Missing required markdown dependency

[dpryan79]

While rolling out the Bioconductor 3.13 release on Bioconda, I ran into issues because cbpManager cannot be loaded unless markdown is installed:

Error in loadNamespace(x) : there is no package called ‘markdown’
Error: unable to load R code in package ‘cbpManager’

Please move markdown from a suggestion to a requirement.

[arsenij-ust]

Dear @dpryan79 ,

unfortunately, I was not able to reproduce your error. We do not use markdown in the package. The vignette uses rmarkdown and therefore its dependency is in Suggests.

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252 LC_NUMERIC=C                   
[5] LC_TIME=German_Germany.1252    

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

other attached packages:
[1] cbpManager_1.1.0     shinydashboard_0.7.1 shiny_1.6.0         

loaded via a namespace (and not attached):
 [1] sass_0.4.0             pkgload_1.2.1          bit64_4.0.5            vroom_1.4.0            jsonlite_1.7.2         bslib_0.2.5.1         
 [7] rintrojs_0.3.0         BiocManager_1.30.15    pander_0.6.3           yaml_2.2.1             remotes_2.4.0          sessioninfo_1.1.1     
[13] pillar_1.6.1           lattice_0.20-44        glue_1.4.2             reticulate_1.20        digest_0.6.27          promises_1.2.0.1      
[19] shinycssloaders_1.0.0  htmltools_0.5.1.1      httpuv_1.6.1           Matrix_1.3-4           plyr_1.8.6             pkgconfig_2.0.3       
[25] devtools_2.4.2         dir.expiry_1.0.0       purrr_0.3.4            xtable_1.8-4           processx_3.5.2         later_1.2.0           
[31] tibble_3.1.2           generics_0.1.0         usethis_2.0.1          ellipsis_0.3.2         DT_0.18                cachem_1.0.5          
[37] withr_2.4.2            cli_2.5.0              magrittr_2.0.1         crayon_1.4.1           mime_0.10              memoise_2.0.0         
[43] ps_1.6.0               fs_1.5.0               fansi_0.5.0            xml2_1.3.2             pkgbuild_1.2.0         rapportools_1.0       
[49] tools_4.1.0            prettyunits_1.1.1      lifecycle_1.0.0        basilisk.utils_1.4.0   stringr_1.4.0          callr_3.7.0           
[55] jquerylib_0.1.4        compiler_4.1.0         rlang_0.4.11           grid_4.1.0             rstudioapi_0.13        htmlwidgets_1.5.3.9000
[61] crosstalk_1.1.1        shinyBS_0.61           basilisk_1.4.0         testthat_3.0.2         curl_4.3.1             roxygen2_7.1.1        
[67] markdown_1.1           R6_2.5.0               knitr_1.33             dplyr_1.0.6            fastmap_1.1.0          bit_4.0.4             
[73] utf8_1.2.1             filelock_1.0.2         rprojroot_2.0.2        desc_1.3.0             stringi_1.6.1          parallel_4.1.0        
[79] Rcpp_1.0.6             vctrs_0.3.8            png_0.1-7              tidyselect_1.1.1       xfun_0.23

[dpryan79]

Yes, I added rmarkdown into the recipe in bioconda, which resolved the issue. I notice you have mardown loaded via a namespace in your session info, which is presumably why you didn't run into this.

[federicomarini]

Hi @dpryan79 , first of all thanks for the massive work in porting all Bioc packages to conda!

What felt strange to me of the error message you reported: we do not explicitly use any call to markdown::whatever_function, and the package correctly builds on the Bioc builders.

We are on the way of setting up the Github Actions for the package, this can maybe help in providing extra insight.

Thanks for flagging this! Federico