, "adventr")` for more info @@ -38,7 +38,7 @@ Run `revdep_details(, "adventr")` for more info * GitHub: https://github.com/MazamaScience/AirSensor * Source code: https://github.com/cran/AirSensor * Date/Publication: 2020-10-08 12:10:02 UTC -* Number of recursive dependencies: 181 +* Number of recursive dependencies: 186 Run `revdep_details(, "AirSensor")` for more info @@ -55,11 +55,11 @@ Run `revdep_details(, "AirSensor")` for more info
-* Version: 1.6.0 +* Version: 1.6.1 * GitHub: https://github.com/csoneson/alevinQC * Source code: https://github.com/cran/alevinQC -* Date/Publication: 2020-10-27 -* Number of recursive dependencies: 91 +* Date/Publication: 2021-02-02 +* Number of recursive dependencies: 100 Run `revdep_details(, "alevinQC")` for more info @@ -82,7 +82,7 @@ Run `revdep_details(, "alevinQC")` for more info * GitHub: https://github.com/itsvenu/ALPS * Source code: https://github.com/cran/ALPS * Date/Publication: 2020-10-27 -* Number of recursive dependencies: 194 +* Number of recursive dependencies: 197 Run `revdep_details(, "ALPS")` for more info @@ -102,10 +102,10 @@ Run `revdep_details(, "ALPS")` for more info
-* Version: 3.0.4 +* Version: 3.0.5 * GitHub: NA * Source code: https://github.com/cran/AlpsNMR -* Date/Publication: 2020-11-19 +* Date/Publication: 2021-01-20 * Number of recursive dependencies: 163 Run `revdep_details(, "AlpsNMR")` for more info @@ -154,7 +154,7 @@ Run `revdep_details(, "AlpsNMR")` for more info * GitHub: https://github.com/sndmrc/BasketballAnalyzeR * Source code: https://github.com/cran/BasketballAnalyzeR * Date/Publication: 2020-06-26 09:00:11 UTC -* Number of recursive dependencies: 91 +* Number of recursive dependencies: 76 Run `revdep_details(, "BasketballAnalyzeR")` for more info @@ -169,6 +169,30 @@ Run `revdep_details(, "BasketballAnalyzeR")` for more info All declared Imports should be used. ``` +# bayestestR + +
+ +* Version: 0.8.2 +* GitHub: https://github.com/easystats/bayestestR +* Source code: https://github.com/cran/bayestestR +* Date/Publication: 2021-01-26 17:40:03 UTC +* Number of recursive dependencies: 209 + +Run `revdep_details(, "bayestestR")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 9.1Mb + sub-directories of 1Mb or more: + doc 7.2Mb + help 1.3Mb + ``` + # BGGM
@@ -177,7 +201,7 @@ Run `revdep_details(, "BasketballAnalyzeR")` for more info * GitHub: https://github.com/donaldRwilliams/BGGM * Source code: https://github.com/cran/BGGM * Date/Publication: 2020-12-03 08:20:06 UTC -* Number of recursive dependencies: 193 +* Number of recursive dependencies: 167 Run `revdep_details(, "BGGM")` for more info @@ -211,7 +235,7 @@ Run `revdep_details(, "bigPint")` for more info * checking installed package size ... NOTE ``` - installed size is 7.7Mb + installed size is 7.8Mb sub-directories of 1Mb or more: data 2.1Mb doc 2.3Mb @@ -226,13 +250,13 @@ Run `revdep_details(, "bigPint")` for more info * GitHub: NA * Source code: https://github.com/cran/bootcluster * Date/Publication: 2020-10-20 14:50:06 UTC -* Number of recursive dependencies: 81 +* Number of recursive dependencies: 68 Run `revdep_details(, "bootcluster")` for more info
-## Newly broken +## In both * checking whether package ‘bootcluster’ can be installed ... WARNING ``` @@ -249,7 +273,7 @@ Run `revdep_details(, "bootcluster")` for more info * GitHub: NA * Source code: https://github.com/cran/CeTF * Date/Publication: 2020-11-23 -* Number of recursive dependencies: 228 +* Number of recursive dependencies: 229 Run `revdep_details(, "CeTF")` for more info @@ -259,7 +283,7 @@ Run `revdep_details(, "CeTF")` for more info * checking installed package size ... NOTE ``` - installed size is 5.2Mb + installed size is 5.3Mb sub-directories of 1Mb or more: data 1.6Mb doc 2.5Mb @@ -269,11 +293,11 @@ Run `revdep_details(, "CeTF")` for more info
-* Version: 1.1.53 +* Version: 1.1.54 * GitHub: NA * Source code: https://github.com/cran/CINNA -* Date/Publication: 2019-02-25 12:50:14 UTC -* Number of recursive dependencies: 152 +* Date/Publication: 2021-01-28 15:00:02 UTC +* Number of recursive dependencies: 138 Run `revdep_details(, "CINNA")` for more info @@ -310,40 +334,51 @@ Run `revdep_details(, "CluMSID")` for more info doc 5.6Mb ``` -# ctsem +# communication
-* Version: 3.4.1 -* GitHub: https://github.com/cdriveraus/ctsem -* Source code: https://github.com/cran/ctsem -* Date/Publication: 2020-12-18 13:00:25 UTC -* Number of recursive dependencies: 132 +* Version: 0.1 +* GitHub: NA +* Source code: https://github.com/cran/communication +* Date/Publication: 2021-02-25 09:20:02 UTC +* Number of recursive dependencies: 89 -Run `revdep_details(, "ctsem")` for more info +Run `revdep_details(, "communication")` for more info
## In both -* checking installed package size ... NOTE - ``` - installed size is 14.5Mb - sub-directories of 1Mb or more: - R 2.1Mb - data 1.6Mb - libs 9.6Mb - ``` - * checking dependencies in R code ... NOTE ``` - Namespace in Imports field not imported from: ‘pkgbuild’ + Namespaces in Imports field not imported from: + ‘GGally’ ‘RColorBrewer’ ‘abind’ ‘diagram’ ‘ggplot2’ ‘grid’ ‘gtable’ + ‘igraph’ ‘magrittr’ ‘plyr’ ‘purrr’ ‘reshape2’ ‘scales’ ‘useful’ All declared Imports should be used. ``` -* checking for GNU extensions in Makefiles ... NOTE +# discourseGT + +
+ +* Version: 1.1.4 +* GitHub: NA +* Source code: https://github.com/cran/discourseGT +* Date/Publication: 2021-02-17 07:20:02 UTC +* Number of recursive dependencies: 106 + +Run `revdep_details(, "discourseGT")` for more info + +
+ +## In both + +* checking dependencies in R code ... NOTE ``` - GNU make is a SystemRequirements. + Namespaces in Imports field not imported from: + ‘BiocManager’ ‘sna’ + All declared Imports should be used. ``` # egoTERGM @@ -354,7 +389,7 @@ Run `revdep_details(, "ctsem")` for more info * GitHub: https://github.com/benjamin-w-campbell/egoTERGM * Source code: https://github.com/cran/egoTERGM * Date/Publication: 2019-05-17 13:20:03 UTC -* Number of recursive dependencies: 90 +* Number of recursive dependencies: 82 Run `revdep_details(, "egoTERGM")` for more info @@ -375,7 +410,7 @@ Run `revdep_details(, "egoTERGM")` for more info * GitHub: https://github.com/chjackson/fic * Source code: https://github.com/cran/fic * Date/Publication: 2019-04-13 08:32:39 UTC -* Number of recursive dependencies: 98 +* Number of recursive dependencies: 104 Run `revdep_details(, "fic")` for more info @@ -397,7 +432,7 @@ Run `revdep_details(, "fic")` for more info * GitHub: https://github.com/NA/NA * Source code: https://github.com/cran/fingerPro * Date/Publication: 2018-08-28 10:04:54 UTC -* Number of recursive dependencies: 165 +* Number of recursive dependencies: 162 Run `revdep_details(, "fingerPro")` for more info @@ -415,11 +450,11 @@ Run `revdep_details(, "fingerPro")` for more info
-* Version: 2.20.0 +* Version: 2.20.1 * GitHub: https://github.com/UW-GAC/GENESIS * Source code: https://github.com/cran/GENESIS -* Date/Publication: 2020-10-27 -* Number of recursive dependencies: 162 +* Date/Publication: 2021-01-28 +* Number of recursive dependencies: 165 Run `revdep_details(, "GENESIS")` for more info @@ -458,7 +493,7 @@ Run `revdep_details(, "GENESIS")` for more info * GitHub: https://github.com/tengfei/ggbio * Source code: https://github.com/cran/ggbio * Date/Publication: 2020-10-27 -* Number of recursive dependencies: 162 +* Number of recursive dependencies: 167 Run `revdep_details(, "ggbio")` for more info @@ -517,7 +552,7 @@ Run `revdep_details(, "ggbio")` for more info * GitHub: https://github.com/dongjunchung/GGPA * Source code: https://github.com/cran/GGPA * Date/Publication: 2020-10-27 -* Number of recursive dependencies: 77 +* Number of recursive dependencies: 70 Run `revdep_details(, "GGPA")` for more info @@ -554,7 +589,7 @@ Run `revdep_details(, "GGPA")` for more info * GitHub: https://github.com/ggPMXdevelopment/ggPMX * Source code: https://github.com/cran/ggPMX * Date/Publication: 2020-06-25 15:50:09 UTC -* Number of recursive dependencies: 71 +* Number of recursive dependencies: 78 Run `revdep_details(, "ggPMX")` for more info @@ -571,11 +606,11 @@ Run `revdep_details(, "ggPMX")` for more info
-* Version: 0.1.9 +* Version: 0.2.0 * GitHub: https://github.com/smouksassi/ggquickeda * Source code: https://github.com/cran/ggquickeda -* Date/Publication: 2020-12-16 13:40:02 UTC -* Number of recursive dependencies: 173 +* Date/Publication: 2021-02-15 12:40:02 UTC +* Number of recursive dependencies: 167 Run `revdep_details(, "ggquickeda")` for more info @@ -587,10 +622,9 @@ Run `revdep_details(, "ggquickeda")` for more info ``` Namespaces in Imports field not imported from: ‘DT’ ‘Formula’ ‘GGally’ ‘Hmisc’ ‘RPostgres’ ‘colourpicker’ ‘dplyr’ - ‘ggpmisc’ ‘ggpubr’ ‘ggrepel’ ‘ggstance’ ‘grDevices’ ‘grid’ - ‘gridExtra’ ‘lazyeval’ ‘markdown’ ‘plotly’ ‘quantreg’ ‘rlang’ - ‘shinyFiles’ ‘shinyjqui’ ‘shinyjs’ ‘survival’ ‘survminer’ ‘table1’ - ‘tidyr’ + ‘ggpmisc’ ‘ggpubr’ ‘ggrepel’ ‘gridExtra’ ‘markdown’ ‘plotly’ + ‘quantreg’ ‘rlang’ ‘shinyFiles’ ‘shinyjqui’ ‘shinyjs’ ‘survival’ + ‘survminer’ ‘table1’ ‘tidyr’ ‘zoo’ All declared Imports should be used. ``` @@ -602,7 +636,7 @@ Run `revdep_details(, "ggquickeda")` for more info * GitHub: https://github.com/USEPA/CompTox-ExpoCast-httk * Source code: https://github.com/cran/httk * Date/Publication: 2020-09-25 11:00:03 UTC -* Number of recursive dependencies: 114 +* Number of recursive dependencies: 104 Run `revdep_details(, "httk")` for more info @@ -618,36 +652,15 @@ Run `revdep_details(, "httk")` for more info doc 2.1Mb ``` -# ICtest - -
- -* Version: 0.3-2 -* GitHub: NA -* Source code: https://github.com/cran/ICtest -* Date/Publication: 2019-08-23 11:50:02 UTC -* Number of recursive dependencies: 83 - -Run `revdep_details(, "ICtest")` for more info - -
- -## In both - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘fICA’ - ``` - # isomiRs
-* Version: 1.18.0 +* Version: 1.18.1 * GitHub: https://github.com/lpantano/isomiRs * Source code: https://github.com/cran/isomiRs -* Date/Publication: 2020-10-27 -* Number of recursive dependencies: 159 +* Date/Publication: 2021-01-29 +* Number of recursive dependencies: 162 Run `revdep_details(, "isomiRs")` for more info @@ -711,7 +724,7 @@ Run `revdep_details(, "isomiRs")` for more info * GitHub: NA * Source code: https://github.com/cran/jmv * Date/Publication: 2020-06-26 10:00:09 UTC -* Number of recursive dependencies: 201 +* Number of recursive dependencies: 189 Run `revdep_details(, "jmv")` for more info @@ -732,11 +745,11 @@ Run `revdep_details(, "jmv")` for more info
-* Version: 1.1.4 +* Version: 1.1.6 * GitHub: https://github.com/jinseob2kim/jsmodule * Source code: https://github.com/cran/jsmodule -* Date/Publication: 2020-12-01 05:30:03 UTC -* Number of recursive dependencies: 200 +* Date/Publication: 2021-02-15 14:20:06 UTC +* Number of recursive dependencies: 214 Run `revdep_details(, "jsmodule")` for more info @@ -759,7 +772,7 @@ Run `revdep_details(, "jsmodule")` for more info * GitHub: NA * Source code: https://github.com/cran/LANDD * Date/Publication: 2016-10-01 01:14:24 -* Number of recursive dependencies: 113 +* Number of recursive dependencies: 107 Run `revdep_details(, "LANDD")` for more info @@ -788,7 +801,7 @@ Run `revdep_details(, "LANDD")` for more info * GitHub: https://github.com/great-northern-diver/loon.ggplot * Source code: https://github.com/cran/loon.ggplot * Date/Publication: 2020-06-26 16:40:03 UTC -* Number of recursive dependencies: 108 +* Number of recursive dependencies: 107 Run `revdep_details(, "loon.ggplot")` for more info @@ -856,7 +869,7 @@ ERROR: lazy loading failed for package ‘loon.ggplot’ * GitHub: NA * Source code: https://github.com/cran/MAINT.Data * Date/Publication: 2020-09-24 20:30:06 UTC -* Number of recursive dependencies: 72 +* Number of recursive dependencies: 63 Run `revdep_details(, "MAINT.Data")` for more info @@ -866,10 +879,10 @@ Run `revdep_details(, "MAINT.Data")` for more info * checking installed package size ... NOTE ``` - installed size is 5.8Mb + installed size is 6.6Mb sub-directories of 1Mb or more: R 2.0Mb - data 2.3Mb + data 3.0Mb libs 1.2Mb ``` @@ -881,7 +894,7 @@ Run `revdep_details(, "MAINT.Data")` for more info * GitHub: https://github.com/RGLab/MAST * Source code: https://github.com/cran/MAST * Date/Publication: 2020-10-27 -* Number of recursive dependencies: 205 +* Number of recursive dependencies: 207 Run `revdep_details(, "MAST")` for more info @@ -889,28 +902,6 @@ Run `revdep_details(, "MAST")` for more info ## In both -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 23. lme4::lFormula(...) - 24. lme4:::chkRank.drop.cols(X, kind = rankX.chk, tol = 1e-07) - 25. Matrix::rankMatrix(X, tol = tol, method = method) - 27. Matrix::qr2rankMatrix(q.r, tol = tol, isBqr = x.dense, do.warn = warn.qr) - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure (test-lmWrapper-glmer.R:22:9): lrt is non-NA ──────────────────────── - all(l1[, "hurdle", "lambda"] > 0) is not TRUE - - `actual`: FALSE - `expected`: TRUE - - [ FAIL 1 | WARN 7 | SKIP 4 | PASS 286 ] - Error: Test failures - Execution halted - ``` - * checking whether package ‘MAST’ can be installed ... WARNING ``` Found the following significant warnings: @@ -950,7 +941,7 @@ Run `revdep_details(, "MAST")` for more info * GitHub: NA * Source code: https://github.com/cran/MCbiclust * Date/Publication: 2020-10-27 -* Number of recursive dependencies: 178 +* Number of recursive dependencies: 182 Run `revdep_details(, "MCbiclust")` for more info @@ -974,7 +965,7 @@ Run `revdep_details(, "MCbiclust")` for more info * GitHub: https://github.com/mfasiolo/mgcViz * Source code: https://github.com/cran/mgcViz * Date/Publication: 2020-03-04 15:10:02 UTC -* Number of recursive dependencies: 100 +* Number of recursive dependencies: 112 Run `revdep_details(, "mgcViz")` for more info @@ -984,7 +975,7 @@ Run `revdep_details(, "mgcViz")` for more info * checking installed package size ... NOTE ``` - installed size is 5.2Mb + installed size is 5.1Mb sub-directories of 1Mb or more: doc 4.4Mb ``` @@ -997,7 +988,7 @@ Run `revdep_details(, "mgcViz")` for more info * GitHub: NA * Source code: https://github.com/cran/MissingDataGUI * Date/Publication: 2016-04-25 08:58:53 -* Number of recursive dependencies: 105 +* Number of recursive dependencies: 93 Run `revdep_details(, "MissingDataGUI")` for more info @@ -1008,7 +999,7 @@ Run `revdep_details(, "MissingDataGUI")` for more info * checking S3 generic/method consistency ... WARNING ``` - (R:56419): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() + (R:14605): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. ``` @@ -1016,7 +1007,7 @@ Run `revdep_details(, "MissingDataGUI")` for more info * checking replacement functions ... WARNING ``` - (R:56430): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() + (R:14779): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() The argument of a replacement function which corresponds to the right hand side must be named ‘value’. ``` @@ -1024,7 +1015,7 @@ Run `revdep_details(, "MissingDataGUI")` for more info * checking for missing documentation entries ... WARNING ``` - (R:56715): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() + (R:15107): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. @@ -1033,23 +1024,23 @@ Run `revdep_details(, "MissingDataGUI")` for more info * checking for code/documentation mismatches ... WARNING ``` - (R:56733): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() + (R:15132): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() - (R:56749): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() + (R:15259): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() - (R:56765): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() + (R:15357): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() ``` * checking dependencies in R code ... NOTE ``` - (R:56284): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() + (R:14396): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() ``` * checking foreign function calls ... NOTE ``` - (R:56469): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() + (R:14814): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. ``` @@ -1057,13 +1048,13 @@ Run `revdep_details(, "MissingDataGUI")` for more info * checking R code for possible problems ... NOTE ``` - (R:56517): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() + (R:14905): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() ``` * checking Rd \usage sections ... NOTE ``` - (R:56803): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() + (R:15405): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R @@ -1074,11 +1065,11 @@ Run `revdep_details(, "MissingDataGUI")` for more info
-* Version: 1.6.1 +* Version: 1.6.2 * GitHub: NA * Source code: https://github.com/cran/MOFA -* Date/Publication: 2020-10-28 -* Number of recursive dependencies: 103 +* Date/Publication: 2021-02-09 +* Number of recursive dependencies: 90 Run `revdep_details(, "MOFA")` for more info @@ -1157,7 +1148,7 @@ Run `revdep_details(, "MOFA")` for more info * GitHub: https://github.com/bioFAM/MOFA2 * Source code: https://github.com/cran/MOFA2 * Date/Publication: 2020-11-03 -* Number of recursive dependencies: 219 +* Number of recursive dependencies: 223 Run `revdep_details(, "MOFA2")` for more info @@ -1182,7 +1173,7 @@ Run `revdep_details(, "MOFA2")` for more info * checking installed package size ... NOTE ``` - installed size is 5.5Mb + installed size is 5.6Mb sub-directories of 1Mb or more: doc 3.0Mb extdata 1.7Mb @@ -1239,7 +1230,7 @@ Run `revdep_details(, "MOFA2")` for more info * GitHub: NA * Source code: https://github.com/cran/nanny * Date/Publication: 2020-06-13 13:50:03 UTC -* Number of recursive dependencies: 162 +* Number of recursive dependencies: 167 Run `revdep_details(, "nanny")` for more info @@ -1262,7 +1253,7 @@ Run `revdep_details(, "nanny")` for more info * GitHub: NA * Source code: https://github.com/cran/NetworkChange * Date/Publication: 2020-07-11 22:00:14 UTC -* Number of recursive dependencies: 144 +* Number of recursive dependencies: 126 Run `revdep_details(, "NetworkChange")` for more info @@ -1308,11 +1299,11 @@ Run `revdep_details(, "nzelect")` for more info
-* Version: 1.10.1 +* Version: 1.10.11 * GitHub: https://github.com/Roleren/ORFik * Source code: https://github.com/cran/ORFik -* Date/Publication: 2020-11-09 -* Number of recursive dependencies: 146 +* Date/Publication: 2021-02-09 +* Number of recursive dependencies: 150 Run `revdep_details(, "ORFik")` for more info @@ -1340,9 +1331,9 @@ Run `revdep_details(, "ORFik")` for more info * checking installed package size ... NOTE ``` - installed size is 5.5Mb + installed size is 6.4Mb sub-directories of 1Mb or more: - doc 3.2Mb + doc 3.9Mb ``` * checking dependencies in R code ... NOTE @@ -1352,30 +1343,33 @@ Run `revdep_details(, "ORFik")` for more info ‘IRanges:::regroupBySupergroup’ ‘S4Vectors:::normarg_mcols’ ‘biomartr:::getENSEMBL.Seq’ ‘biomartr:::getENSEMBL.gtf’ See the note in ?`:::` about the use of this operator. + There are ::: calls to the package's namespace in its code. A package + almost never needs to use ::: for its own objects: + ‘findFa’ ‘find_url_ebi’ ‘hasHits’ ‘trimming.table’ ``` * checking R code for possible problems ... NOTE ``` ... - collapseDuplicatedReads,GRanges: no visible binding for global variable - ‘size’ - collapseDuplicatedReads,GRanges: no visible global function definition - for ‘.’ - Undefined global functions or variables: - . CDS CDSGrouping Hx LEADERS ORFGrouping ORFScores RRS RSS Run Sample - StartCodons StopCodons TOP chr cigar1 cigar2 codonSums count countRFP - count_seq_pos_with_count detectCores dif difPer disengagementScores - distORFCDS entropyRFP exon_rank feature forward fpkmRFP fpkmRNA - fraction fraction.x fraction.y fractionLengths fraction_min fractions - frame frame_one_RP frame_two_RP gene_id gene_sum grnames inFrameCDS - ioScore isOverlappingCds kozak leaders mRNA mean_per_gene - median_per_gene median_score name ones pShifted pick position random - rankInTx ranks ratio_cds_leader ratio_cds_mrna ratio_mrna_aligned - rowSums2 sample_id scalingFactor sd_per_gene seq1 seq2 seq3 seq4 seq5 - size spots start1 start2 startCodonCoverage startRegionRelative - sum.count sum_per_gene te trailers tx utr3_len utr5_len value - variable widths windowMean windowSD zscore + . CDS CDSGrouping Hx IR LEADERS LFC_TE ORFGrouping ORFScores RRS RSS + Regulation Run StartCodons StopCodons TE_log2 TOP chr cigar1 cigar2 + codonSums count countRFP count_seq_pos_with_count counts_per_sample + detectCores df.rfp df.rna dif difPer disengagementScores distORFCDS + entropyRFP exon_rank feature forward fpkmRFP fpkmRNA fraction + fraction.x fraction.y fractionLengths fraction_min fractions frame + frame_one_RP frame_two_RP gene_id gene_sum grnames inFrameCDS ioScore + isOverlappingCds kozak leaders mRNA mean_IR mean_per_gene + median_per_gene median_score name ones pShifted + perc_of_counts_per_sample percent percentage percentage_mrna_aligned + pick position random rankInTx ranks ratio_cds_leader ratio_cds_mrna + read length rfp rfp_log2 rna rna_log10 rna_log2 rowMin rowSums2 + sample_id sample_total scalingFactor sd_per_gene seq1 seq2 seq3 seq4 + seq5 size spots start1 start2 startCodonCoverage startRegionRelative + subtitle sum.count sum_per_gene te trailers tx tx_len + upstream_kozak_strength utr3_len utr5_len value variable widths + windowMean windowSD zscore Consider adding + importFrom("base", "length") importFrom("graphics", "frame") to your NAMESPACE file. ``` @@ -1388,7 +1382,7 @@ Run `revdep_details(, "ORFik")` for more info * GitHub: NA * Source code: https://github.com/cran/PAFway * Date/Publication: 2020-02-05 16:40:02 UTC -* Number of recursive dependencies: 78 +* Number of recursive dependencies: 71 Run `revdep_details(, "PAFway")` for more info @@ -1411,7 +1405,7 @@ Run `revdep_details(, "PAFway")` for more info * GitHub: https://github.com/XiaoruiZhu/PAsso * Source code: https://github.com/cran/PAsso * Date/Publication: 2020-07-13 08:50:07 UTC -* Number of recursive dependencies: 163 +* Number of recursive dependencies: 161 Run `revdep_details(, "PAsso")` for more info @@ -1439,7 +1433,7 @@ Run `revdep_details(, "PAsso")` for more info * GitHub: https://github.com/hfang-bristol/Pi * Source code: https://github.com/cran/Pi * Date/Publication: 2020-11-24 -* Number of recursive dependencies: 241 +* Number of recursive dependencies: 230 Run `revdep_details(, "Pi")` for more info @@ -1458,11 +1452,11 @@ Run `revdep_details(, "Pi")` for more info
-* Version: 4.9.2.2 +* Version: 4.9.3 * GitHub: https://github.com/ropensci/plotly * Source code: https://github.com/cran/plotly -* Date/Publication: 2020-12-19 06:15:37 UTC -* Number of recursive dependencies: 156 +* Date/Publication: 2021-01-10 14:30:02 UTC +* Number of recursive dependencies: 161 Run `revdep_details(, "plotly")` for more info @@ -1472,9 +1466,9 @@ Run `revdep_details(, "plotly")` for more info * checking installed package size ... NOTE ``` - installed size is 6.5Mb + installed size is 6.8Mb sub-directories of 1Mb or more: - htmlwidgets 3.7Mb + htmlwidgets 3.8Mb ``` # PopGenReport @@ -1485,7 +1479,7 @@ Run `revdep_details(, "plotly")` for more info * GitHub: https://github.com/green-striped-gecko/PopGenReport * Source code: https://github.com/cran/PopGenReport * Date/Publication: 2019-02-04 12:13:23 UTC -* Number of recursive dependencies: 124 +* Number of recursive dependencies: 119 Run `revdep_details(, "PopGenReport")` for more info @@ -1502,11 +1496,11 @@ Run `revdep_details(, "PopGenReport")` for more info
-* Version: 1.1.19 +* Version: 1.1.20 * GitHub: https://github.com/josie-athens/pubh * Source code: https://github.com/cran/pubh -* Date/Publication: 2020-12-03 08:20:02 UTC -* Number of recursive dependencies: 204 +* Date/Publication: 2021-02-16 17:30:06 UTC +* Number of recursive dependencies: 202 Run `revdep_details(, "pubh")` for more info @@ -1528,7 +1522,7 @@ Run `revdep_details(, "pubh")` for more info * GitHub: NA * Source code: https://github.com/cran/robCompositions * Date/Publication: 2020-11-18 21:10:02 UTC -* Number of recursive dependencies: 146 +* Number of recursive dependencies: 148 Run `revdep_details(, "robCompositions")` for more info @@ -1545,11 +1539,11 @@ Run `revdep_details(, "robCompositions")` for more info
-* Version: 0.93-6 +* Version: 0.93-7 * GitHub: NA * Source code: https://github.com/cran/robustbase -* Date/Publication: 2020-03-23 17:40:02 UTC -* Number of recursive dependencies: 76 +* Date/Publication: 2021-01-04 15:30:03 UTC +* Number of recursive dependencies: 67 Run `revdep_details(, "robustbase")` for more info @@ -1557,6 +1551,11 @@ Run `revdep_details(, "robustbase")` for more info ## In both +* checking package dependencies ... NOTE + ``` + Package which this enhances but not available for checking: ‘robustX’ + ``` + * checking Rd cross-references ... NOTE ``` Package unavailable to check Rd xrefs: ‘robustX’ @@ -1592,7 +1591,7 @@ Run `revdep_details(, "rrr")` for more info * GitHub: https://github.com/LuyiTian/scPipe * Source code: https://github.com/cran/scPipe * Date/Publication: 2020-10-27 -* Number of recursive dependencies: 144 +* Number of recursive dependencies: 149 Run `revdep_details(, "scPipe")` for more info @@ -1657,7 +1656,7 @@ Run `revdep_details(, "scPipe")` for more info * GitHub: NA * Source code: https://github.com/cran/seer * Date/Publication: 2020-06-08 05:00:02 UTC -* Number of recursive dependencies: 111 +* Number of recursive dependencies: 112 Run `revdep_details(, "seer")` for more info @@ -1679,7 +1678,7 @@ Run `revdep_details(, "seer")` for more info * GitHub: https://github.com/Liubuntu/SeqSQC * Source code: https://github.com/cran/SeqSQC * Date/Publication: 2020-10-27 -* Number of recursive dependencies: 133 +* Number of recursive dependencies: 141 Run `revdep_details(, "SeqSQC")` for more info @@ -1699,16 +1698,16 @@ Run `revdep_details(, "SeqSQC")` for more info Genotype matrix is being transposed ... Optimize the access efficiency ... Clean up the fragments of GDS file: - open the file '/var/folders/0k/bxg5lhr92sq74mb1d446ql540000gp/T//RtmprkZ7pQ/file78b615f5a092' (12.4K) + open the file '/var/folders/0k/bxg5lhr92sq74mb1d446ql540000gp/T//RtmpjeDD22/file1054219e79e09' (12.4K) # of fragments: 48 - save to '/var/folders/0k/bxg5lhr92sq74mb1d446ql540000gp/T//RtmprkZ7pQ/file78b615f5a092.tmp' - rename '/var/folders/0k/bxg5lhr92sq74mb1d446ql540000gp/T//RtmprkZ7pQ/file78b615f5a092.tmp' (10.7K, reduced: 1.6K) + save to '/var/folders/0k/bxg5lhr92sq74mb1d446ql540000gp/T//RtmpjeDD22/file1054219e79e09.tmp' + rename '/var/folders/0k/bxg5lhr92sq74mb1d446ql540000gp/T//RtmpjeDD22/file1054219e79e09.tmp' (10.7K, reduced: 1.6K) # of fragments: 20 Load study cohort annotation file ... Load 1kg data to temp directory... Error: Corrupt Cache: sqlite file See vignette section on corrupt cache - cache: /Users/barret/Library/Caches/ExperimentHub + cache: ~/Library/Caches/ExperimentHub filename: experimenthub.sqlite3 Execution halted ``` @@ -1741,7 +1740,7 @@ Run `revdep_details(, "SeqSQC")` for more info * GitHub: https://github.com/daya6489/SmartEDA * Source code: https://github.com/cran/SmartEDA * Date/Publication: 2020-07-10 10:20:17 UTC -* Number of recursive dependencies: 115 +* Number of recursive dependencies: 124 Run `revdep_details(, "SmartEDA")` for more info @@ -1758,11 +1757,11 @@ Run `revdep_details(, "SmartEDA")` for more info
-* Version: 3.0.3 +* Version: 3.1.4 * GitHub: https://github.com/BioSystemsUM/specmine * Source code: https://github.com/cran/specmine -* Date/Publication: 2020-12-17 23:30:02 UTC -* Number of recursive dependencies: 281 +* Date/Publication: 2021-03-04 23:10:02 UTC +* Number of recursive dependencies: 284 Run `revdep_details(, "specmine")` for more info @@ -1795,7 +1794,7 @@ Run `revdep_details(, "specmine")` for more info * GitHub: https://github.com/nspyrison/spinifex * Source code: https://github.com/cran/spinifex * Date/Publication: 2020-11-18 15:00:02 UTC -* Number of recursive dependencies: 101 +* Number of recursive dependencies: 107 Run `revdep_details(, "spinifex")` for more info @@ -1820,7 +1819,7 @@ Run `revdep_details(, "spinifex")` for more info 7. └─args$renderer(frames_vars$frame_source, args$fps) 8. └─magick::image_animate(anim, fps, loop = if (loop) 0 else 1) - [ FAIL 2 | WARN 14 | SKIP 0 | PASS 53 ] + [ FAIL 2 | WARN 12 | SKIP 0 | PASS 53 ] Error: Test failures Execution halted ``` @@ -1839,7 +1838,7 @@ Run `revdep_details(, "spinifex")` for more info * GitHub: NA * Source code: https://github.com/cran/spup * Date/Publication: 2020-04-30 22:20:06 UTC -* Number of recursive dependencies: 83 +* Number of recursive dependencies: 85 Run `revdep_details(, "spup")` for more info @@ -1861,7 +1860,7 @@ Run `revdep_details(, "spup")` for more info * GitHub: NA * Source code: https://github.com/cran/statVisual * Date/Publication: 2020-02-20 19:30:02 UTC -* Number of recursive dependencies: 176 +* Number of recursive dependencies: 165 Run `revdep_details(, "statVisual")` for more info @@ -1892,7 +1891,7 @@ Run `revdep_details(, "statVisual")` for more info * GitHub: NA * Source code: https://github.com/cran/tidybulk * Date/Publication: 2020-10-27 -* Number of recursive dependencies: 265 +* Number of recursive dependencies: 269 Run `revdep_details(, "tidybulk")` for more info @@ -1962,7 +1961,7 @@ Run `revdep_details(, "tidybulk")` for more info * GitHub: NA * Source code: https://github.com/cran/tidySingleCellExperiment * Date/Publication: 2020-10-27 -* Number of recursive dependencies: 200 +* Number of recursive dependencies: 205 Run `revdep_details(, "tidySingleCellExperiment")` for more info @@ -2024,7 +2023,7 @@ Run `revdep_details(, "tidySingleCellExperiment")` for more info * GitHub: NA * Source code: https://github.com/cran/TNBC.CMS * Date/Publication: 2020-10-27 -* Number of recursive dependencies: 164 +* Number of recursive dependencies: 151 Run `revdep_details(, "TNBC.CMS")` for more info @@ -2054,7 +2053,7 @@ Run `revdep_details(, "TNBC.CMS")` for more info * GitHub: https://github.com/kevinrue/TVTB * Source code: https://github.com/cran/TVTB * Date/Publication: 2020-10-27 -* Number of recursive dependencies: 164 +* Number of recursive dependencies: 172 Run `revdep_details(, "TVTB")` for more info @@ -2078,7 +2077,7 @@ Run `revdep_details(, "TVTB")` for more info * GitHub: https://github.com/john-harrold/ubiquity * Source code: https://github.com/cran/ubiquity * Date/Publication: 2020-09-13 16:40:02 UTC -* Number of recursive dependencies: 110 +* Number of recursive dependencies: 117 Run `revdep_details(, "ubiquity")` for more info @@ -2088,39 +2087,12 @@ Run `revdep_details(, "ubiquity")` for more info * checking installed package size ... NOTE ``` - installed size is 9.5Mb + installed size is 9.6Mb sub-directories of 1Mb or more: doc 6.5Mb ubinc 2.1Mb ``` -# ufs - -
- -* Version: 0.4.0 -* GitHub: NA -* Source code: https://github.com/cran/ufs -* Date/Publication: 2020-11-10 11:40:03 UTC -* Number of recursive dependencies: 159 - -Run `revdep_details(, "ufs")` for more info - -
- -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘viridis’ - All declared Imports should be used. - ``` - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘behaviorchange’ - ``` - # vidger
@@ -2129,7 +2101,7 @@ Run `revdep_details(, "ufs")` for more info * GitHub: https://github.com/btmonier/vidger * Source code: https://github.com/cran/vidger * Date/Publication: 2020-10-27 -* Number of recursive dependencies: 123 +* Number of recursive dependencies: 126 Run `revdep_details(, "vidger")` for more info