Windows Builds

Overview

This document attempts to track Windows builds for Bioconductor packages for the devel and release branches:

  • http://bioc.r-universe.dev builds the Bioconductor devel branch
  • http://bioc-release.r-universe.dev builds the Bioconductor release branch

Because R universe build for multiple versions of R whereas Bioconductor branches build for a specific version, the following tables display only the package builds corresponding the Bioconductor branch’s specific R version.

Code 
library(universe)
library(BiocPkgTools)
library(biocUniTools)
library(dplyr)
library(reactable)
library(tibble)

# set max.print to get all packages
options(max.print = 3000L)

r_version <- "4.6.0"
bioc_version <- "3.23"
uni <- "bioc"
uni_os_branch <- "devel"
os <- "windows"
ru_builds <- biocUniTools::get_binaries_by_os(uni, uni_os_branch, r_version,
                                              bioc_version, os)
bbs_pkgs_i <- BiocPkgTools::biocBuildReport(version = bioc_version,
                                            pkgType = "software")

Bioconductor Devel Windows on bioc.r-universe.dev

Note: The following packages may not have the same version or commit hash in R Universe and the BBS. Only packages with the same version and commit hash are currently propagated.

Code 
bbs_builds <- bbs_pkgs_i |>
    dplyr::filter(node == "nebbiolo1", stage == "checksrc") |>
    dplyr::select(pkg, version, Deprecated, git_last_commit, result) |>
    dplyr::rename(Package = pkg, Version = version, BBS_commit = git_last_commit,
                  Check = result)

devel_builds <- merge(bbs_builds, ru_builds, by = "Package")
devel_builds <- devel_builds |>
    dplyr::rename(`RU Version` = `Version.x`, `BBS Version` = `Version.y`,
                  `BBS Commit` = `BBS_commit`, `RU Commit` = `RemoteSha`,
                  `BBS Check` = Check, `RU Job Check` = `_jobs_check`,
                  `RU Binaries Check` = `_binaries_check`,
                  `RU Binary Status` = `_binaries_status`, `Job Url` = JobUrl) |>
dplyr::select(Package, `RU Version`, `BBS Version`, `BBS Commit`,
              `RU Commit`, `BBS Check`, `RU Job Check`, `RU Binaries Check`,
              `RU Binary Status`, `Job Url`, Deprecated)

reactable::reactable(subset(devel_builds, select = -`Job Url`),
                     defaultPageSize = 50,
                     compact = TRUE,
                     columns = list(
                        `RU Commit` = reactable::colDef(cell = function(value, index) {
                            substr(value, 1, 7)
                        }),
                        `RU Job Check` = reactable::colDef(cell = function(value, index) {
                            if (is.na(value)) {
                                "No url"
                            } else {
                                htmltools::tags$a(href = devel_builds[index, "Job Url"],
                                                  target = "_blank",
                                                  as.character(value))
                            }}))
)

Bioconductor Release Windows on bioc-release.r-universe.dev

Note: The following packages may not have the same version or commit hash in R Universe and the BBS. Only packages with the same version and commit hash are currently propagated.

Code 
r_version <- "4.5.0"
bioc_version <- "3.22"
uni <- "bioc-release"
uni_os_branch <- "release"
os <- "windows"
ru_builds <- biocUniTools::get_binaries_by_os(uni, uni_os_branch, r_version,
                                              bioc_version, os)
bbs_pkgs_i <- BiocPkgTools::biocBuildReport(version = bioc_version,
                                            pkgType = "software")

bbs_builds <- bbs_pkgs_i |>
    dplyr::filter(node == "nebbiolo2", stage == "checksrc") |>
    dplyr::select(pkg, version, Deprecated, git_last_commit, result) |>
    dplyr::rename(Package = pkg, Version = version, BBS_commit = git_last_commit,
                  Check = result)

release_builds <- merge(bbs_builds, ru_builds, by = "Package")
release_builds <- release_builds |>
    dplyr::rename(`RU Version` = `Version.x`, `BBS Version` = `Version.y`,
                  `BBS Commit` = `BBS_commit`, `RU Commit` = RemoteSha,
                  `BBS Check` = Check, `RU Job Check` = `_jobs_check`,
                  `RU Binaries Check` = `_binaries_check`,
                  `RU Binary Status` = `_binaries_status`, `Job Url` = JobUrl) |>
dplyr::select(Package, `RU Version`, `BBS Version`, `BBS Commit`,
              `RU Commit`, `BBS Check`, `RU Job Check`, `RU Binaries Check`,
              `RU Binary Status`, `Job Url`, Deprecated)

reactable::reactable(subset(devel_builds, select = -`Job Url`),
                     defaultPageSize = 50,
                     compact = TRUE,
                     columns = list(
                        `RU Commit` = reactable::colDef(cell = function(value, index) {
                            substr(value, 1, 7)
                        }),
                        `RU Job Check` = reactable::colDef(cell = function(value, index) {
                            if (is.na(value)) {
                                "No url"
                            } else {
                                htmltools::tags$a(href = devel_builds[index, "Job Url"],
                                                  target = "_blank",
                                                  as.character(value))
                            }}))
)

Understanding the error

For more details about the error, click on the link. The Latest Check will go to the latest GitHub Action Workflow run’s R CMD check on the package whereas the Binary Check will go to the GitHub Action Workflow associated with the R CMD check associated with the binary. It may not take you to the specific location of the error. You need to look at the Build R-release for Windows (on left), which builds the same package version as Bioconductor devel for the correct version of R. You can then either expand the Annotations or expand R CMD check to see more details about the error. You must be logged in to see more details.

annotations

r_cmd_check

sessionInfo()

Code 
sessionInfo()
R version 4.5.2 (2025-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] tibble_3.3.1        reactable_0.4.5     dplyr_1.2.0        
[4] biocUniTools_0.0.99 BiocPkgTools_1.28.3 htmlwidgets_1.6.4  
[7] universe_1.0.0.9000

loaded via a namespace (and not attached):
 [1] xfun_0.57           httr2_1.2.2         gh_1.5.0           
 [4] Biobase_2.70.0      tzdb_0.5.0          crosstalk_1.2.2    
 [7] vctrs_0.7.2         tools_4.5.2         bitops_1.0-9       
[10] generics_0.1.4      stats4_4.5.2        curl_7.0.0         
[13] RUnit_0.4.33.1      RSQLite_2.4.6       blob_1.3.0         
[16] pkgconfig_2.0.3     dbplyr_2.5.2        graph_1.88.1       
[19] lifecycle_1.0.5     compiler_4.5.2      stringr_1.6.0      
[22] biocViews_1.78.1    htmltools_0.5.9     RCurl_1.98-1.18    
[25] yaml_2.3.12         pillar_1.11.1       tidyr_1.3.2        
[28] DT_0.34.0           cachem_1.1.0        tidyselect_1.2.1   
[31] rvest_1.0.5         digest_0.6.39       stringi_1.8.7      
[34] purrr_1.2.1         fastmap_1.2.0       cli_3.6.5          
[37] magrittr_2.0.4      RBGL_1.86.0         XML_3.99-0.23      
[40] reactR_0.6.1        readr_2.2.0         withr_3.0.2        
[43] filelock_1.0.3      rappdirs_0.3.4      bit64_4.6.0-1      
[46] lubridate_1.9.5     timechange_0.4.0    rmarkdown_2.31     
[49] httr_1.4.8          igraph_2.2.2        bit_4.6.0          
[52] otel_0.2.0          hms_1.1.4           memoise_2.0.1      
[55] evaluate_1.0.5      knitr_1.51          BiocFileCache_3.0.0
[58] rlang_1.1.7         glue_1.8.0          DBI_1.3.0          
[61] BiocManager_1.30.27 xml2_1.5.2          BiocGenerics_0.56.0
[64] jsonlite_2.0.0      R6_2.6.1