Deprecating old initialization code in packages using RcppArmadillo

[eddelbuettel]

When we updated RcppArmadillo recently to help package Matrix propagate a change, we encountered a small change in Armadillo made between the 11.2.0 and 11.2.3 releases that marked our previous and current release. A number of packages would now throw deprecation warnings as Armadillo upstream activated those.

CRAN of course frowns on this so we temporarily disabled the warning in RcppArmadillo. Going forward we should aim to patch this in all affected packages, and we will try to provide PRs. This affects these packages:

• [x] ACEt (at https://r-forge.r-project.org/R/?group_id=2167) (patch created, tested and emailed 2022-09-01) (heard back 2022-09-04: "within a few weeks") (version 1.8.2 on CRAN 2022-09-26)
• [x] autostsm (at https://bitbucket.org/ajhubb/autostsm.git) (pull request made 2022-09-01) (version 3.0.2 at CRAN)
• [x] BAMBI (at https://github.com/c7rishi/BAMBI/) (already addressed by upstream) (version 2.3.4 on CRAN)
• [x] BayesPPD (no known repo) (patch created, tested, and emailed 2022-09-04) (version 1.1.0 on CRAN 2022-11-12) (new patch emailed 2023-01-15, email reply 2023-05-11, fixed on CRAN 2023-05-09 (!!))
• [x] BNPMIXcluster (at https://github.com/chriscarmona/BNPMIXcluster) (PR created 2022-09-04) (merged 2022-09-09) (no longer on CRAN as of 2022-11-20)
• [x] cccp (at https://github.com/bpfaff/cccp) (PR created 2022-09-04) (merged 2022-09-06) (version 0.2-9 on CRAN 2022-09-09) (Second PR created 2023-01-15) (new version on CRAN 2023-12-09)
• [x] finity (at https://github.com/x0range/finity) (PR created 2022-09-05) (merged 2023-11-19) (new version 0.1.5 on CRAN 2023-12-20)
• [x] greed (at https://github.com/comeetie/greed) (PR created 2022-09-05) (heard back 2022-09-06 'within days') (merged 2022-09-07) (version 0.6.1 on CRAN 2022-10-03)
• [x] gren (at https://github.com/magnusmunch/gren) (PR created 2023-01-15 for updated insert_rows() signature) (no longer on CRAN as of 2023-12-07)
• [x] grove (at https://github.com/jacsor/grove) (PR created 2022-09-05) (new version on CRAN 2023-12-10)
• [x] growfunctions (no known repo) (patch for updated insert_rows() signature created, tested and emailed 2023-01-15) (new version on CRAN 2023-12-12)
• [x] handwriter (at https://github.com/CSAFE-ISU/handwriter) (PR created 2022-09-06) (merged 2022-09-09) (see this issue dated 2023-01-11 about possible maintainer transition) (new version 2.0.2 on CRAN 2023-10-13, got heads-up 2023-10-20) (new version on CRAN 2023-12-07)
• [x] HARModel (at https://github.com/emilsjoerup/HARModel) (PR created 2022-09-07) (merged 2023-01-08) (stated 2023-01-09 that package will not get updated at CRAN) (off CRAN as of 2023-12-19)
• [x] mdgc (at https://github.com/boennecd/mdgc) (PR create 2022-09-08) (merged 2022-09-08) (version 0.1.6 on CRAN 2022-09-10)
• [x] minimaxdesign (no known repo) (patch created, tested and emailed 2022-09-10) (heard back 2022-09-12, "in the coming months") (no longer on CRAN as of 2024-01-12)
• [x] MRS (at https://github.com/jacsor/MRS) (PR created 2022-09-10) (merged 2022-10-07) (new version on CRAN 2023-12-09)
• [x] nlmixr (at https://github.com/nlmixrdevelopment/nlmixr) (PR created 2022-09-10) (no longer on CRAN as of 2022-10-10)
• [x] nlmixr2est (at https://github.com/nlmixr2/nlmixr2est) (fix created and merged by upstream 2022-09-01) (new version 2.1.0 on CRAN 2022-10-22)
• [x] pedmod (at https://github.com/boennecd/pedmod) (committed upstream 2022-09-08) (new version 0.2.4 on CRAN 2022-09-11)
• [x] robustHD (at https://github.com/aalfons/robustHD) (PR created 2023-01-15 for updated insert_rows() signature) (merged 2023-01-18) (version 0.7.4 on CRAN 2023-01-18)
• [x] smog (at https://github.com/chongma8903/smog) (PR made 2022-09-11) (merged 2022-09-12) (no longer on CRAN as of 2024-01-12)
• [x] SparseFactorAnalysis (no known repo) (patch created, tested and emailed 2022-09-12) (no longer on CRAN as of 2024-01-12)
• [x] spBFA (at https://github.com/berchuck/spBFA) (committed upstream 2022-09-04, on CRAN as 1.2, 2022-09-04)
• [x] spCP (at https://github.com/berchuck/spCP) (committed upstream 2022-09-04, on CRAN as 1.3, 2022-09-05)
• [x] specs (at https://github.com/wijler/specs) (PR made 2022-09-12) (no longer on CRAN as of 2023-12-07)
• [x] TreeBUGS (at https://github.com/danheck/TreeBUGS) (heard back from upstream 2022-09-06, "at CRAN in 1.4.9")
• [x] UComp (at https://github.com/djpedregal/UComp) (PR made 2022-09-13) (no longer on CRAN as of 2023-01-24)
• [x] womblR (at https://github.com/berchuck/womblR) (committed upstream 2022-09-04, on CRAN as 1.0.5, 2022-09-05)
• [x] bayesm (no known repo) (detected in re-run 2023-09-16) (patch emailed 2023-09-20) (incorporated upstream 2023-09-22) (on CRAN as 3.1-6 on 2023-09-23)
• [x] ordinalClust (no known repo) (detected in re-run 2023-09-16) (patch emailed 2023-09-20) (no longer on CRAN as of 2024-01-12)
• [x] mixedClust (no known repo) (deteced in re-run 2023-10-29) (patch email 2023-10-31) (no longer on CRAN as of 2024-01-12)

The full log from the CRAN check (before we amended the now-uploaded version 0.11.2.3.1 to no flag deprecation) follows

``` Changes to worse in reverse depends: Package: ACEt Check: whether package can be installed New result: WARNING Found the following significant warnings: AtCtEt.cpp:87:35: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEt.cpp:88:35: warning: ‘arma::mat_injector > arma::Row::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEt.cpp:122:35: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEt.cpp:123:35: warning: ‘arma::mat_injector > arma::Row::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEt.cpp:198:35: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEt.cpp:199:35: warning: ‘arma::mat_injector > arma::Row::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEt.cpp:262:35: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEt.cpp:263:35: warning: ‘arma::mat_injector > arma::Row::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEt.cpp:395:35: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEt.cpp:396:35: warning: ‘arma::mat_injector > arma::Row::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEt.cpp:429:35: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEt.cpp:430:35: warning: ‘arma::mat_injector > arma::Row::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:108:35: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:109:35: warning: ‘arma::mat_injector > arma::Row::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:142:35: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:143:35: warning: ‘arma::mat_injector > arma::Row::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:345:35: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:346:35: warning: ‘arma::mat_injector > arma::Row::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:374:35: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:375:35: warning: ‘arma::mat_injector > arma::Row::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:461:35: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:462:35: warning: ‘arma::mat_injector > arma::Row::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:507:35: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:508:35: warning: ‘arma::mat_injector > arma::Row::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:644:35: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:645:35: warning: ‘arma::mat_injector > arma::Row::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:678:35: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:679:35: warning: ‘arma::mat_injector > arma::Row::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:84:35: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:85:35: warning: ‘arma::mat_injector > arma::Row::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:111:35: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:112:35: warning: ‘arma::mat_injector > arma::Row::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:251:35: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:252:35: warning: ‘arma::mat_injector > arma::Row::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:272:35: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:273:35: warning: ‘arma::mat_injector > arma::Row::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:337:35: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:338:35: warning: ‘arma::mat_injector > arma::Row::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:367:35: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:368:35: warning: ‘arma::mat_injector > arma::Row::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:468:35: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:469:35: warning: ‘arma::mat_injector > arma::Row::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:494:35: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:495:35: warning: ‘arma::mat_injector > arma::Row::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] Package: autostsm Check: whether package can be installed New result: WARNING Found the following significant warnings: kalmanfilter.cpp:108:13: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] Package: BAMBI Check: whether package can be installed New result: WARNING Found the following significant warnings: vmcos_llik_grad.cpp:185:28: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] vmcos_llik_grad.cpp:212:54: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] vmsin_llik_grad.cpp:154:21: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] vmsin_llik_grad.cpp:163:21: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] vmsin_llik_grad.cpp:473:10: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] Package: BayesPPD Check: whether package can be installed New result: WARNING Found the following significant warnings: PP_fixed_glm.cpp:98:12: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] PP_random_glm.cpp:96:10: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] Package: BNPMIXcluster Check: whether package can be installed New result: WARNING Found the following significant warnings: get_latents.cpp:44:19: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] Package: cccp Check: whether package can be installed New result: WARNING Found the following significant warnings: DCP.cpp:409:13: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] DLP.cpp:470:13: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] DNL.cpp:317:13: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] DQP.cpp:340:13: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] GPP.cpp:276:13: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] RPP.cpp:225:13: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] Package: finity Check: whether package can be installed New result: WARNING Found the following significant warnings: finite_moment_test.cpp:412:22: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] Package: greed Check: whether package can be installed New result: WARNING Found the following significant warnings: DcSbm.cpp:210:9: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] DcSbm.cpp:212:10: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] DcSbmUndirected.cpp:91:9: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] DcSbmUndirected.cpp:93:10: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] MultSbm.cpp:198:9: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] MultSbm.cpp:200:10: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] MultSbmUndirected.cpp:77:9: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] MultSbmUndirected.cpp:79:10: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] Sbm.cpp:153:9: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] Sbm.cpp:155:10: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] SbmUndirected.cpp:63:9: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] SbmUndirected.cpp:65:10: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] Package: grove Check: whether package can be installed New result: WARNING Found the following significant warnings: hmg.cpp:202:25: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] hmg.cpp:203:40: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] hmg.cpp:453:33: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] Package: handwriter Check: whether package can be installed New result: WARNING Found the following significant warnings: CleanBinaryImage.cpp:265:23: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] ThinImageCpp.cpp:113:32: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] ThinImageCpp.cpp:207:30: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] ThinImageCpp.cpp:220:32: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] ThinImageCpp.cpp:233:32: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] ThinImageCpp.cpp:246:32: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] ThinImageCpp.cpp:261:32: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] ThinImageCpp.cpp:280:27: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] Package: HARModel Check: whether package can be installed New result: WARNING Found the following significant warnings: HARDataCreationC.cpp:43:31: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] Package: mdgc Check: whether package can be installed New result: WARNING Found the following significant warnings: test-pmvnorm.cpp:40:15: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-pmvnorm.cpp:41:14: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-pmvnorm.cpp:42:13: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-pmvnorm.cpp:44:14: warning: ‘arma::mat_injector > arma::Mat::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:33:14: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:35:14: warning: ‘arma::mat_injector > arma::Mat::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:91:15: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:92:14: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:93:15: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:95:14: warning: ‘arma::mat_injector > arma::Mat::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:141:13: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:142:12: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:143:15: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:203:13: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:204:12: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:205:15: warning: ‘arma::mat_injector > arma::Mat::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:292:14: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:294:14: warning: ‘arma::mat_injector > arma::Mat::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:301:15: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:374:15: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:375:14: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:376:14: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:378:14: warning: ‘arma::mat_injector > arma::Mat::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:385:15: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] Package: minimaxdesign Check: whether package can be installed New result: WARNING Found the following significant warnings: subfunc.cpp:322:20: warning: ‘arma::mat_injector > arma::Mat::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] Package: MRS Check: whether package can be installed New result: WARNING Found the following significant warnings: main.cpp:41:34: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] recursion.cpp:645:13: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] Package: nlmixr Check: whether package can be installed New result: WARNING Found the following significant warnings: saem.cpp:746:51: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] Package: nlmixr2est Check: whether package can be installed New result: WARNING Found the following significant warnings: saem.cpp:948:51: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] Package: pedmod Check: whether package can be installed New result: WARNING Found the following significant warnings: test-cdfaprx.cpp:319:15: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:320:14: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:321:15: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:323:14: warning: ‘arma::mat_injector > arma::Mat::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:471:13: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:472:12: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:473:15: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:544:13: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:545:12: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:614:13: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:615:12: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:616:15: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:617:11: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:620:11: warning: ‘arma::mat_injector > arma::Mat::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:745:13: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:746:12: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:747:15: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:748:11: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:751:11: warning: ‘arma::mat_injector > arma::Mat::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:752:11: warning: ‘arma::mat_injector > arma::Mat::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] Package: smog Check: whether package can be installed New result: WARNING Found the following significant warnings: glog.cpp:151:10: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] glog.cpp:253:10: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] glog.cpp:286:15: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] glog.cpp:320:13: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] glog.cpp:369:10: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] Package: SparseFactorAnalysis Check: whether package can be installed New result: WARNING Found the following significant warnings: grad_est.cpp:33:19: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] grad_est.cpp:98:19: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] grad_est.cpp:116:10: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] grad_est.cpp:133:19: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] grad_est.cpp:160:20: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] hmc4sfa.cpp:45:14: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] test_gamma_pois.cpp:30:13: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] Package: spBFA Check: whether package can be installed New result: WARNING Found the following significant warnings: DIAG_GetLogLik.cpp:51:19: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] DIAG_SamplePPD.cpp:37:19: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] PRED_EtaKrigging.cpp:33:19: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] PRED_YKrigging.cpp:33:19: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] Package: spCP Check: whether package can be installed New result: WARNING Found the following significant warnings: DIAG_NormalLogLik.cpp:30:17: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] DIAG_ProbitLogLik.cpp:30:17: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] DIAG_SamplePPD.cpp:40:17: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] DIAG_TobitLogLik.cpp:30:17: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] PRED_PredictFuture.cpp:33:17: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] Package: specs Check: whether package can be installed New result: WARNING Found the following significant warnings: specs.cpp:43:23: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] Package: TreeBUGS Check: whether package can be installed New result: WARNING Found the following significant warnings: betaMPT.cpp:51:9: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] betaMPT.cpp:76:9: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] Package: UComp Check: whether package can be installed New result: WARNING Found the following significant warnings: SSpace.h:1214:16: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] SSpace.h:1216:16: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] SSpace.h:1218:12: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] Package: womblR Check: whether package can be installed New result: WARNING Found the following significant warnings: DIAG_NormalLogLik.cpp:30:17: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] DIAG_SamplePPD.cpp:34:17: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] DIAG_TobitLogLik.cpp:29:17: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] PRED_ThetaKrigging.cpp:36:17: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] PRED_YKrigging.cpp:28:17: warning: ‘arma::mat_injector > arma::Col::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] ```

I have not looked at every one of these in detail but it seems that most if not all are from the change in Armadillo which deprecated the long-used form of initialization via << (which we turned off unconditionally in the most recent CRAN release). What is in the mainline here now (so install_github() works), and can also be installed from the drat repo via install.packages("RcppArmadillo", repos=c("https://RcppCore.github.io/drat")) has a conditional toggle which a) defaults to no deprecation for now to permit CRAN use and b) permits to re-enable deprecation to test your code. The code in the next 'detail' snippet has a minimal example. You need the newer RcppArmadillo from this repo or the drat to make it work.

```c++ // keep uncommented to see the effect, or comment our for silence #define RCPPARMADILLO_FORCE_NO_DEPRECATE 1 #include // [[Rcpp::depends(RcppArmadillo)]] constexpr double alpha = 1.23; // mock variables and values constexpr double beta = 4.56; // [[Rcpp::export]] arma::vec oldCode() { arma::vec res(2); res << alpha << beta; // deprecated OLD initialization return(res); } // [[Rcpp::export]] arma::vec newCode() { arma::vec res({ alpha, beta }); // new standard modern C++ brace initialization return(res); } /*** R stopifnot(packageVersion("RcppArmadillo") >= "0.11.2.3.1.1") oldCode() newCode() */ ```

You see the difference betweeb oldCode() and newCode(): initialization by << (which Conrad wants to deprecate, but which we still allow to not get your package at CRAN) and initialization by the newer and preferred brace initialization common since C++11.

ChangeLog:

• maintainers emailed 2022-09-01 with initial story
• maintainers emailed 2022-09-02 re fix on define
• patches or PRs to all remaining packages made by 2022-09-13 (while several packages were already updated by their maintainers -- thank you!)

[eddelbuettel]

As of 2022-09-26 status of open packages:

library(data.table)
db <- as.data.table(tools::CRAN_package_db())
pkgs <- c("ACEt", "BayesPPD", "BNPMIXcluster", "finity", "greed","grove","handwriter","HARModel","minimaxdesign", "MRS", "nlmixr", "nlmixr2est", "smog","SparseFactorAnalysis","specs","UComp") 
db[Package %in% pkgs,.(Package,Version,Date,Published)][order(-Published)] 

yields

                  Package Version       Date  Published                                                                                                                                                            
                   <char>  <char>     <char>     <char>                                                                                                                                                            
  1:                UComp   2.2.3 2022-08-17 2022-08-17                                                                                                                                                            
  2:             BayesPPD   1.0.7 2022-07-24 2022-08-12                                                                                                                                                            
  3:           nlmixr2est   2.0.8       <NA> 2022-06-22                                                                                                                                                            
  4:               nlmixr   2.0.7       <NA> 2022-03-27                                                                                                                                                            
  5:                greed   0.6.0 2022-03-18 2022-03-18                                                                                                                                                            
  6:           handwriter   1.0.1       <NA> 2021-08-16                                                                                                                                                            
  7:        minimaxdesign   0.1.5       <NA> 2021-07-12                                                                                                                                                            
  8:        BNPMIXcluster     1.3 2020-11-28 2020-11-30                                                                                                                                                            
  9:                 ACEt   1.8.1 2020-10-20 2020-10-21                                                                                                                                                            
 10:                 smog   2.1.0 2020-08-01 2020-08-10                                                                                                                                                            
 11:                specs   0.1.1       <NA> 2020-07-17                                                                                                                                                            
 12:               finity 0.1.4.1 2020-04-22 2020-04-23                                                                                                                                                            
 13:             HARModel     1.0 2019-08-30 2019-08-31                                                                                                                                                            
 14:                  MRS   1.2.4 2018-01-13 2018-01-23                                                                                                                                                            
 15:                grove     1.1 2018-01-07 2018-01-07                                                                                                                                                            
 16: SparseFactorAnalysis     1.0 2015-07-20 2015-07-23     

[eddelbuettel]

As of 2022-10-10 status of open packages:

library(data.table) 
db <- as.data.table(tools::CRAN_package_db()) 
pkgs <- c("BayesPPD", "BNPMIXcluster", "finity", "grove","handwriter","HARModel","minimaxdesign", "MRS", "nlmixr2est", "smog","SparseFactorAnalysis","specs","UComp") 
db[Package %in% pkgs,.(Package,Version,Date,Published)][order(-Published)] 

yields

                 Package Version       Date  Published
                  <char>  <char>     <char>     <char>
 1:                UComp   2.2.3 2022-08-17 2022-08-17
 2:             BayesPPD   1.0.7 2022-07-24 2022-08-12
 3:           nlmixr2est   2.0.8       <NA> 2022-06-22
 4:           handwriter   1.0.1       <NA> 2021-08-16
 5:        minimaxdesign   0.1.5       <NA> 2021-07-12
 6:        BNPMIXcluster     1.3 2020-11-28 2020-11-30
 7:                 smog   2.1.0 2020-08-01 2020-08-10
 8:                specs   0.1.1       <NA> 2020-07-17
 9:               finity 0.1.4.1 2020-04-22 2020-04-23
10:             HARModel     1.0 2019-08-30 2019-08-31
11:                  MRS   1.2.4 2018-01-13 2018-01-23
12:                grove     1.1 2018-01-07 2018-01-07
13: SparseFactorAnalysis     1.0 2015-07-20 2015-07-23
> 

[eddelbuettel]

As of 2022-10-27:

> db <- as.data.table(tools::CRAN_package_db())
> pkgs <- c("BayesPPD", "BNPMIXcluster", "finity", "grove","handwriter","HARModel","minimaxdesign", "MRS", "smog","SparseFactorAnalysis","specs","UComp") 
> db[Package %in% pkgs,.(Package,Version,Date,Published)][order(-Published)]  
                  Package Version       Date  Published        
  1:                UComp   2.2.3 2022-08-17 2022-08-17  
  2:             BayesPPD   1.0.7 2022-07-24 2022-08-12
  3:           handwriter   1.0.1       <NA> 2021-08-16      
  4:        minimaxdesign   0.1.5       <NA> 2021-07-12  
  5:        BNPMIXcluster     1.3 2020-11-28 2020-11-30
  6:                 smog   2.1.0 2020-08-01 2020-08-10     
  7:                specs   0.1.1       <NA> 2020-07-17         
  8:               finity 0.1.4.1 2020-04-22 2020-04-23        
  9:             HARModel     1.0 2019-08-30 2019-08-31  
 10:                  MRS   1.2.4 2018-01-13 2018-01-23    
 11:                grove     1.1 2018-01-07 2018-01-07      
 12: SparseFactorAnalysis     1.0 2015-07-20 2015-07-23 

[eddelbuettel]

As of 2022-11-18:

> library(data.table)
> db <- as.data.table(tools::CRAN_package_db())                                                                                                                                                                    
> pkgs <- c("BNPMIXcluster", "finity", "grove","handwriter","HARModel","minimaxdesign", "MRS", "smog","SparseFactorAnalysis","specs","UComp")                                                                      
> db[Package %in% pkgs,.(Package,Version,Date,Published)][order(-Published)]                                                                                                                                       
                 Package Version       Date  Published                                                                                                                                                             
 1:                UComp   2.2.3 2022-08-17 2022-08-17                                                                                                                                                             
 2:           handwriter   1.0.1       <NA> 2021-08-16                                                                                                                                                             
 3:        minimaxdesign   0.1.5       <NA> 2021-07-12                                                                                                                                                             
 4:        BNPMIXcluster     1.3 2020-11-28 2020-11-30                                                                                                                                                             
 5:                 smog   2.1.0 2020-08-01 2020-08-10                                                                                                                                                             
 6:                specs   0.1.1       <NA> 2020-07-17                                                                                                                                                             
 7:               finity 0.1.4.1 2020-04-22 2020-04-23                                                                                                                                                             
 8:             HARModel     1.0 2019-08-30 2019-08-31                                                                                                                                                             
 9:                  MRS   1.2.4 2018-01-13 2018-01-23                                                                                                                                                             
10:                grove     1.1 2018-01-07 2018-01-07                                                                                                                                                             
11: SparseFactorAnalysis     1.0 2015-07-20 2015-07-23                                                                                                                                                             
>  

[eddelbuettel]

As of 2022-12-21

> library(data.table)
> db <- as.data.table(tools::CRAN_package_db())
> pkgs <- c("finity", "grove","handwriter","HARModel","minimaxdesign", "MRS", "smog","SparseFactorAnalysis","specs","UComp") 
> db[Package %in% pkgs,.(Package,Version,Date,Published)][order(-Published)]
                 Package Version       Date  Published
                  <char>  <char>     <char>     <char>
 1:                UComp   2.2.3 2022-08-17 2022-08-17
 2:           handwriter   1.0.1       <NA> 2021-08-16
 3:        minimaxdesign   0.1.5       <NA> 2021-07-12
 4:                 smog   2.1.0 2020-08-01 2020-08-10
 5:                specs   0.1.1       <NA> 2020-07-17
 6:               finity 0.1.4.1 2020-04-22 2020-04-23
 7:             HARModel     1.0 2019-08-30 2019-08-31
 8:                  MRS   1.2.4 2018-01-13 2018-01-23
 9:                grove     1.1 2018-01-07 2018-01-07
10: SparseFactorAnalysis     1.0 2015-07-20 2015-07-23
> 

[eddelbuettel]

As of 2023-01-07

> db <- as.data.table(tools::CRAN_package_db())
> pkgs <- c("finity", "grove","handwriter","HARModel","minimaxdesign", "MRS", "smog","SparseFactorAnalysis","specs","UComp")
> db[Package %in% pkgs,.(Package,Version,Date,Published)][order(-Published)]
                 Package Version       Date  Published
                  <char>  <char>     <char>     <char>
 1:                UComp   2.2.3 2022-08-17 2022-08-17
 2:           handwriter   1.0.1       <NA> 2021-08-16
 3:        minimaxdesign   0.1.5       <NA> 2021-07-12
 4:                 smog   2.1.0 2020-08-01 2020-08-10
 5:                specs   0.1.1       <NA> 2020-07-17
 6:               finity 0.1.4.1 2020-04-22 2020-04-23
 7:             HARModel     1.0 2019-08-30 2019-08-31
 8:                  MRS   1.2.4 2018-01-13 2018-01-23
 9:                grove     1.1 2018-01-07 2018-01-07
10: SparseFactorAnalysis     1.0 2015-07-20 2015-07-23
> 

Another reminder email sent

``` Dear fellow maintainers, In late August and early September I wrote to the twenty-five maintainers of packages affected by a change in upstream Armadillo which marks an (old) version of initialization as 'deprecated'. As I wrote to you then, "for now" the warning would be suppressed in RcppArmadillo. Details are at https://github.com/RcppCore/RcppArmadillo/issues/391 I also prepared twenty-five patches and/or pull requests for all these packages. By now, fourteen packages have been updated at CRAN, and one has been removed from CRAN leaving ten packages in need of work. This leaves ten packages in need of change. You maintain one of these packages. As I plan to update RcppArmadillo to the current version 0.11.4.3.0 (based on upstream release 11.4.3), you will likely hear from CRAN requesting a change in your package. Having had this issue open since early September (for the last PRs), I hope sufficient time has been made available to make the (generally small) change of accepting a PR or patch. I am planning to release the current RcppArmadillo version to CRAN in about a week. I hope I can count on your cooperation here. If you have questions please do not hesiate to reach out (via reply here, or DM, or on the issue ticket at https://github.com/RcppCore/RcppArmadillo/issues/391). Cheers, Dirk ```

[eddelbuettel]

Version 0.11.4.3.1 of RcppArmadillo has now been uploaded to CRAN, is pending inspection, and will trigger deprecation warnings for the two handful of packages that have not been updated as this issue urged them to.

It revealed at least two packages where my patch or PR might have been incomplete (my bad), and a set of new packages where a new deprecation warning ‘void arma::set_cerr_stream(std::ostream&)’ is deprecated arises that I may have to look into. We will update / refresh this issue ticket, and address the added ones in its ticket #402.

[eddelbuettel]

As of 2023-01-22, with the enlarged list following the 0.11.4.3.1 upload:

> db <- as.data.table(tools::CRAN_package_db())
> pkgs <- c("BayesPPD", "cccp", "finity", "gren", "grove", "growfunctions", "handwriter", "HARModel", "minimaxdesign", "MRS", "smog", "SparseFactorAnalysis", "specs","UComp")
> db[Package %in% pkgs,.(Package,Version,Date,Published)][order(-Published)]
                 Package Version       Date  Published
                  <char>  <char>     <char>     <char>
 1:             BayesPPD   1.1.0 2022-11-11 2022-11-12
 2:                 cccp   0.2-9 2022-09-06 2022-09-09
 3:                UComp   2.2.3 2022-08-17 2022-08-17
 4:           handwriter   1.0.1       <NA> 2021-08-16
 5:        growfunctions    0.15 2021-06-23 2021-07-16
 6:        minimaxdesign   0.1.5       <NA> 2021-07-12
 7:                 smog   2.1.0 2020-08-01 2020-08-10
 8:                specs   0.1.1       <NA> 2020-07-17
 9:               finity 0.1.4.1 2020-04-22 2020-04-23
10:             HARModel     1.0 2019-08-30 2019-08-31
11:                 gren   0.0.1 2018-07-19 2018-07-30
12:                  MRS   1.2.4 2018-01-13 2018-01-23
13:                grove     1.1 2018-01-07 2018-01-07
14: SparseFactorAnalysis     1.0 2015-07-20 2015-07-23
> 

[eddelbuettel]

Now without UComp, otherwise unchanged

> suppressMessages(library(data.table))
> db <- data.table(tools::CRAN_package_db())
> pkgs <- c("BayesPPD", "cccp", "finity", "gren", "grove", "growfunctions", "handwriter", "HARModel", "minimaxdesign", "MRS", "smog", "SparseFactorAnalysis", "specs")
> db[Package %in% pkgs,.(Package,Version,Date,Published)][order(-Published)]
                 Package Version       Date  Published
 1:             BayesPPD   1.1.0 2022-11-11 2022-11-12
 2:                 cccp   0.2-9 2022-09-06 2022-09-09
 3:           handwriter   1.0.1       <NA> 2021-08-16
 4:        growfunctions    0.15 2021-06-23 2021-07-16
 5:        minimaxdesign   0.1.5       <NA> 2021-07-12
 6:                 smog   2.1.0 2020-08-01 2020-08-10
 7:                specs   0.1.1       <NA> 2020-07-17
 8:               finity 0.1.4.1 2020-04-22 2020-04-23
 9:             HARModel     1.0 2019-08-30 2019-08-31
10:                 gren   0.0.1 2018-07-19 2018-07-30
11:                  MRS   1.2.4 2018-01-13 2018-01-23
12:                grove     1.1 2018-01-07 2018-01-07
13: SparseFactorAnalysis     1.0 2015-07-20 2015-07-23
> 

[eddelbuettel]

BayesPPD was taken care of, so the list is one element shorter by otherwise unchanged:

> suppressMessages(library(data.table))
> db <- data.table(tools::CRAN_package_db())
> pkgs <- c("cccp", "finity", "gren", "grove", "growfunctions", "handwriter", "HARModel", "minimaxdesign", "MRS", "smog", "SparseFactorAnalysis", "specs")
> db[Package %in% pkgs,.(Package,Version,Date,Published)][order(-Published)]
                 Package Version       Date  Published
                  <char>  <char>     <char>     <char>
 1:                 cccp   0.2-9 2022-09-06 2022-09-09
 2:           handwriter   1.0.1       <NA> 2021-08-16
 3:        growfunctions    0.15 2021-06-23 2021-07-16
 4:        minimaxdesign   0.1.5       <NA> 2021-07-12
 5:                 smog   2.1.0 2020-08-01 2020-08-10
 6:                specs   0.1.1       <NA> 2020-07-17
 7:               finity 0.1.4.1 2020-04-22 2020-04-23
 8:             HARModel     1.0 2019-08-30 2019-08-31
 9:                 gren   0.0.1 2018-07-19 2018-07-30
10:                  MRS   1.2.4 2018-01-13 2018-01-23
11:                grove     1.1 2018-01-07 2018-01-07
12: SparseFactorAnalysis     1.0 2015-07-20 2015-07-23
> 

[eddelbuettel]

handwriter was taken care of, so now one element shorter.

> library(data.table)
> db <- data.table(tools::CRAN_package_db())
> pkgs <- c("cccp", "finity", "gren", "grove", "growfunctions", "HARModel", "minimaxdesign", "MRS", "smog", "SparseFactorAnalysis", "specs")
> db[Package %in% pkgs,.(Package,Version,Date,Published)][order(-Published)]
                 Package Version       Date  Published
                  <char>  <char>     <char>     <char>
 1:                 cccp   0.2-9 2022-09-06 2022-09-09
 2:        growfunctions    0.15 2021-06-23 2021-07-16
 3:        minimaxdesign   0.1.5       <NA> 2021-07-12
 4:                 smog   2.1.0 2020-08-01 2020-08-10
 5:                specs   0.1.1       <NA> 2020-07-17
 6:               finity 0.1.4.1 2020-04-22 2020-04-23
 7:             HARModel     1.0 2019-08-30 2019-08-31
 8:                 gren   0.0.1 2018-07-19 2018-07-30
 9:                  MRS   1.2.4 2018-01-13 2018-01-23
10:                grove     1.1 2018-01-07 2018-01-07
11: SparseFactorAnalysis     1.0 2015-07-20 2015-07-23
> 

PS Edit 2023-10-30: Apparently handwriter is not fully fixed.

[eddelbuettel]

mixedClust and ordinalClust added, handwriter re-added:

 > suppressMessages(library(data.table))                                                                                                                                                                           
 > db <- data.table(tools::CRAN_package_db())                                                                                                                                                                      
 > pkgs <- c("cccp", "finity", "gren", "grove", "growfunctions", "handwriter", "HARModel", "minimaxdesign", "mixedClust", "ordinalClust", "MRS", "smog", "SparseFactorAnalysis", "specs")                          
!> db[Package %in% pkgs,.(Package,Version,Date,Published)][order(-Published)]                                                                                                                                      
                  Package Version       Date  Published                                                                                                                                                            
                   <char>  <char>     <char>     <char>                                                                                                                                                            
  1:           handwriter   2.0.2       <NA> 2023-10-13                                                                                                                                                            
  2:                 cccp   0.2-9 2022-09-06 2022-09-09                                                                                                                                                            
  3:        growfunctions    0.15 2021-06-23 2021-07-16                                                                                                                                                            
  4:        minimaxdesign   0.1.5       <NA> 2021-07-12                                                                                                                                                            
  5:           mixedClust   1.0.2 2021-03-21 2021-03-29                                                                                                                                                            
  6:         ordinalClust   1.3.5 2020-10-26 2020-11-19                                                                                                                                                            
  7:                 smog   2.1.0 2020-08-01 2020-08-10                                                                                                                                                            
  8:                specs   0.1.1       <NA> 2020-07-17                                                                                                                                                            
  9:               finity 0.1.4.1 2020-04-22 2020-04-23                                                                                                                                                            
 10:             HARModel     1.0 2019-08-30 2019-08-31                                                                                                                                                            
 11:                 gren   0.0.1 2018-07-19 2018-07-30                                                                                                                                                            
 12:                  MRS   1.2.4 2018-01-13 2018-01-23                                                                                                                                                            
 13:                grove     1.1 2018-01-07 2018-01-07                                                                                                                                                            
 14: SparseFactorAnalysis     1.0 2015-07-20 2015-07-23                                                                                                                                                            
 > 

[eddelbuettel]

RcppArmadillo release 0.12.6.6.1 is now on CRAN, and no longer defines ARMA_IGNORE_DEPRECATED_MARKER.

[eddelbuettel]

As of 2023-12-10, gren and specs are no longer on CRAN (maintainer email bounce), and packages handwriter, MRS, cccp and grove have been updated.

> suppressMessages(library(data.table))    
> db <- data.table(tools::CRAN_package_db())
> pkgs <- c("finity","growfunctions","HARModel","minimaxdesign","mixedClust","ordinalClust","smog","SparseFactorAnalysis") 
> db[Package %in% pkgs,.(Package,Version,Date,Published)][order(-Published)]      
                Package Version       Date  Published
                 <char>  <char>     <char>     <char>
1:        growfunctions    0.15 2021-06-23 2021-07-16
2:        minimaxdesign   0.1.5       <NA> 2021-07-12
3:           mixedClust   1.0.2 2021-03-21 2021-03-29
4:         ordinalClust   1.3.5 2020-10-26 2020-11-19
5:                 smog   2.1.0 2020-08-01 2020-08-10
6:               finity 0.1.4.1 2020-04-22 2020-04-23
7:             HARModel     1.0 2019-08-30 2019-08-31
8: SparseFactorAnalysis     1.0 2015-07-20 2015-07-23
> 

[eddelbuettel]

Remainder of #391 and #402 as of 2023-12-18:

> suppressMessages(library(data.table))
> db <- data.table(tools::CRAN_package_db())
> pkgs <- c("Rphylopars","finity","HARModel","minimaxdesign","mixedClust","ordinalClust","smog","SparseFactorAnalysis")
> db[Package %in% pkgs,.(Package,Version,Date,Published)][order(-Published)]
                Package Version       Date  Published
                 <char>  <char>     <char>     <char>
1:           Rphylopars   0.3.9 2022-05-08 2022-05-09
2:        minimaxdesign   0.1.5       <NA> 2021-07-12
3:           mixedClust   1.0.2 2021-03-21 2021-03-29
4:         ordinalClust   1.3.5 2020-10-26 2020-11-19
5:                 smog   2.1.0 2020-08-01 2020-08-10
6:               finity 0.1.4.1 2020-04-22 2020-04-23
7:             HARModel     1.0 2019-08-30 2019-08-31
8: SparseFactorAnalysis     1.0 2015-07-20 2015-07-23
> 

Edit: As of 2023-12-20, HARModel is off CRAN, and finity has been updated so the list is down to six.

[eddelbuettel]

As of 2023-12-28:

> suppressMessages(library(data.table))
> db <- data.table(tools::CRAN_package_db())
> pkgs <- c("Rphylopars","minimaxdesign","mixedClust","ordinalClust","smog","SparseFactorAnalysis")
> db[Package %in% pkgs,.(Package,Version,Date,Published)][order(-Published)]
                Package Version       Date  Published
                 <char>  <char>     <char>     <char>
1:           Rphylopars   0.3.9 2022-05-08 2022-05-09
2:        minimaxdesign   0.1.5       <NA> 2021-07-12
3:           mixedClust   1.0.2 2021-03-21 2021-03-29
4:         ordinalClust   1.3.5 2020-10-26 2020-11-19
5:                 smog   2.1.0 2020-08-01 2020-08-10
6: SparseFactorAnalysis     1.0 2015-07-20 2015-07-23
> 

[eddelbuettel]

All packages still listed in the previous update are now off CRAN. So this concludes the transition: a really large number of packages helped along and update, while a much smaller number of packages could not or would not but is no longer at CRAN.

The transition is complete and the issue can now be closed.