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Do you know of a way around this issue of finding the DESCRIPTION file during tests more generally (couldn't find any explicit examples in your test folder)?
Could you possibly expose to users the step in which the DESCRIPTION file is imported via a new argument (named something like d or description that expects an object of the class "description")? I have some other functions for (usually) more robustly finding and importing the DESCRIPTION file across a wider variety of scenarios (rworkflows::get_description). Specifically, this step:
Hi there,
I'm trying to incorporate the
biocViews::recommendBiocViews
function into of my my package's functions:rworkflows::infer_biocviews
:https://github.com/neurogenomics/rworkflows/blob/master/R/infer_biocviews.R
However when I go to run unit tests with it using
testthat
, it can't find the DESCRIPTION file. My usual hacks for getting around this directory-specific issue (e.g.setwd("../../")
aren't working either.https://github.com/neurogenomics/rworkflows/blob/master/tests/testthat/test-infer_biocviews.R
So my question is twofold:
d
ordescription
that expects an object of the class "description")? I have some other functions for (usually) more robustly finding and importing the DESCRIPTION file across a wider variety of scenarios (rworkflows::get_description
). Specifically, this step:biocViews/R/recommendBiocViews.R
Line 108 in 58eda22
Many thanks in advance!,
Brian
Session info
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rworkflows_0.99.7
loaded via a namespace (and not attached):
[1] Biobase_2.58.0 pkgload_1.3.2 jsonlite_1.8.4 here_1.0.1 brio_1.1.3 shiny_1.7.4
[7] BiocManager_1.30.20 rvcheck_0.2.1 stats4_4.2.1 yulab.utils_0.0.6 RBGL_1.74.0 renv_0.17.0
[13] yaml_2.3.7 remotes_2.4.2 sessioninfo_1.2.2 pillar_1.8.1 glue_1.6.2 RUnit_0.4.32
[19] digest_0.6.31 RColorBrewer_1.1-3 promises_1.2.0.1 colorspace_2.1-0 htmltools_0.5.4 httpuv_1.6.9
[25] XML_3.99-0.13 pkgconfig_2.0.3 devtools_2.4.5 purrr_1.0.1 xtable_1.8-4 scales_1.2.1
[31] processx_3.8.0 later_1.3.0 tibble_3.1.8 biocViews_1.66.2 generics_0.1.3 ggplot2_3.4.1
[37] usethis_2.1.6 ellipsis_0.3.2 cachem_1.0.6 withr_2.5.0 BiocGenerics_0.44.0 cli_3.6.0
[43] magrittr_2.0.3 crayon_1.5.2 mime_0.12 evaluate_0.20 memoise_2.0.1 ps_1.7.2
[49] badger_0.2.3 fs_1.6.1 fansi_1.0.4 xml2_1.3.3 pkgbuild_1.4.0 graph_1.76.0
[55] profvis_0.3.7 tools_4.2.1 prettyunits_1.1.1 lifecycle_1.0.3 stringr_1.5.0 munsell_0.5.0
[61] callr_3.7.3 compiler_4.2.1 rlang_1.0.6 grid_4.2.1 RCurl_1.98-1.10 rstudioapi_0.14
[67] htmlwidgets_1.6.1 miniUI_0.1.1.1 rmarkdown_2.20.1 bitops_1.0-7 testthat_3.1.6 gtable_0.3.1
[73] roxygen2_7.2.3 R6_2.5.1 knitr_1.42 dplyr_1.1.0 fastmap_1.1.0 utf8_1.2.3
[79] rprojroot_2.0.3 dlstats_0.1.6 desc_1.4.2 stringi_1.7.12 Rcpp_1.0.10 vctrs_0.5.2
[85] tidyselect_1.2.0 xfun_0.37 urlchecker_1.0.1
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