From fefaac86cb96ccaccb5c1eb700a1497938b718dc Mon Sep 17 00:00:00 2001 From: igor <6363505+igordot@users.noreply.github.com> Date: Wed, 5 May 2021 13:04:21 -0400 Subject: [PATCH] Prepare for CRAN release 7.4.1 --- .gitignore | 3 +- DESCRIPTION | 2 +- NEWS.md | 2 +- R/functions.R | 5 -- README.md | 2 +- cran-comments.md | 8 ++- revdep/.gitignore | 1 + revdep/README.md | 31 +++++++---- revdep/cran.md | 2 +- revdep/failures.md | 26 ++++++--- revdep/problems.md | 108 ++++++++++++++++++++---------------- vignettes/msigdbr-intro.Rmd | 6 +- 12 files changed, 113 insertions(+), 83 deletions(-) diff --git a/.gitignore b/.gitignore index 0f95aa7..b32ff9c 100644 --- a/.gitignore +++ b/.gitignore @@ -27,6 +27,8 @@ inst/doc # Temporary files created by R markdown *.utf8.md *.knit.md +# pkgdown +docs ### macOS ### *.DS_Store @@ -67,4 +69,3 @@ $RECYCLE.BIN/ *.msp # Windows shortcuts *.lnk -docs diff --git a/DESCRIPTION b/DESCRIPTION index 2477db1..327f33a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: msigdbr Type: Package Title: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format -Version: 7.2.1.9002 +Version: 7.4.1 Authors@R: person("Igor", "Dolgalev", email = "igor.dolgalev@nyumc.org", role = c("aut", "cre")) Description: Provides the 'Molecular Signatures Database' (MSigDB) gene sets typically used with the 'Gene Set Enrichment Analysis' (GSEA) software diff --git a/NEWS.md b/NEWS.md index e9b8321..4b778ad 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# msigdbr (development version) +# msigdbr 7.4.1 * Based on MSigDB v7.4 release. * Added Ensembl gene IDs to the returned gene sets. diff --git a/R/functions.R b/R/functions.R index 33b5d81..049af4d 100644 --- a/R/functions.R +++ b/R/functions.R @@ -145,11 +145,6 @@ msigdbr <- function(species = "Homo sapiens", category = NULL, subcategory = NUL ) } - # confirm that the species exists in the database - if (nrow(orthologs_subset) == 0) { - stop("species does not exist in the database: ", species) - } - # combine gene sets and orthologs genesets_subset %>% inner_join(orthologs_subset, by = "human_ensembl_gene") %>% diff --git a/README.md b/README.md index e55628c..7bf20d7 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ The `msigdbr` R package provides Molecular Signatures Database (MSigDB) gene set * in an R-friendly tidy/long format with one gene per row * for multiple frequently studied model organisms, such as mouse, rat, pig, zebrafish, fly, and yeast, in addition to the original human genes -* as both gene symbols and NCBI Entrez Gene IDs for better compatibility with pathway enrichment tools +* as gene symbols as well as NCBI Entrez and Ensembl IDs * that can be installed and loaded as a package without requiring additional external files ## Installation diff --git a/cran-comments.md b/cran-comments.md index cc677fb..0799865 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,6 +1,7 @@ ## Test environments -* local R installation, R 4.0.2 -* ubuntu 16.04 (on travis-ci), R 4.0.2 +* local R installation, R 4.0.3 +* ubuntu 20.04 (on GitHub Actions), R 3.3, R 3.6, R-release, R-devel +* macOS (on GitHub Actions), R-release * win-builder (devel) ## R CMD check results @@ -9,7 +10,8 @@ ## revdepcheck results -We checked 7 reverse dependencies (3 from CRAN + 4 from BioConductor), comparing R CMD check results across CRAN and dev versions of this package. +We checked 14 reverse dependencies (5 from CRAN + 9 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/.gitignore b/revdep/.gitignore index 31f6c40..bc768ae 100644 --- a/revdep/.gitignore +++ b/revdep/.gitignore @@ -4,3 +4,4 @@ checks.noindex library.noindex data.sqlite *.html +cloud.noindex diff --git a/revdep/README.md b/revdep/README.md index 3c1d844..59e8ed8 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -2,7 +2,7 @@ |field |value | |:--------|:----------------------------| -|version |R version 4.0.2 (2020-06-22) | +|version |R version 4.0.3 (2020-10-10) | |os |macOS Mojave 10.14.6 | |system |x86_64, darwin17.0 | |ui |RStudio | @@ -10,25 +10,34 @@ |collate |en_US.UTF-8 | |ctype |en_US.UTF-8 | |tz |America/New_York | -|date |2020-10-02 | +|date |2021-05-04 | # Dependencies -|package |old |new |Δ | -|:-------|:-----|:-----|:--| -|msigdbr |7.1.1 |7.2.1 |* | +|package |old |new |Δ | +|:----------|:-----|:------|:--| +|msigdbr |7.2.1 |7.4.1 |* | +|cli |NA |2.5.0 |* | +|ellipsis |NA |0.3.2 |* | +|fansi |NA |0.4.2 |* | +|pillar |NA |1.6.0 |* | +|rlang |NA |0.4.11 |* | +|tibble |NA |3.1.1 |* | +|tidyselect |NA |1.1.1 |* | +|utf8 |NA |1.2.1 |* | +|vctrs |NA |0.3.8 |* | # Revdeps ## Failed to check (1) -|package |version |error |warning |note | -|:--------|:-------|:-----|:-------|:----| -|tidybulk |? | | | | +|package |version |error |warning |note | +|:------------------|:-------|:-----|:-------|:----| +|simplifyEnrichment |? | | | | ## New problems (1) -|package |version |error |warning |note | -|:--------------------------|:-------|:-----|:-------|:----| -|[hypeR](problems.md#hyper) |1.4.0 | |__+1__ |2 | +|package |version |error |warning |note | +|:----------------------------------------|:-------|:------|:-------|:----| +|[singleCellTK](problems.md#singlecelltk) |2.0.0 |__+2__ |1 |1 | diff --git a/revdep/cran.md b/revdep/cran.md index 87b7619..62b8228 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,6 +1,6 @@ ## revdepcheck results -We checked 7 reverse dependencies (3 from CRAN + 4 from BioConductor), comparing R CMD check results across CRAN and dev versions of this package. +We checked 14 reverse dependencies (5 from CRAN + 9 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/failures.md b/revdep/failures.md index 7d70243..e24b313 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -1,4 +1,4 @@ -# tidybulk +# simplifyEnrichment
@@ -15,14 +15,18 @@ ``` - There is a binary version available but the source version is later: - binary source needs_compilation -RSQLite 2.2.0 2.2.1 TRUE + There are binary versions available but the source versions are later: + binary source needs_compilation +class 7.3-18 7.3-19 TRUE +colorspace 2.0-0 2.0-1 TRUE +MASS 7.3-53.1 7.3-54 TRUE +Matrix 1.3-2 1.3-3 TRUE +RcppParallel 5.1.3 5.1.4 TRUE Binaries will be installed -installing the source packages ‘EGSEAdata’, ‘hgu133a.db’, ‘hgu133plus2.db’, ‘KEGGdzPathwaysGEO’, ‘org.Mm.eg.db’, ‘org.Rn.eg.db’ +installing the source package ‘reactome.db’ @@ -31,14 +35,18 @@ installing the source packages ‘EGSEAdata’, ‘hgu133a.db’, ‘hgu133plus2 ``` - There is a binary version available but the source version is later: - binary source needs_compilation -RSQLite 2.2.0 2.2.1 TRUE + There are binary versions available but the source versions are later: + binary source needs_compilation +class 7.3-18 7.3-19 TRUE +colorspace 2.0-0 2.0-1 TRUE +MASS 7.3-53.1 7.3-54 TRUE +Matrix 1.3-2 1.3-3 TRUE +RcppParallel 5.1.3 5.1.4 TRUE Binaries will be installed -installing the source packages ‘EGSEAdata’, ‘hgu133a.db’, ‘hgu133plus2.db’, ‘KEGGdzPathwaysGEO’, ‘org.Mm.eg.db’, ‘org.Rn.eg.db’ +installing the source package ‘reactome.db’ diff --git a/revdep/problems.md b/revdep/problems.md index 72cacc0..1961c9a 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,68 +1,82 @@ -# hypeR +# singleCellTK
-* Version: 1.4.0 -* GitHub: https://github.com/montilab/hypeR -* Source code: https://github.com/cran/hypeR -* Date/Publication: 2020-04-27 -* Number of recursive dependencies: 111 +* Version: 2.0.0 +* GitHub: https://github.com/compbiomed/singleCellTK +* Source code: https://github.com/cran/singleCellTK +* Date/Publication: 2020-10-27 +* Number of recursive dependencies: 339 -Run `revdep_details(, "hypeR")` for more info +Run `revdep_details(, "singleCellTK")` for more info
## Newly broken -* checking examples ... WARNING +* checking examples ... ERROR ``` - Found the following significant warnings: + Running examples in ‘singleCellTK-Ex.R’ failed + The error most likely occurred in: - Warning: 'msigdbr::msigdbr_show_species' is deprecated. - Warning: 'msigdbr::msigdbr_show_species' is deprecated. - Warning: 'msigdbr::msigdbr_show_species' is deprecated. - Warning: 'msigdbr::msigdbr_show_species' is deprecated. - Warning: 'msigdbr::msigdbr_show_species' is deprecated. - Warning: 'msigdbr::msigdbr_show_species' is deprecated. - Warning: 'msigdbr::msigdbr_show_species' is deprecated. - Warning: 'msigdbr::msigdbr_show_species' is deprecated. - Warning: 'msigdbr::msigdbr_show_species' is deprecated. - Warning: 'msigdbr::msigdbr_show_species' is deprecated. - Deprecated functions may be defunct as soon as of the next release of - R. - See ?Deprecated. + > ### Name: importGeneSetsFromMSigDB + > ### Title: Imports gene sets from MSigDB + > ### Aliases: importGeneSetsFromMSigDB + > + > ### ** Examples + > + > data(scExample) + ... + > sce <- importGeneSetsFromMSigDB(inSCE = sce, + + categoryIDs = "H", + + species = "Homo sapiens", + + mapping = "gene_symbol", + + by = "feature_name") + Tue May 4 13:37:02 2021 .. Importing 'H' gene sets (n = 50) + Error in validObject(.Object) : + invalid class “GeneSet” object: gene symbols must be unique + Calls: importGeneSetsFromMSigDB ... -> initialize -> initialize -> validObject + Execution halted + ``` + +* checking tests ... + ``` + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Error: invalid class "GeneSet" object: gene symbols must be unique + Backtrace: + █ + 1. └─singleCellTK::importGeneSetsFromMSigDB(...) test-import.R:107:2 + 2. ├─GSEABase::GeneSet(...) + 3. └─GSEABase::GeneSet(...) + 4. ├─base::do.call(new, c("GeneSet", list(... = ..., setIdentifier = setIdentifier))) + 5. └─(function (Class, ...) ... + 6. ├─methods::initialize(value, ...) + 7. └─methods::initialize(value, ...) + 8. └─methods::validObject(.Object) + + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 36 ] + Error: Test failures + Execution halted ``` ## In both -* checking R code for possible problems ... NOTE +* checking whether package ‘singleCellTK’ can be installed ... WARNING ``` - ... - ‘is’ - hyp_to_table: no visible global function definition for ‘is’ - hyp_to_table: no visible global function definition for - ‘packageVersion’ - hyp_to_table: no visible global function definition for ‘write.table’ - hypeR: no visible global function definition for ‘is’ - msigdb_available: no visible binding for global variable ‘gs_cat’ - msigdb_available: no visible binding for global variable ‘gs_subcat’ - msigdb_download: no visible binding for global variable ‘gs_name’ - msigdb_download: no visible binding for global variable ‘gene_symbol’ - msigdb_download: no visible binding for global variable ‘.’ - msigdb_version: no visible global function definition for - ‘packageVersion’ - Undefined global functions or variables: - . fdr from gene_symbol gs_cat gs_name gs_subcat is label - packageVersion pval significance size to write.table x y - Consider adding - importFrom("methods", "is") - importFrom("utils", "packageVersion", "write.table") - to your NAMESPACE file (and ensure that your DESCRIPTION Imports field - contains 'methods'). + Found the following significant warnings: + Warning: package ‘BiocGenerics’ was built under R version 4.0.5 + Warning: package ‘GenomeInfoDb’ was built under R version 4.0.5 + Warning: package ‘DelayedArray’ was built under R version 4.0.4 + See ‘/Users/id460/repos/msigdbr/revdep/checks.noindex/singleCellTK/new/singleCellTK.Rcheck/00install.out’ for details. ``` -* checking for unstated dependencies in vignettes ... NOTE +* checking dependencies in R code ... NOTE ``` - 'library' or 'require' call not declared from: ‘tidyverse’ + Namespaces in Imports field not imported from: + 'BiocGenerics' 'ggplotify' 'kableExtra' 'shinyBS' 'shinyFiles' + 'shinyWidgets' 'shinyjqui' 'shinythemes' + All declared Imports should be used. ``` diff --git a/vignettes/msigdbr-intro.Rmd b/vignettes/msigdbr-intro.Rmd index f47256f..3002aef 100644 --- a/vignettes/msigdbr-intro.Rmd +++ b/vignettes/msigdbr-intro.Rmd @@ -31,7 +31,7 @@ The `msigdbr` R package provides Molecular Signatures Database (MSigDB) gene set * in an R-friendly tidy/long format with one gene per row * for multiple frequently studied model organisms, such as mouse, rat, pig, zebrafish, fly, and yeast, in addition to the original human genes -* as both gene symbols and NCBI Entrez Gene IDs for better compatibility with pathway enrichment tools +* as gene symbols as well as NCBI Entrez and Ensembl IDs * that can be installed and loaded as a package without requiring additional external files Please be aware that the homologs were computationally predicted for distinct genes. @@ -101,14 +101,14 @@ The `msigdbr` output can be used with various popular pathway analysis packages. Use the gene sets data frame for `clusterProfiler` with genes as Entrez Gene IDs. ```{r cp-entrez, eval=FALSE} -msigdbr_t2g = msigdbr_df %>% dplyr::select(gs_name, entrez_gene) %>% as.data.frame() +msigdbr_t2g = msigdbr_df %>% dplyr::distinct(gs_name, entrez_gene) %>% as.data.frame() enricher(gene = gene_ids_vector, TERM2GENE = msigdbr_t2g, ...) ``` Use the gene sets data frame for `clusterProfiler` with genes as gene symbols. ```{r cp-symbols, eval=FALSE} -msigdbr_t2g = msigdbr_df %>% dplyr::select(gs_name, gene_symbol) %>% as.data.frame() +msigdbr_t2g = msigdbr_df %>% dplyr::distinct(gs_name, gene_symbol) %>% as.data.frame() enricher(gene = gene_symbols_vector, TERM2GENE = msigdbr_t2g, ...) ```