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https://remotes.r-lib.org/
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Correct reporting of remote repositories #695

Closed llrs closed 10 months ago

llrs commented 2 years ago

I was debugging a new instance of github actions where they were unable to install packages and found the following piece:

 package_deps("BioCor")
# Not on CRAN ----------------------------
#  package installed available is_cran remote
#  BioCor  1.18.0    NA        TRUE    CRAN

BioCor is a package on Bioconducto but it reports as from CRAN. I'm not sure but this is probably because remotes find the right way to install it via getOption("repos") and so it decides it is CRAN. It would be nice and might be helpful if it used the name of the repository to report which remote it comes from (Additionaly probably is_cran column should be replaced by is_available).

This is related to #275 where the assumption is that packages come from CRAN.

Session ─ Session info ────────────────────────────────────────────────────────────────────────────── setting value version R version 4.1.2 (2021-11-01) os Ubuntu 20.04.3 LTS system x86_64, linux-gnu ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz Europe/Madrid date 2022-02-11 rstudio 2021.09.2+382 Ghost Orchid (desktop) pandoc 2.14.0.3 @ /usr/lib/rstudio/bin/pandoc/ (via rmarkdown) ─ Packages ────────────────────────────────────────────────────────────────────────────────── package * version date (UTC) lib source annotate 1.72.0 2021-10-26 [1] Bioconductor AnnotationDbi 1.56.2 2021-11-09 [1] Bioconductor Biobase 2.54.0 2021-10-26 [1] Bioconductor BiocGenerics 0.40.0 2021-10-26 [1] Bioconductor BiocManager * 1.30.16 2021-06-15 [1] CRAN (R 4.1.2) BioCor 1.18.0 2021-10-26 [1] Bioconductor BiocParallel 1.28.3 2021-12-09 [1] Bioconductor Biostrings 2.62.0 2021-10-26 [1] Bioconductor bit 4.0.4 2020-08-04 [1] CRAN (R 4.1.2) bit64 4.0.5 2020-08-30 [1] CRAN (R 4.1.2) bitops 1.0-7 2021-04-24 [1] CRAN (R 4.1.2) blob 1.2.2 2021-07-23 [1] CRAN (R 4.1.2) brio 1.1.3 2021-11-30 [1] CRAN (R 4.1.2) cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.2) callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.2) cli 3.1.1 2022-01-20 [1] CRAN (R 4.1.2) crayon 1.4.2 2021-10-29 [1] CRAN (R 4.1.2) curl 4.3.2 2021-06-23 [1] CRAN (R 4.1.2) cyclocomp * 1.1.0 2016-09-10 [1] CRAN (R 4.1.2) DBI 1.1.2 2021-12-20 [1] CRAN (R 4.1.2) desc 1.4.0 2021-09-28 [1] CRAN (R 4.1.2) devtools * 2.4.3 2021-11-30 [1] CRAN (R 4.1.2) digest 0.6.29 2021-12-01 [1] CRAN (R 4.1.2) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.2) evaluate 0.14 2019-05-28 [1] CRAN (R 4.1.2) fansi 1.0.2 2022-01-14 [1] CRAN (R 4.1.2) fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.2) fs 1.5.2 2021-12-08 [1] CRAN (R 4.1.2) GenomeInfoDb 1.30.1 2022-01-30 [1] Bioconductor GenomeInfoDbData 1.2.7 2022-01-10 [1] Bioconductor gh 1.3.0 2021-04-30 [1] CRAN (R 4.1.2) gitcreds 0.1.1 2020-12-04 [1] CRAN (R 4.1.2) glue 1.6.1 2022-01-22 [1] CRAN (R 4.1.2) GO.db 3.14.0 2022-01-10 [1] Bioconductor GOSemSim 2.20.0 2021-10-26 [1] Bioconductor graph 1.72.0 2021-10-26 [1] Bioconductor GSEABase 1.56.0 2021-10-26 [1] Bioconductor htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.1.2) httr 1.4.2 2020-07-20 [1] CRAN (R 4.1.2) IRanges 2.28.0 2021-10-26 [1] Bioconductor jsonlite 1.7.3 2022-01-17 [1] CRAN (R 4.1.2) KEGGREST 1.34.0 2021-10-26 [1] Bioconductor knitr 1.37 2021-12-16 [1] CRAN (R 4.1.2) lattice 0.20-45 2021-09-22 [1] CRAN (R 4.1.2) lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.2) magrittr 2.0.2 2022-01-26 [1] CRAN (R 4.1.2) Matrix 1.4-0 2021-12-08 [1] CRAN (R 4.1.2) memoise 2.0.1 2021-11-26 [1] CRAN (R 4.1.2) pillar 1.7.0 2022-02-01 [1] CRAN (R 4.1.2) pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.1.2) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.2) pkgload 1.2.4 2021-11-30 [1] CRAN (R 4.1.2) png 0.1-7 2013-12-03 [1] CRAN (R 4.1.2) prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.2) processx 3.5.2 2021-04-30 [1] CRAN (R 4.1.2) ps 1.6.0 2021-02-28 [1] CRAN (R 4.1.2) purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.2) R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.2) Rcpp 1.0.8 2022-01-13 [1] CRAN (R 4.1.2) RCurl 1.98-1.6 2022-02-08 [1] CRAN (R 4.1.2) remotes * 2.4.2 2021-11-30 [1] CRAN (R 4.1.2) rlang 1.0.1 2022-02-03 [1] CRAN (R 4.1.2) rmarkdown 2.11 2021-09-14 [1] CRAN (R 4.1.2) rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.1.2) RSQLite 2.2.9 2021-12-06 [1] CRAN (R 4.1.2) rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.2) S4Vectors 0.32.3 2021-11-21 [1] Bioconductor sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.2) testthat * 3.1.2 2022-01-20 [1] CRAN (R 4.1.2) tibble 3.1.6 2021-11-07 [1] CRAN (R 4.1.2) usethis * 2.1.5 2021-12-09 [1] CRAN (R 4.1.2) utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.2) vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.2) withr 2.4.3 2021-11-30 [1] CRAN (R 4.1.2) xfun 0.29 2021-12-14 [1] CRAN (R 4.1.2) XML 3.99-0.8 2021-09-17 [1] CRAN (R 4.1.2) xtable 1.8-4 2019-04-21 [1] CRAN (R 4.1.2) XVector 0.34.0 2021-10-26 [1] Bioconductor yaml 2.2.2 2022-01-25 [1] CRAN (R 4.1.2) zlibbioc 1.40.0 2021-10-26 [1] Bioconductor [1] /home/lluis/bin/R/4.1.2/lib/R/library ─────────────────────────────────────────────────────────────────────────────────────────────
gaborcsardi commented 2 years ago

I think is_cran here simply means "it is coming from a CRAN-like repository", and it does not actually mean that it is a package on CRAN.