The BiocPkgDash package provides an interactive Shiny application to visualize the status of Bioconductor packages. Primarily, users can filter packages by maintainer email to display a status badge wall for all packages maintained by that email. It allows users to filter packages based on various criteria, such as Bioconductor version, package type, and GitHub topics. The dashboard displays badges indicating the build status and code coverage for each package. The tool is primarily designed for Bioconductor package maintainers to monitor the status of their packages.
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("BiocPkgDash")library(BiocPkgDash)BiocPkgDash()
Note that the dashboard and this document is organized by the tab panels. Each tab in the dashboard is described in the following sections.
One can filter packages by name, Bioconductor version, biocViews package type, maintainer email, and GitHub topics. The dashboard will display the status badges for all packages that match the selected criteria. Typically, a user with use one of the methods to filter for packages. Primarily, the user will filter by the relevant maintainer email.
The GitHub topic filter allows users to filter packages based on specific topics associated with R / Bioconductor packages on GitHub. This can be useful for organizations that maintain multiple packages related to a specific project, theme, or grant. For example, one can filter for all packages related to a particular grant code, e.g., “u24ca289073”. Note that repositories will have to have the topic added to them for the filter to work.
The badge wall displays the build status and code coverage for each package. Clicking on a badge will take you to the relevant page for more details.
Note that the coverage badges can be turned off if the maintainer does not use codecov.io for testing package coverage.
The dashboard allows users to download the badge wall as a partial HTML
file. This can be useful for including the badges on personal websites
or other HTML documentation. The HTML file is generated on the fly by
the shiny app after clicking the Download HTML button on the sidebar
panel.
The dashboard also provides a visualization of the package build statuses across different stages of the Bioconductor Build System (BBS). This helps maintainers quickly identify any issues with their packages.
Note that clicking on any of the status bars in the plot takes the user to the detailed build report for that specific builder, stage, and status combination.
The Dependencies tab displays the package reverse dependencies for a
selected package. This can help maintainers understand the dependency
tree of their packages and identify any potential issues.
The Metadata tab displays additional information about the selected
package(s) such as the package title, version, and additional fields
from the DESCRIPTION file as obtained from the internal biocViews
database. This can help maintainers quickly access information about
their package(s).
sessionInfo()
#> R Under development (unstable) (2025-10-28 r88973)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.4 LTS
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#> Matrix products: default
#> BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
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#> time zone: America/New_York
#> tzcode source: system (glibc)
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#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
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#> other attached packages:
#> [1] BiocPkgDash_0.99.39 shiny_1.12.1 colorout_1.3-2
#>
#> loaded via a namespace (and not attached):
#> [1] tidyselect_1.2.1 viridisLite_0.4.2 dplyr_1.1.4 farver_2.1.2
#> [5] blob_1.2.4 filelock_1.0.3 S7_0.2.1 bitops_1.0-9
#> [9] fastmap_1.2.0 RCurl_1.98-1.17 lazyeval_0.2.2 gh_1.5.0
#> [13] BiocFileCache_3.1.0 BiocPkgTools_1.29.2 promises_1.5.0 XML_3.99-0.20
#> [17] digest_0.6.39 timechange_0.4.0 mime_0.13 lifecycle_1.0.4
#> [21] processx_3.8.6 RSQLite_2.4.5 magrittr_2.0.4 compiler_4.6.0
#> [25] rlang_1.1.6 tools_4.6.0 igraph_2.2.1 yaml_2.3.12
#> [29] data.table_1.18.2.1 knitr_1.51 htmlwidgets_1.6.4 bit_4.6.0
#> [33] curl_7.0.0 xml2_1.5.1 RColorBrewer_1.1-3 rsconnect_1.7.0
#> [37] websocket_1.4.4 purrr_1.2.0 BiocGenerics_0.57.0 grid_4.6.0
#> [41] stats4_4.6.0 xtable_1.8-4 ggplot2_4.0.1 scales_1.4.0
#> [45] dichromat_2.0-0.1 cli_3.6.5 rmarkdown_2.30 generics_0.1.4
#> [49] otel_0.2.0 rstudioapi_0.18.0 httr_1.4.7 tzdb_0.5.0
#> [53] BiocBaseUtils_1.13.0 RUnit_0.4.33.1 DBI_1.2.3 cachem_1.1.0
#> [57] chromote_0.5.1 stringr_1.6.0 rvest_1.0.5 BiocManager_1.30.27
#> [61] vctrs_0.6.5 jsonlite_2.0.0 hms_1.1.4 bit64_4.6.0-1
#> [65] RBGL_1.87.0 plotly_4.11.0 tidyr_1.3.1 glue_1.8.0
#> [69] codetools_0.2-20 ps_1.9.1 DT_0.34.0 lubridate_1.9.4
#> [73] stringi_1.8.7 gtable_0.3.6 later_1.4.4 tibble_3.3.0
#> [77] pillar_1.11.1 rappdirs_0.3.4 htmltools_0.5.9 graph_1.89.1
#> [81] R6_2.6.1 dbplyr_2.5.1 httr2_1.2.2 evaluate_1.0.5
#> [85] Biobase_2.71.0 readr_2.1.6 memoise_2.0.1 httpuv_1.6.16
#> [89] Rcpp_1.1.1 xfun_0.56 whisker_0.4.1 biocViews_1.79.0
#> [93] pkgconfig_2.0.3