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:

• 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)
• autostsm (at https://bitbucket.org/ajhubb/autostsm.git) (pull request made 2022-09-01) (version 3.0.2 at CRAN)
• BAMBI (at https://github.com/c7rishi/BAMBI/) (already addressed by upstream) (version 2.3.4 on CRAN)
• 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 (!!))
• 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)
• 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)
• 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)
• 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)
• 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)
• grove (at https://github.com/jacsor/grove) (PR created 2022-09-05) (new version on CRAN 2023-12-10)
• growfunctions (no known repo) (patch for updated insert_rows() signature created, tested and emailed 2023-01-15) (new version on CRAN 2023-12-12)
• 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)
• 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)
• 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)
• 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)
• MRS (at https://github.com/jacsor/MRS) (PR created 2022-09-10) (merged 2022-10-07) (new version on CRAN 2023-12-09)
• nlmixr (at https://github.com/nlmixrdevelopment/nlmixr) (PR created 2022-09-10) (no longer on CRAN as of 2022-10-10)
• 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)
• pedmod (at https://github.com/boennecd/pedmod) (committed upstream 2022-09-08) (new version 0.2.4 on CRAN 2022-09-11)
• 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)
• 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)
• SparseFactorAnalysis (no known repo) (patch created, tested and emailed 2022-09-12) (no longer on CRAN as of 2024-01-12)
• spBFA (at https://github.com/berchuck/spBFA) (committed upstream 2022-09-04, on CRAN as 1.2, 2022-09-04)
• spCP (at https://github.com/berchuck/spCP) (committed upstream 2022-09-04, on CRAN as 1.3, 2022-09-05)
• specs (at https://github.com/wijler/specs) (PR made 2022-09-12) (no longer on CRAN as of 2023-12-07)
• TreeBUGS (at https://github.com/danheck/TreeBUGS) (heard back from upstream 2022-09-06, "at CRAN in 1.4.9")
• UComp (at https://github.com/djpedregal/UComp) (PR made 2022-09-13) (no longer on CRAN as of 2023-01-24)
• womblR (at https://github.com/berchuck/womblR) (committed upstream 2022-09-04, on CRAN as 1.0.5, 2022-09-05)
• 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)
• 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)
• 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

Details

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<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEt.cpp:88:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEt.cpp:122:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEt.cpp:123:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEt.cpp:198:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEt.cpp:199:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEt.cpp:262:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEt.cpp:263:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEt.cpp:395:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEt.cpp:396:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEt.cpp:429:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEt.cpp:430:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEtp.cpp:108:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEtp.cpp:109:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEtp.cpp:142:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEtp.cpp:143:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEtp.cpp:345:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEtp.cpp:346:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEtp.cpp:374:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEtp.cpp:375:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEtp.cpp:461:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEtp.cpp:462:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEtp.cpp:507:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEtp.cpp:508:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEtp.cpp:644:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEtp.cpp:645:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEtp.cpp:678:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtCtEtp.cpp:679:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtEtp.cpp:84:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtEtp.cpp:85:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtEtp.cpp:111:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtEtp.cpp:112:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtEtp.cpp:251:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtEtp.cpp:252:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtEtp.cpp:272:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtEtp.cpp:273:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtEtp.cpp:337:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtEtp.cpp:338:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtEtp.cpp:367:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtEtp.cpp:368:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtEtp.cpp:468:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtEtp.cpp:469:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtEtp.cpp:494:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    AtEtp.cpp:495:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::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<eT> > arma::Col<eT>::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<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    vmcos_llik_grad.cpp:212:54: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    vmsin_llik_grad.cpp:154:21: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    vmsin_llik_grad.cpp:163:21: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    vmsin_llik_grad.cpp:473:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::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<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]
    PP_random_glm.cpp:96:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::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<eT> > arma::Col<eT>::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<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    DLP.cpp:470:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    DNL.cpp:317:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    DQP.cpp:340:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    GPP.cpp:276:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    RPP.cpp:225:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::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<eT> > arma::Col<eT>::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<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]
    DcSbm.cpp:212:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]
    DcSbmUndirected.cpp:91:9: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]
    DcSbmUndirected.cpp:93:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]
    MultSbm.cpp:198:9: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]
    MultSbm.cpp:200:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]
    MultSbmUndirected.cpp:77:9: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]
    MultSbmUndirected.cpp:79:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]
    Sbm.cpp:153:9: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]
    Sbm.cpp:155:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]
    SbmUndirected.cpp:63:9: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]
    SbmUndirected.cpp:65:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::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<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    hmg.cpp:203:40: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    hmg.cpp:453:33: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::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<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    ThinImageCpp.cpp:113:32: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    ThinImageCpp.cpp:207:30: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    ThinImageCpp.cpp:220:32: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    ThinImageCpp.cpp:233:32: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    ThinImageCpp.cpp:246:32: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    ThinImageCpp.cpp:261:32: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    ThinImageCpp.cpp:280:27: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::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<eT> > arma::Col<eT>::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<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-pmvnorm.cpp:41:14: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-pmvnorm.cpp:42:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-pmvnorm.cpp:44:14: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-restrict-cdf.cpp:33:14: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-restrict-cdf.cpp:35:14: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-restrict-cdf.cpp:91:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-restrict-cdf.cpp:92:14: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-restrict-cdf.cpp:93:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-restrict-cdf.cpp:95:14: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-restrict-cdf.cpp:141:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-restrict-cdf.cpp:142:12: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-restrict-cdf.cpp:143:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-restrict-cdf.cpp:203:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-restrict-cdf.cpp:204:12: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-restrict-cdf.cpp:205:15: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-restrict-cdf.cpp:292:14: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-restrict-cdf.cpp:294:14: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-restrict-cdf.cpp:301:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-restrict-cdf.cpp:374:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-restrict-cdf.cpp:375:14: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-restrict-cdf.cpp:376:14: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-restrict-cdf.cpp:378:14: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-restrict-cdf.cpp:385:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::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<eT> > arma::Mat<eT>::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<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    recursion.cpp:645:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::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<eT> > arma::Col<eT>::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<eT> > arma::Col<eT>::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<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-cdfaprx.cpp:320:14: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-cdfaprx.cpp:321:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-cdfaprx.cpp:323:14: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-cdfaprx.cpp:471:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-cdfaprx.cpp:472:12: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-cdfaprx.cpp:473:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-cdfaprx.cpp:544:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-cdfaprx.cpp:545:12: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-cdfaprx.cpp:614:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-cdfaprx.cpp:615:12: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-cdfaprx.cpp:616:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-cdfaprx.cpp:617:11: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-cdfaprx.cpp:620:11: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-cdfaprx.cpp:745:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-cdfaprx.cpp:746:12: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-cdfaprx.cpp:747:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-cdfaprx.cpp:748:11: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-cdfaprx.cpp:751:11: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    test-cdfaprx.cpp:752:11: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::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<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]
    glog.cpp:253:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]
    glog.cpp:286:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]
    glog.cpp:320:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]
    glog.cpp:369:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::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<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    grad_est.cpp:98:19: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    grad_est.cpp:116:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    grad_est.cpp:133:19: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    grad_est.cpp:160:20: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    hmc4sfa.cpp:45:14: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]
    test_gamma_pois.cpp:30:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::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<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    DIAG_SamplePPD.cpp:37:19: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    PRED_EtaKrigging.cpp:33:19: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    PRED_YKrigging.cpp:33:19: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::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<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    DIAG_ProbitLogLik.cpp:30:17: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    DIAG_SamplePPD.cpp:40:17: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    DIAG_TobitLogLik.cpp:30:17: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    PRED_PredictFuture.cpp:33:17: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::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<eT> > arma::Col<eT>::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<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    betaMPT.cpp:76:9: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::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<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]
    SSpace.h:1216:16: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]
    SSpace.h:1218:12: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::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<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    DIAG_SamplePPD.cpp:34:17: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    DIAG_TobitLogLik.cpp:29:17: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    PRED_ThetaKrigging.cpp:36:17: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]
    PRED_YKrigging.cpp:28:17: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::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.

Details

// keep uncommented to see the effect, or comment our for silence
#define RCPPARMADILLO_FORCE_NO_DEPRECATE 1


#include <RcppArmadillo.h>
// [[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!)