diff --git a/.github/workflows/revdep.yaml b/.github/workflows/revdep.yaml deleted file mode 100644 index 32fab9bd..00000000 --- a/.github/workflows/revdep.yaml +++ /dev/null @@ -1,94 +0,0 @@ -on: - push: - branches: - - master - -name: revdep - -jobs: - revdep: - runs-on: ${{ matrix.config.os }} - name: ${{ matrix.config.os }} (${{ matrix.config.r }}) - strategy: - fail-fast: false - matrix: - config: - - {os: ubuntu-18.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"} - - env: - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - RSPM: ${{ matrix.config.rspm }} - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - - if: "!contains(github.event.head_commit.message, 'revdepcheck run - No changes to commit')" - steps: - - - uses: actions/checkout@v2 - - - uses: r-lib/actions/setup-r@v1 - with: - r-version: ${{ matrix.config.r }} - http-user-agent: ${{ matrix.config.http-user-agent }} - - - uses: r-lib/actions/setup-pandoc@v1 - - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Restore R package cache - uses: actions/cache@v2 - with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- - - - name: Install system dependencies - if: runner.os == 'Linux' - run: | - while read -r cmd - do - eval sudo $cmd - done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "18.04"))') - - name: Install dependencies - run: | - remotes::install_deps(dependencies = TRUE) - remotes::install_cran("rcmdcheck") - remotes::install_github("r-lib/revdepcheck") - shell: Rscript {0} - - - name: Session info - run: | - options(width = 100) - pkgs <- installed.packages()[, "Package"] - sessioninfo::session_info(pkgs, include_base = TRUE) - shell: Rscript {0} - - - name: Run revdepcheck - run: | - revdepcheck::revdep_reset() - revdepcheck::revdep_check(num_workers=4) - revdepcheck::revdep_report() - revdepcheck::revdep_report_summary() - shell: Rscript {0} - - - - name: Commit results - run: | - git config --local user.email "actions@github.com" - git config --local user.name "GitHub Actions" - git add revdep/README.md - git add revdep/problems.md - git add revdep/failures.md - git add revdep/cran.md - git commit -m "revdepcheck run - No changes to commit" || echo "No changes to commit" - git push origin || echo "No changes to commit" - - - name: Upload check results - uses: actions/upload-artifact@v2 - with: - name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: revdep/ \ No newline at end of file diff --git a/revdep/.gitignore b/revdep/.gitignore deleted file mode 100644 index 0371c751..00000000 --- a/revdep/.gitignore +++ /dev/null @@ -1,6 +0,0 @@ -library -checks -checks.noindex -library.noindex -data.sqlite -*.html diff --git a/revdep/README.md b/revdep/README.md deleted file mode 100644 index 976d0d29..00000000 --- a/revdep/README.md +++ /dev/null @@ -1,66 +0,0 @@ -# Platform - -|field |value | -|:--------|:----------------------------| -|version |R version 4.1.3 (2022-03-10) | -|os |Ubuntu 18.04.6 LTS | -|system |x86_64, linux-gnu | -|ui |X11 | -|language |(EN) | -|collate |C.UTF-8 | -|ctype |C.UTF-8 | -|tz |UTC | -|date |2022-03-20 | -|pandoc |2.7.3 @ /usr/bin/pandoc | - -# Dependencies - -|package |old |new |Δ | -|:--------|:-------|:----------|:--| -|openxlsx |4.2.5 |4.2.5.9000 |* | -|Rcpp |1.0.8.3 |1.0.8.3 | | -|stringi |1.7.6 |1.7.6 | | -|zip |2.2.0 |2.2.0 | | - -# Revdeps - -## Failed to check (35) - -|package |version |error |warning |note | -|:--------------|:-------|:-----|:-------|:----| -|appreci8R |? | | | | -|artMS |? | | | | -|bibliometrix |3.2.1 |1 | | | -|BoneProfileR |? | | | | -|breakaway |? | | | | -|bruceR |? | | | | -|cbaf |? | | | | -|CHRONOS |? | | | | -|CNVPanelizer |? | | | | -|CoTiMA |? | | | | -|DAPAR |? | | | | -|ddPCRclust |? | | | | -|Ecfun |? | | | | -|fedup |? | | | | -|GA4GHshiny |? | | | | -|genekitr |? | | | | -|hypeR |1.10.0 |1 | | | -|maEndToEnd |? | | | | -|MatrixQCvis |? | | | | -|MicroSEC |? | | | | -|nanotatoR |? | | | | -|openPrimeR |? | | | | -|parameters |? | | | | -|Pigengene |? | | | | -|PloGO2 |? | | | | -|rbiom |? | | | | -|RIPAT |? | | | | -|sangeranalyseR |? | | | | -|SEtools |? | | | | -|sigFeature |? | | | | -|struct |? | | | | -|structToolbox |? | | | | -|TarSeqQC |? | | | | -|TPP |3.22.1 |1 | |3 | -|uncoverappLib |? | | | | - diff --git a/revdep/cran.md b/revdep/cran.md deleted file mode 100644 index b23b351b..00000000 --- a/revdep/cran.md +++ /dev/null @@ -1,7 +0,0 @@ -## revdepcheck results - -We checked 141 reverse dependencies (0 from CRAN + 141 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. - - * We saw 0 new problems - * We failed to check 0 packages - diff --git a/revdep/email.yml b/revdep/email.yml deleted file mode 100644 index 406360d0..00000000 --- a/revdep/email.yml +++ /dev/null @@ -1,5 +0,0 @@ -release_date: 15.06.2021 -rel_release_date: 5 days -my_news_url: https://ycphs.github.io/openxlsx/news/index.html -release_version: 4.2.4 -my_version: 4.2.3 diff --git a/revdep/failures.md b/revdep/failures.md deleted file mode 100644 index 520ed92a..00000000 --- a/revdep/failures.md +++ /dev/null @@ -1,1242 +0,0 @@ -# appreci8R - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# artMS - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# bibliometrix - -
- -* Version: 3.2.1 -* GitHub: https://github.com/massimoaria/bibliometrix -* Source code: https://github.com/cran/bibliometrix -* Date/Publication: 2022-02-21 09:50:07 UTC -* Number of recursive dependencies: 160 - -Run `revdep_details(, "bibliometrix")` for more info - -
- -## In both - -* checking whether package ‘bibliometrix’ can be installed ... ERROR - ``` - Installation failed. - See ‘/home/runner/work/openxlsx/openxlsx/revdep/checks/bibliometrix/new/bibliometrix.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘bibliometrix’ ... -** package ‘bibliometrix’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -** inst -** byte-compile and prepare package for lazy loading -Error in dyn.load(file, DLLpath = DLLpath, ...) : - unable to load shared object '/home/runner/work/openxlsx/openxlsx/revdep/library/bibliometrix/igraph/libs/igraph.so': - libglpk.so.40: cannot open shared object file: No such file or directory -Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load -Execution halted -ERROR: lazy loading failed for package ‘bibliometrix’ -* removing ‘/home/runner/work/openxlsx/openxlsx/revdep/checks/bibliometrix/new/bibliometrix.Rcheck/bibliometrix’ - - -``` -### CRAN - -``` -* installing *source* package ‘bibliometrix’ ... -** package ‘bibliometrix’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -** inst -** byte-compile and prepare package for lazy loading -Error in dyn.load(file, DLLpath = DLLpath, ...) : - unable to load shared object '/home/runner/work/openxlsx/openxlsx/revdep/library/bibliometrix/igraph/libs/igraph.so': - libglpk.so.40: cannot open shared object file: No such file or directory -Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load -Execution halted -ERROR: lazy loading failed for package ‘bibliometrix’ -* removing ‘/home/runner/work/openxlsx/openxlsx/revdep/checks/bibliometrix/old/bibliometrix.Rcheck/bibliometrix’ - - -``` -# BoneProfileR - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# breakaway - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# bruceR - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# cbaf - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# CHRONOS - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# CNVPanelizer - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# CoTiMA - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# DAPAR - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# ddPCRclust - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# Ecfun - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# fedup - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# GA4GHshiny - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# genekitr - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# hypeR - -
- -* Version: 1.10.0 -* GitHub: https://github.com/montilab/hypeR -* Source code: https://github.com/cran/hypeR -* Date/Publication: 2021-10-26 -* Number of recursive dependencies: 154 - -Run `revdep_details(, "hypeR")` for more info - -
- -## In both - -* checking whether package ‘hypeR’ can be installed ... ERROR - ``` - Installation failed. - See ‘/home/runner/work/openxlsx/openxlsx/revdep/checks/hypeR/new/hypeR.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘hypeR’ ... -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in dyn.load(file, DLLpath = DLLpath, ...) : - unable to load shared object '/home/runner/work/openxlsx/openxlsx/revdep/library/hypeR/igraph/libs/igraph.so': - libglpk.so.40: cannot open shared object file: No such file or directory -Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load -Execution halted -ERROR: lazy loading failed for package ‘hypeR’ -* removing ‘/home/runner/work/openxlsx/openxlsx/revdep/checks/hypeR/new/hypeR.Rcheck/hypeR’ - - -``` -### CRAN - -``` -* installing *source* package ‘hypeR’ ... -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in dyn.load(file, DLLpath = DLLpath, ...) : - unable to load shared object '/home/runner/work/openxlsx/openxlsx/revdep/library/hypeR/igraph/libs/igraph.so': - libglpk.so.40: cannot open shared object file: No such file or directory -Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load -Execution halted -ERROR: lazy loading failed for package ‘hypeR’ -* removing ‘/home/runner/work/openxlsx/openxlsx/revdep/checks/hypeR/old/hypeR.Rcheck/hypeR’ - - -``` -# maEndToEnd - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# MatrixQCvis - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# MicroSEC - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# nanotatoR - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# openPrimeR - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# parameters - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# Pigengene - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# PloGO2 - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# rbiom - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# RIPAT - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# sangeranalyseR - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# SEtools - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# sigFeature - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# struct - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# structToolbox - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# TarSeqQC - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# TPP - -
- -* Version: 3.22.1 -* GitHub: NA -* Source code: https://github.com/cran/TPP -* Date/Publication: 2021-11-04 -* Number of recursive dependencies: 99 - -Run `revdep_details(, "TPP")` for more info - -
- -## In both - -* R CMD check timed out - - -* checking installed package size ... NOTE - ``` - installed size is 13.5Mb - sub-directories of 1Mb or more: - data 1.9Mb - example_data 8.0Mb - test_data 1.9Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘broom’ - All declared Imports should be used. - Unexported objects imported by ':::' calls: - ‘doParallel:::.options’ ‘mefa:::rep.data.frame’ - See the note in ?`:::` about the use of this operator. - ``` - -* checking R code for possible problems ... NOTE - ``` - File ‘TPP/R/TPP.R’: - .onLoad calls: - packageStartupMessage(msgText, "\n") - - See section ‘Good practice’ in '?.onAttach'. - - fitSigmoidCCR: no visible global function definition for - ‘capture.output’ - modelSelector: no visible binding for global variable ‘testHypothesis’ - modelSelector: no visible binding for global variable ‘fitMetric’ - ... - ‘Protein_ID’ - tpp2dExport: no visible binding for global variable ‘temperature’ - tpp2dImport: no visible binding for global variable ‘temperature’ - tpp2dNormalize: no visible binding for global variable ‘temperature’ - Undefined global functions or variables: - ..density.. Protein_ID capture.output fitMetric meltcurve_plot - minMetric temperature testHypothesis - Consider adding - importFrom("utils", "capture.output") - to your NAMESPACE file. - ``` - -# uncoverappLib - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` diff --git a/revdep/problems.md b/revdep/problems.md deleted file mode 100644 index 9a207363..00000000 --- a/revdep/problems.md +++ /dev/null @@ -1 +0,0 @@ -*Wow, no problems at all. :)* \ No newline at end of file