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Prepare for CRAN release
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‎DESCRIPTION‎

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Type: Package
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Package: babelgene
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Title: Gene Orthologs for Model Organisms in a Tidy Data Format
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Version: 22.3.9001
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Version: 22.9
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Authors@R:
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person("Igor", "Dolgalev", , "igor.dolgalev@nyumc.org", role = c("aut", "cre"),
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comment = c(ORCID = "0000-0003-4451-126X"))

‎NEWS.md‎

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# babelgene (development version)
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# babelgene 22.9
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* Updated the database.
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* Added a check for NAs in input genes (#3).

‎cran-comments.md‎

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## Test environments
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* local R installation, R 4.1.2
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* local R installation, R 4.2.1
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* ubuntu-latest (on GitHub Actions), R 3.4, R 3.6, R-release, R-devel
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* macOS-latest (on GitHub Actions), R-release
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* windows-latest (on GitHub Actions), R-release
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* win-builder (devel)
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## R CMD check results
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‎revdep/README.md‎

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# Platform
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|field |value |
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|:--------|:------------------------------------|
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|version |R version 4.1.2 (2021-11-01) |
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|os |macOS Monterey 12.2.1 |
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|system |x86_64, darwin17.0 |
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|ui |RStudio |
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|language |(EN) |
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|collate |en_US.UTF-8 |
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|ctype |en_US.UTF-8 |
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|tz |America/New_York |
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|date |2022-03-30 |
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|rstudio |2021.09.2+382 Ghost Orchid (desktop) |
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|pandoc |NA |
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|field |value |
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|:--------|:----------------------------------------|
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|version |R version 4.2.1 (2022-06-23) |
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|os |macOS Monterey 12.5.1 |
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|system |x86_64, darwin17.0 |
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|ui |RStudio |
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|language |(EN) |
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|collate |en_US.UTF-8 |
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|ctype |en_US.UTF-8 |
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|tz |America/New_York |
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|date |2022-09-28 |
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|rstudio |2022.02.3+492 Prairie Trillium (desktop) |
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|pandoc |2.19 @ /usr/local/bin/pandoc |
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# Dependencies
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|package | old|new |Δ |
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|:----------|----:|:---------|:--|
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|babelgene | 21.4|21.4.9001 |* |
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|cli | NA|3.2.0 |* |
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|crayon | NA|1.5.1 |* |
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|fansi | NA|1.0.3 |* |
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|glue | NA|1.6.2 |* |
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|magrittr | NA|2.0.2 |* |
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|rlang | NA|1.0.2 |* |
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|tidyselect | NA|1.1.2 |* |
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|vctrs | NA|0.3.8 |* |
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|package | old| new|Δ |
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|:---------|----:|----:|:--|
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|babelgene | 22.3| 22.9|* |
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# Revdeps
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## New problems (1)
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|package |version |error |warning |note |
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|:----------------------------------|:-------|:------|:-------|:----|
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|[orthogene](problems.md#orthogene) |1.0.0 |__+1__ | | |
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|package |version |error |warning |note |
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|:---------|:-------|:------|:-------|:----|
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|[orthogene](problems.md#orthogene)|1.2.0 |__+1__ | |1 |
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‎revdep/failures.md‎

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```
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There are binary versions available but the source versions are later:
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binary source needs_compilation
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cluster 2.1.2 2.1.3 TRUE
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magrittr 2.0.2 2.0.3 TRUE
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mgcv 1.8-39 1.8-40 TRUE
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msigdbr 7.4.1 7.5.1 FALSE
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S4Vectors 0.32.3 0.32.4 TRUE
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testthat 3.1.2 3.1.3 TRUE
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vctrs 0.3.8 0.4.0 TRUE
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There is a binary version available but the source version is later:
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binary source needs_compilation
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webshot 0.5.3 0.5.4 FALSE
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Binaries will be installed
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installing the source packages ‘geneLenDataBase’, ‘msigdbr’, ‘PANTHER.db’, ‘reactome.db’
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installing the source packages ‘geneLenDataBase’, ‘GO.db’, ‘PANTHER.db’, ‘reactome.db’, ‘webshot’
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```
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There are binary versions available but the source versions are later:
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binary source needs_compilation
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cluster 2.1.2 2.1.3 TRUE
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magrittr 2.0.2 2.0.3 TRUE
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mgcv 1.8-39 1.8-40 TRUE
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msigdbr 7.4.1 7.5.1 FALSE
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S4Vectors 0.32.3 0.32.4 TRUE
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testthat 3.1.2 3.1.3 TRUE
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vctrs 0.3.8 0.4.0 TRUE
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There is a binary version available but the source version is later:
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binary source needs_compilation
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webshot 0.5.3 0.5.4 FALSE
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Binaries will be installed
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installing the source packages ‘geneLenDataBase’, ‘msigdbr’, ‘PANTHER.db’, ‘reactome.db’
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installing the source packages ‘geneLenDataBase’, ‘GO.db’, ‘PANTHER.db’, ‘reactome.db’, ‘webshot’
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‎revdep/problems.md‎

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<details>
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* Version: 1.0.0
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* Version: 1.2.0
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* GitHub: https://github.com/neurogenomics/orthogene
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* Source code: https://github.com/cran/orthogene
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* Date/Publication: 2021-10-26
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* Number of recursive dependencies: 167
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* Date/Publication: 2022-04-26
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* Number of recursive dependencies: 210
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Run `revdep_details(, "orthogene")` for more info
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ERROR
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Running the tests in ‘tests/testthat.R’ failed.
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Last 13 lines of output:
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3,849 / 4,492 (86%)
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Total genes remaining after convert_orthologs :
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643 / 4,492 (14%)
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Finisheddmelanogasterin0.232minutes.
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Saving benchmarking results ==> /var/folders/lj/80zz6n91631_lb6h3l2m3hq4f503zw/T//Rtmpmg1Vml/file37766fe58c9d.csv
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WARNING: Species ' monkeytypo ' not found in taxa dict.
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[ FAIL 1 | WARN 0 | SKIP 0 | PASS 100 ]
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[ FAIL 4 | WARN 0 | SKIP 0 | PASS 141 ]
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══ Failed tests ════════════════════════════════════════════════════════════════
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── Failure (test-map_orthologs_babelgene.R:18:5): map_orthologs_babelgene works ──
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nrow(gene_map2) is not more than 13000. Difference: -1.3e+04
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── Failure (test-map_orthologs_babelgene.R:12:5): map_orthologs_babelgene works ──
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nrow(gene_map_b1) is not more than 13100. Difference: -34
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── Failure (test-map_orthologs_babelgene.R:29:5): map_orthologs_babelgene works ──
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nrow(gene_map_b3) is not more than 15900. Difference: -27
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── Failure (test-map_orthologs_babelgene.R:42:5): map_orthologs_babelgene works ──
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nrow(gene_map1) is not more than 29700. Difference: -49
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── Failure (test-map_orthologs_babelgene.R:60:5): map_orthologs_babelgene works ──
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nrow(gene_map2) is not more than 29700. Difference: -49
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[ FAIL 1 | WARN 0 | SKIP 0 | PASS 100 ]
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[ FAIL 4 | WARN 0 | SKIP 0 | PASS 141 ]
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Error: Test failures
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Execution halted
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```
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## In both
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* checking dependencies in R code ... NOTE
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```
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Namespace in Imports field not imported from: ‘DelayedMatrixStats’
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All declared Imports should be used.
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There are ::: calls to the package's namespace in its code. A package
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almost never needs to use ::: for its own objects:
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‘aggregate_rows’
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```
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