I'm building a personal ChipDb annotation package, and I'm currently trying to add and export a new function to the package. When I run devtools::load_all()
the first time (in a fresh R session), everything runs smoothly and behaves as expected. However, if I run it a second time, even after making no changes or modifications to the code or my environment, I get the following error message:
> devtools::load_all(".")
Error in (function () :
{packageName}PROSITE is defunct. Please use select() if you need access to PFAM or PROSITE accessions.
Calls: <Anonymous> ... unregister -> unregister_namespace -> eapply -> <Anonymous>
Restarting R session...
Sometimes it says PROSITE is defunct, sometimes it says PFAM is defunct. What could be causing this error to appear? Is it related to my environment? Any advice on how I can work around this or resolve it? As it stands, I have to restart my R session every time I need to run devtools::load_all()
, which is very cumbersome. I also can't index into my package using ::
, or the same error will be thrown.
FYI: I've replaced the name of my personal package with {packageName}
, where appropriate.
Looks like this isn't the first time this issue has popped up, but the solution doesn't apply to my case: Error: hgu95av2PFAM is defunct
Here is my sessionInfo()
:
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/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] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] {packageName}.db_0.99.0 org.Hs.eg.db_3.16.0 AnnotationDbi_1.60.0 IRanges_2.32.0 S4Vectors_0.36.1 Biobase_2.58.0
[7] BiocGenerics_0.44.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 prettyunits_1.1.1 png_0.1-8 ps_1.7.2 Biostrings_2.66.0
[6] rprojroot_2.0.3 digest_0.6.31 mime_0.12 R6_2.5.1 GenomeInfoDb_1.34.7
[11] RSQLite_2.2.20 httr_1.4.4 zlibbioc_1.44.0 rlang_1.0.6 rstudioapi_0.14
[16] miniUI_0.1.1.1 callr_3.7.3 urlchecker_1.0.1 blob_1.2.3 desc_1.4.2
[21] devtools_2.4.5 stringr_1.5.0 htmlwidgets_1.6.1 RCurl_1.98-1.10 bit_4.0.5
[26] shiny_1.7.4 compiler_4.2.2 httpuv_1.6.7 pkgconfig_2.0.3 pkgbuild_1.4.0
[31] htmltools_0.5.4 KEGGREST_1.38.0 GenomeInfoDbData_1.2.9 crayon_1.5.2 withr_2.5.0
[36] later_1.3.0 bitops_1.0-7 brio_1.1.3 xtable_1.8-4 lifecycle_1.0.3
[41] DBI_1.1.3 magrittr_2.0.3 cli_3.5.0 stringi_1.7.8 cachem_1.0.6
[46] XVector_0.38.0 fs_1.5.2 promises_1.2.0.1 remotes_2.4.2 testthat_3.1.6
[51] ellipsis_0.3.2 vctrs_0.5.1 tools_4.2.2 bit64_4.0.5 glue_1.6.2
[56] purrr_1.0.0 processx_3.8.0 pkgload_1.3.2 fastmap_1.1.0 sessioninfo_1.2.2
[61] memoise_2.0.1 profvis_0.3.7 usethis_2.1.6
Thanks in advance!