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Rd cross-references do not pass CRAN checks #664

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HenningLorenzen-ext-bayer opened this issue Oct 4, 2024 · 0 comments · Fixed by #663
Closed

Rd cross-references do not pass CRAN checks #664

HenningLorenzen-ext-bayer opened this issue Oct 4, 2024 · 0 comments · Fixed by #663

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@HenningLorenzen-ext-bayer
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HenningLorenzen-ext-bayer commented Oct 4, 2024

Expected behavior

✔  checking Rd cross-references

Actual behavior

checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggadjustedcurves.Rd: coxph.object, coxph
  ggcompetingrisks.Rd: survfit
  ggcoxdiagnostics.Rd: coxph, coxph.object, residuals.coxph,
    geom_hline, geom_smooth
  ggcoxfunctional.Rd: coxph, Surv, coxph.object, arrangeGrob,
    grid.arrange
  ggcoxzph.Rd: plot.cox.zph, cox.zph, arrangeGrob, grid.arrange
  ggsurvevents.Rd: Surv, survfit
  ggsurvplot.Rd: grid.arrange
  surv_cutpoint.Rd: theme_classic, grid.arrange
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.

Steps to reproduce the problem

devtools::check(args = c('--as-cran'))

session_info()

─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R Under development (unstable) (2024-10-01 r87205 ucrt)
 os       Windows 11 x64 (build 22621)
 system   x86_64, mingw32
 ui       RStudio
 language (EN)
 collate  German_Germany.utf8
 ctype    German_Germany.utf8
 tz       Europe/Berlin
 date     2024-10-04
 rstudio  2024.09.0+375 Cranberry Hibiscus (desktop)
 pandoc   NA

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package     * version    date (UTC) lib source
 cachem        1.1.0      2024-05-16 [1] CRAN (R 4.5.0)
 callr         3.7.6      2024-03-25 [1] CRAN (R 4.5.0)
 cli           3.6.3.9000 2024-09-02 [1] Github (r-lib/cli@d33aeee)
 curl          5.2.3      2024-09-20 [1] CRAN (R 4.5.0)
 desc          1.4.3      2023-12-10 [1] CRAN (R 4.5.0)
 devtools      2.4.5      2022-10-11 [1] CRAN (R 4.5.0)
 digest        0.6.37     2024-08-19 [1] CRAN (R 4.5.0)
 ellipsis      0.3.2      2021-04-29 [1] CRAN (R 4.5.0)
 fansi         1.0.6      2023-12-08 [1] CRAN (R 4.5.0)
 fastmap       1.2.0      2024-05-15 [1] CRAN (R 4.5.0)
 fs            1.6.4      2024-04-25 [1] CRAN (R 4.5.0)
 glue          1.8.0      2024-09-30 [1] CRAN (R 4.5.0)
 htmltools     0.5.8.1    2024-04-04 [1] CRAN (R 4.5.0)
 htmlwidgets   1.6.4      2023-12-06 [1] CRAN (R 4.5.0)
 httpuv        1.6.15     2024-03-26 [1] CRAN (R 4.5.0)
 later         1.3.2      2023-12-06 [1] CRAN (R 4.5.0)
 lifecycle     1.0.4      2023-11-07 [1] CRAN (R 4.5.0)
 magrittr      2.0.3      2022-03-30 [1] CRAN (R 4.5.0)
 memoise       2.0.1      2021-11-26 [1] CRAN (R 4.5.0)
 mime          0.12       2021-09-28 [1] CRAN (R 4.5.0)
 miniUI        0.1.1.1    2018-05-18 [1] CRAN (R 4.5.0)
 pillar        1.9.0      2023-03-22 [1] CRAN (R 4.5.0)
 pkgbuild      1.4.4      2024-03-17 [1] CRAN (R 4.5.0)
 pkgconfig     2.0.3      2019-09-22 [1] CRAN (R 4.5.0)
 pkgload       1.4.0.9000 2024-08-20 [1] Github (r-lib/pkgload@3fe8258)
 prettyunits   1.2.0      2023-09-24 [1] CRAN (R 4.5.0)
 processx      3.8.4      2024-03-16 [1] CRAN (R 4.5.0)
 profvis       0.4.0      2024-09-20 [1] CRAN (R 4.5.0)
 promises      1.3.0      2024-04-05 [1] CRAN (R 4.5.0)
 ps            1.8.0      2024-09-12 [1] CRAN (R 4.5.0)
 purrr         1.0.2      2023-08-10 [1] CRAN (R 4.5.0)
 R6            2.5.1      2021-08-19 [1] CRAN (R 4.5.0)
 rcmdcheck     1.4.0      2021-09-27 [1] CRAN (R 4.5.0)
 Rcpp          1.0.13     2024-07-17 [1] CRAN (R 4.5.0)
 remotes       2.5.0      2024-03-17 [1] CRAN (R 4.5.0)
 rlang         1.1.4.9000 2024-08-20 [1] Github (r-lib/rlang@69659c4)
 rprojroot     2.0.4      2023-11-05 [1] CRAN (R 4.5.0)
 rstudioapi    0.16.0     2024-03-24 [1] CRAN (R 4.5.0)
 sessioninfo   1.2.2      2021-12-06 [1] CRAN (R 4.5.0)
 shiny         1.9.1      2024-08-01 [1] CRAN (R 4.5.0)
 tibble        3.2.1      2023-03-20 [1] CRAN (R 4.5.0)
 urlchecker    1.0.1      2021-11-30 [1] CRAN (R 4.5.0)
 usethis       3.0.0.9000 2024-09-02 [1] Github (r-lib/usethis@2cc9e5a)
 utf8          1.2.4      2023-10-22 [1] CRAN (R 4.5.0)
 vctrs         0.6.5      2023-12-01 [1] CRAN (R 4.5.0)
 withr         3.0.1      2024-07-31 [1] CRAN (R 4.5.0)
 xopen         1.0.1      2024-04-25 [1] CRAN (R 4.5.0)
 xtable        1.8-4      2019-04-21 [1] CRAN (R 4.5.0)

 [1] C:/Users/[redacted]/AppData/Local/Programs/R/R-devel/site-library
 [2] C:/Users/[redacted]/AppData/Local/Programs/R/R-devel/library

──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
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