diff --git a/README.md b/README.md index d21bdc0..7bed760 100644 --- a/README.md +++ b/README.md @@ -22,6 +22,12 @@ The package can be installed from [CRAN](https://cran.r-project.org/package=msig install.packages("msigdbr") ``` +Releases that are not available on CRAN can be installed from GitHub (specific release or version can be specified): + +```{r} +remotes::install_github("igordot/msigdbr", ref = "v2022.1.1") +``` + ## Usage The package data can be accessed using the `msigdbr()` function, which returns a data frame of gene sets and their member genes. For example, you can retrieve mouse genes from the C2 (curated) CGP (chemical and genetic perturbations) gene sets. diff --git a/cran-comments.md b/cran-comments.md deleted file mode 100644 index a63ca9b..0000000 --- a/cran-comments.md +++ /dev/null @@ -1,16 +0,0 @@ -## Test environments -* local R installation, R 4.1.2 -* ubuntu-latest (on GitHub Actions), R 3.4, R 3.6, R-release, R-devel -* macOS (on GitHub Actions), R-release -* win-builder (devel) - -## R CMD check results - -0 errors | 0 warnings | 1 note - -## revdepcheck results - -We checked 24 reverse dependencies (10 from CRAN + 14 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. - - * We saw 0 new problems - * We failed to check 1 packages diff --git a/revdep/.gitignore b/revdep/.gitignore deleted file mode 100644 index bc768ae..0000000 --- a/revdep/.gitignore +++ /dev/null @@ -1,7 +0,0 @@ -checks -library -checks.noindex -library.noindex -data.sqlite -*.html -cloud.noindex diff --git a/revdep/README.md b/revdep/README.md deleted file mode 100644 index 291c5ce..0000000 --- a/revdep/README.md +++ /dev/null @@ -1,41 +0,0 @@ -# Platform - -|field |value | -|:--------|:------------------------------------| -|version |R version 4.1.2 (2021-11-01) | -|os |macOS Monterey 12.2.1 | -|system |x86_64, darwin17.0 | -|ui |RStudio | -|language |(EN) | -|collate |en_US.UTF-8 | -|ctype |en_US.UTF-8 | -|tz |America/New_York | -|date |2022-03-29 | -|rstudio |2021.09.2+382 Ghost Orchid (desktop) | -|pandoc |NA | - -# Dependencies - -|package |old |new |Δ | -|:----------|:-----|:-----|:--| -|msigdbr |7.4.1 |7.5.1 |* | -|cli |NA |3.2.0 |* | -|crayon |NA |1.5.1 |* | -|fansi |NA |1.0.3 |* | -|glue |NA |1.6.2 |* | -|rlang |NA |1.0.2 |* | -|tidyselect |NA |1.1.2 |* | - -# Revdeps - -## Failed to check (6) - -|package |version |error |warning |note | -|:------------------|:-------|:-----|:-------|:----| -|ChromSCape |1.4.0 |1 | |5 | -|OSCA.advanced |? | | | | -|pathfindR |1.6.3 |1 | | | -|simplifyEnrichment |? | | | | -|singleCellTK |2.4.0 |1 | |2 | -|sparrow |? | | | | - diff --git a/revdep/cran.md b/revdep/cran.md deleted file mode 100644 index 7908e06..0000000 --- a/revdep/cran.md +++ /dev/null @@ -1,12 +0,0 @@ -## revdepcheck results - -We checked 24 reverse dependencies (10 from CRAN + 14 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. - - * We saw 0 new problems - * We failed to check 1 packages - -Issues with CRAN packages are summarised below. - -### Failed to check - -* pathfindR (NA) diff --git a/revdep/email.yml b/revdep/email.yml deleted file mode 100644 index 0c5cef8..0000000 --- a/revdep/email.yml +++ /dev/null @@ -1,5 +0,0 @@ -release_date: ??? -rel_release_date: ??? -my_news_url: ??? -release_version: ??? -release_details: ??? diff --git a/revdep/failures.md b/revdep/failures.md deleted file mode 100644 index 4e882e8..0000000 --- a/revdep/failures.md +++ /dev/null @@ -1,337 +0,0 @@ -# ChromSCape - -
- -* Version: 1.4.0 -* GitHub: https://github.com/vallotlab/ChromSCape -* Source code: https://github.com/cran/ChromSCape -* Date/Publication: 2021-10-26 -* Number of recursive dependencies: 272 - -Run `revdep_details(, "ChromSCape")` for more info - -
- -## In both - -* R CMD check timed out - - -* checking for hidden files and directories ... NOTE - ``` - Found the following hidden files and directories: - .BBSoptions - These were most likely included in error. See section ‘Package - structure’ in the ‘Writing R Extensions’ manual. - ``` - -* checking installed package size ... NOTE - ``` - installed size is 7.4Mb - sub-directories of 1Mb or more: - data 1.3Mb - doc 2.9Mb - www 2.1Mb - ``` - -* checking R code for possible problems ... NOTE - ``` - CompareWilcox: no visible binding for global variable ‘annot.’ - bams_to_matrix_indexes: no visible binding for global variable - ‘files_dir_list’ - filter_correlated_cell_scExp: no visible binding for global variable - ‘run_tsne’ - generate_analysis: no visible binding for global variable ‘k’ - generate_analysis: no visible binding for global variable - ‘clusterConsensus’ - get_most_variable_cyto: no visible binding for global variable - ‘cytoBand’ - ... - plot_reduced_dim_scExp: no visible binding for global variable ‘V1’ - plot_reduced_dim_scExp: no visible binding for global variable ‘V2’ - plot_reduced_dim_scExp: no visible binding for global variable - ‘cluster’ - subset_bam_call_peaks: no visible binding for global variable - ‘merged_bam’ - Undefined global functions or variables: - Fri_cyto Gain_or_Loss V1 V2 absolute_value annot. cluster - clusterConsensus cytoBand files_dir_list genes k merged_bam ncells - run_tsne sample_id total_counts - ``` - -* checking Rd files ... NOTE - ``` - prepare_Rd: raw_counts_to_sparse_matrix.Rd:6-8: Dropping empty section \source - ``` - -* checking files in ‘vignettes’ ... NOTE - ``` - Files named as vignettes but with no recognized vignette engine: - ‘vignettes/PairedTag_Zhu_H3K4me1.Rmd’ - ‘vignettes/scChIC_Ku_H3K4me3.Rmd’ - (Is a VignetteBuilder field missing?) - ``` - -# OSCA.advanced - -
- -* Version: -* GitHub: https://github.com/igordot/msigdbr -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - There are binary versions available but the source versions are later: - binary source needs_compilation -cluster 2.1.2 2.1.3 TRUE -mgcv 1.8-39 1.8-40 TRUE -S4Vectors 0.32.3 0.32.4 TRUE - - Binaries will be installed - - -installing the source packages ‘celldex’, ‘DropletTestFiles’, ‘EnsDb.Hsapiens.v86’, ‘HCAData’, ‘MouseGastrulationData’, ‘OSCA.basic’, ‘OSCA.multisample’, ‘OSCA.workflows’, ‘scRNAseq’, ‘TENxBrainData’, ‘TENxPBMCData’ - - - -``` -### CRAN - -``` - - There are binary versions available but the source versions are later: - binary source needs_compilation -cluster 2.1.2 2.1.3 TRUE -mgcv 1.8-39 1.8-40 TRUE -S4Vectors 0.32.3 0.32.4 TRUE - - Binaries will be installed - - -installing the source packages ‘celldex’, ‘DropletTestFiles’, ‘EnsDb.Hsapiens.v86’, ‘HCAData’, ‘MouseGastrulationData’, ‘OSCA.basic’, ‘OSCA.multisample’, ‘OSCA.workflows’, ‘scRNAseq’, ‘TENxBrainData’, ‘TENxPBMCData’ - - - -``` -# pathfindR - -
- -* Version: 1.6.3 -* GitHub: https://github.com/egeulgen/pathfindR -* Source code: https://github.com/cran/pathfindR -* Date/Publication: 2021-11-15 09:20:04 UTC -* Number of recursive dependencies: 141 - -Run `revdep_details(, "pathfindR")` for more info - -
- -## In both - -* checking whether package ‘pathfindR’ can be installed ... ERROR - ``` - Installation failed. - See ‘/Users/id460/repos/msigdbr/revdep/checks.noindex/pathfindR/new/pathfindR.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘pathfindR’ ... -** package ‘pathfindR’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -** help -*** installing help indices -*** copying figures -** building package indices -... -Warning in system2(java, "-version", stderr = TRUE, stdout = TRUE) : - running command ''/usr/bin/java' -version 2>&1' had status 1 -Error: package or namespace load failed for ‘pathfindR’: - .onAttach failed in attachNamespace() for 'pathfindR', details: - call: check_java_version() - error: Java version detected but couldn't parse version from The operation couldn’t be completed. Unable to locate a Java Runtime. - Please visit http://www.java.com for information on installing Java. - -Error: loading failed -Execution halted -ERROR: loading failed -* removing ‘/Users/id460/repos/msigdbr/revdep/checks.noindex/pathfindR/new/pathfindR.Rcheck/pathfindR’ - - -``` -### CRAN - -``` -* installing *source* package ‘pathfindR’ ... -** package ‘pathfindR’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -** help -*** installing help indices -*** copying figures -** building package indices -... -Warning in system2(java, "-version", stderr = TRUE, stdout = TRUE) : - running command ''/usr/bin/java' -version 2>&1' had status 1 -Error: package or namespace load failed for ‘pathfindR’: - .onAttach failed in attachNamespace() for 'pathfindR', details: - call: check_java_version() - error: Java version detected but couldn't parse version from The operation couldn’t be completed. Unable to locate a Java Runtime. - Please visit http://www.java.com for information on installing Java. - -Error: loading failed -Execution halted -ERROR: loading failed -* removing ‘/Users/id460/repos/msigdbr/revdep/checks.noindex/pathfindR/old/pathfindR.Rcheck/pathfindR’ - - -``` -# simplifyEnrichment - -
- -* Version: -* GitHub: https://github.com/igordot/msigdbr -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - There are binary versions available but the source versions are later: - binary source needs_compilation -cluster 2.1.2 2.1.3 TRUE -mgcv 1.8-39 1.8-40 TRUE -S4Vectors 0.32.3 0.32.4 TRUE -testthat 3.1.2 3.1.3 TRUE - - Binaries will be installed - - -installing the source packages ‘hu6800.db’, ‘reactome.db’ - - - -``` -### CRAN - -``` - - There are binary versions available but the source versions are later: - binary source needs_compilation -cluster 2.1.2 2.1.3 TRUE -mgcv 1.8-39 1.8-40 TRUE -S4Vectors 0.32.3 0.32.4 TRUE -testthat 3.1.2 3.1.3 TRUE - - Binaries will be installed - - -installing the source packages ‘hu6800.db’, ‘reactome.db’ - - - -``` -# singleCellTK - -
- -* Version: 2.4.0 -* GitHub: https://github.com/compbiomed/singleCellTK -* Source code: https://github.com/cran/singleCellTK -* Date/Publication: 2021-10-27 -* Number of recursive dependencies: 379 - -Run `revdep_details(, "singleCellTK")` for more info - -
- -## In both - -* R CMD check timed out - - -* checking installed package size ... NOTE - ``` - installed size is 7.0Mb - sub-directories of 1Mb or more: - extdata 1.5Mb - shiny 2.8Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - 'AnnotationDbi' 'RColorBrewer' - All declared Imports should be used. - ``` - -# sparrow - -
- -* Version: -* GitHub: https://github.com/igordot/msigdbr -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - There are binary versions available but the source versions are later: - binary source needs_compilation -cluster 2.1.2 2.1.3 TRUE -mgcv 1.8-39 1.8-40 TRUE -S4Vectors 0.32.3 0.32.4 TRUE -testthat 3.1.2 3.1.3 TRUE - - Binaries will be installed - - -installing the source packages ‘geneLenDataBase’, ‘PANTHER.db’, ‘reactome.db’ - - - -``` -### CRAN - -``` - - There are binary versions available but the source versions are later: - binary source needs_compilation -cluster 2.1.2 2.1.3 TRUE -mgcv 1.8-39 1.8-40 TRUE -S4Vectors 0.32.3 0.32.4 TRUE -testthat 3.1.2 3.1.3 TRUE - - Binaries will be installed - - -installing the source packages ‘geneLenDataBase’, ‘PANTHER.db’, ‘reactome.db’ - - - -``` diff --git a/revdep/problems.md b/revdep/problems.md deleted file mode 100644 index 9a20736..0000000 --- a/revdep/problems.md +++ /dev/null @@ -1 +0,0 @@ -*Wow, no problems at all. :)* \ No newline at end of file