Prepare for CRAN release 7.4.1

igordot · May 5, 2021 · fefaac8 · fefaac8
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diff --git 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
@@ -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 = "[email protected]", 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -4,3 +4,4 @@ checks.noindex
 library.noindex
 data.sqlite
 *.html
+cloud.noindex
diff --git a/revdep/README.md b/revdep/README.md
@@ -2,33 +2,42 @@
 
 |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                      |
 |language |(EN)                         |
 |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
@@ -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
@@ -1,4 +1,4 @@
-# tidybulk
+# simplifyEnrichment
 
 <details>
 
@@ -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
@@ -1,68 +1,82 @@
-# hypeR
+# singleCellTK
 
 <details>
 
-* 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
 
 </details>
 
 ## 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 ... <Anonymous> -> 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
@@ -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, ...)
 ```