PRs (or patches) for packages with deprecation warnings, ordered by rev.deps #491

Similar to #489, we have taken the list of packages with deprecation warning identified in #485 and sorted them by (recursive) reverse dependencies. Focussing for now on packages with two or more we get

> N[order(-nrevdep), c(1:2,70)][nrevdep >= 2]
                        Package     Version nrevdep
                         <char>      <char>   <int>
 1:                      bayesm       3.1-6      32
 2:                      Rfast2     0.1.5.4      29
 3:                      smooth       4.3.0      24
 4:                    ClusterR       1.3.4      18
 5:                    cellWise       2.5.3      17
 6:                    unmarked       1.5.0      13
 7:                    stochvol       3.2.7       9
 8:                      maotai       0.2.6       8
 9:                    robustHD       0.8.1       8
10:                   Rdimtools       1.1.2       7
11:                      sdsfun       0.8.0       7
12:                        cccp       0.3-2       6
13:                   robslopes       1.1.3       5
14:                       simts       0.2.2       5
15:                         GSE       4.2-1       4
16:                       comat       0.9.5       4
17:                     fdasrvf       2.4.0       3
18:                       updog       2.1.5       3
19: SuperpixelImageSegmentation       1.0.6       2
20:                      eulerr       7.0.2       2
21:                      fclust       2.1.2       2
22:                        phyr       1.1.0       2
23:               simStateSpace      1.2.10       2
24:             strucchangeRcpp 1.5-4-1.0.0       2
25:                          wv       0.1.2       2
                        Package     Version nrevdep
> 

and will collect patches and PRs here.

• Rfast PR #130 filed 2025-09-10, merged 2025-10-06, new version 2.1.5.2 on CRAN 2025-10-10
• bayesm patch emailed 2025-09-22, new version 3.1-7 on CRAN 2025-11-11
• Rfast2 PR #28 filed 2025-09-22, merged 2025-10-06, version 0.1.5.5 on CRAN 2025-10-14
• smooth PR #273 filed 2025-09-22, version 4.3.1 on CRAN 2025-10-27
• ClusterR already taken care of in recent upload 1.3.4 dated 2025-09-14
• cellWise patch emailed 2025-09-23; new version 2.5.4 on CRAN 2025-09-23
• unmarked addressed upstream in ecoverseR/unmarked@22143aa on 2025-09-19, version 1.5.1 on CRAN 2025-09-26
• stochvol PR #31 filed 2025-09-23 merged 2025-09-23, version 3.2.8 on CRAN 2025-10-14
• maotai PR #6 filed 2025-09-23, new version 0.2.7 on CRAN 2025-09-24
• robustHD PR #40 filed 2025-09-23, merged 2025-09-29, version 0.8.2 on CRAN 2025-10-02
• Rdimtools taken care of in CRAN version 1.1.3 dated 2025-09-22
• sdsfun taken care of in CRAN version 0.8.1 dated 2025-09-22
• cccp patch emailed 2025-09-23, version 0.3.3 on CRAN 2025-09-27
• robslopes patch emailed 2025-09-23, version 1.1.4 on CRAN 2025-12-19 (!!)
• simts PR #36 filed 2025-09-23, merged 2025-10-07; new version 0.2.3 on CRAN 2025-10-08
• GSE patch emailed 2025-09-23, verion 0.2-3 on CRAN 2025-10-10
• comat PR #19 files 2025-09-23 merged 2025-09-25, version 0.9.6 on CRAN 2025-09-26
• fdasrvf taken care of upstream in jdtuck/fdasrvf_R@578496f#r166368061 on 2025-09-23, fixed in version on CRAN 2.4.1 dated 2025-09-23
• updog taken care of upstream in dcgerard/updog@cf3a67d#r166368319 on 2025-09-23, version 2.1.6 on CRAN 2025-09-24
• SuperpixelImageSegmentation already taken care of in recent upload 1.0.6 dated 2025-09-15
• eulerr addressed in version 7.0.4 dated 2025-09-23, on CRAN 2025-09-24
• fclust patch emailed 2025-09-24, new version 2.1.3 on CRAN 2025-10-18
• phyr PR #93 filed 2025-09-24 merged 2025-09-24, new version 1.1.3 on CRAN 2025-11-11
• simStateSpace already fixed upstream in version 1.2.11, issue #1 filed asking for upload, version 1.2.11 on CRAN 2025-09-26
• strucchangeRcpp PR #42 filed 2025-09-24 merged 2025-09-25, version 1.5-4-1.0.1 on CRAN 2025-09-26
• wv PR #18 filed 2025-09-24; merged 2024-10-07; version 0.1.3 on CRAN 2025-10-08
• KODAMA PR #2 filed 2025-10-11
• fdacluster already addressed in upstream repo, CRAN release ?
• imagine PR #8 filed 2025-10-11, merged 2025-10-27, version 2.1.3 on CRAN 2025-10-27
• pacotest already addressed in upstream repo, CRAN release 0.4.3 on 2025-10-15
• psychonetrics PR #489 filed 2025-10-11, new version 0.13.2 on CRAN 2025-10-22

Edit on 2025-10-09: There were also some patches I sent earlier such as this one that should have been on this list but were not.

Edit 2 on 2025-10-11: We are added five more packages with a reverse-depends count of one.