Deprecating old initialization code in packages using RcppArmadillo #391

eddelbuettel · 2022-08-26T19:57:11Z

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:

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<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.

// 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!)

The text was updated successfully, but these errors were encountered:

…lo#391

This one-line change updates RcppArmadillo from the now deprecated `<<` initialization to brace initialization allowed since C++11 and long been minimal standard with R too. It would be great if you could merge this, and release and updated package "in the next little while" -- see the two prior emails I sent, and the transition log at RcppCore/RcppArmadillo#391

These six one-line changes update RcppArmadillo from the now deprecated `<<` initialization to brace initialization allowed since C++11 and long been the minimal standard with R too. It would be great if you could merge this, and release and updated package "in the next little while" -- see the two prior emails I sent, and the transition log at RcppCore/RcppArmadillo#391

This one-line change updates RcppArmadillo from the now deprecated << initialization to brace initialization allowed since C++11 and long been minimal standard with R too -- and which you already had, albeit commented out. It would be great if you could merge this, and release and updated package "in the next little while" -- see the two prior emails I sent, and the transition log at RcppCore/RcppArmadillo#391

These six two-line changes update RcppArmadillo from the now deprecated `<<` initialization to brace initialization allowed since C++11 and long been the minimal standard with R too. It would be great if you could merge this, and release and updated package "in the next little while" -- see the two prior emails I sent, and the transition log at RcppCore/RcppArmadillo#391

These two simple changes update RcppArmadillo from the now deprecated `<<` initialization to brace initialization allowed since C++11 and long been the minimal standard with R too. It would be great if you could merge this, and release and updated package "in the next little while" -- see the two prior emails I sent, and the transition log at RcppCore/RcppArmadillo#391

These simple changes update RcppArmadillo from the now deprecated `<<` initialization to brace initialization allowed since C++11 and long been the minimal standard with R too. It would be great if you could merge this, and release and updated package "in the next little while" -- see the two prior emails I sent, and the transition log at RcppCore/RcppArmadillo#391

This one-line change updates RcppArmadillo from the now deprecated `<<` initialization to brace initialization allowed since C++11 and long been the minimal standard with R too. It would be great if you could merge this, and release and updated package "in the next little while" -- see the two prior emails I sent, and the transition log at RcppCore/RcppArmadillo#391

These changes update RcppArmadillo from the now deprecated `<<` initialization to brace initialization allowed since C++11 and long been the minimal standard with R too. It would be great if you could merge this, and release and updated package "in the next little while" -- see the two prior emails I sent, and the transition log at RcppCore/RcppArmadillo#391

see RcppCore/RcppArmadillo#391

One simple change to update RcppArmadillo use from the now deprecated `<<` initialization to brace initialization allowed since C++11 and long been the minimal standard with R too. It would be great if you could merge this, and release and updated package "in the next little while" -- see the two prior emails I sent, and the transition log at RcppCore/RcppArmadillo#391

A second simple change to update RcppArmadillo use from the now deprecated `<<` initialization to brace initialization allowed since C++11 and long been the minimal standard with R too. It would be great if you could merge this, and release and updated package "in the next little while" -- see the two prior emails I sent, and the transition log at RcppCore/RcppArmadillo#391

Two simple changes to update RcppArmadillo use from the now deprecated `<<` initialization to brace initialization allowed since C++11 and long been the minimal standard with R too. It would be great if you could merge this, and release and updated package "in the next little while" -- see the two prior emails I sent, and the transition log at RcppCore/RcppArmadillo#391

One simple one-line change to update RcppArmadillo use from the now deprecated `<<` initialization to brace initialization allowed since C++11 and long been the minimal standard with R too. It would be great if you could merge this, and release and updated package "in the next little while" -- see the two prior emails I sent, and the transition log at RcppCore/RcppArmadillo#391

These changes update RcppArmadillo from the now deprecated << initialization to brace initialization allowed since C++11 and long been the minimal standard with R too. It would be great if you could merge this, and release and updated package "in the next little while" -- see the two prior emails I sent, and the transition log at RcppCore/RcppArmadillo#391

This one-line change updates RcppArmadillo from the now deprecated `<<` initialization to brace initialization allowed since C++11 and long been the minimal standard with R too. It would be great if you could merge this, and release and updated package "in the next little while" -- see the two prior emails I sent, and the transition log at RcppCore/RcppArmadillo#391

These three one-line change update RcppArmadillo from the now deprecated << initialization to brace initialization allowed since C++11 and long been the minimal standard with R too. It would be great if you could merge this, and release and updated package "in the next little while" -- see the two prior emails I sent, and the transition log at RcppCore/RcppArmadillo#391

eddelbuettel · 2022-09-26T12:19:57Z

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 · 2022-10-10T16:38:42Z

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 · 2022-10-27T16:26:36Z

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 · 2022-11-18T16:08:26Z

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 · 2022-12-22T05:29:02Z

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 · 2023-01-07T18:45:47Z

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 · 2023-01-14T16:53:50Z

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 · 2023-01-23T00:05:17Z

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 · 2023-03-12T16:09:54Z

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 · 2023-09-10T14:33:10Z

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 · 2023-10-21T07:18:34Z

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 · 2023-11-01T01:18:25Z

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                                                                                                                                                            
 >

For reasons related to issues discussed in RcppCore/RcppArmadillo#391 and RcppCore/RcppArmadillo#402, RcppArmadillo is building with deprecation warnings suppressed. I plan to change that ... and when I do r2sundials with create three warnings from your use of a three-argument form of `insert_cols` that is now deprecated. This is simple: use the two-argument form. I tested the change and R CMD check still passes. It would be great if you could update r2sundials in the next few weeks. I plan to update RcppArmadillo in about a month and then stop suppressing warnings.

eddelbuettel · 2023-12-04T13:00:40Z

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

eddelbuettel · 2023-12-10T16:06:12Z

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 · 2023-12-18T13:20:07Z

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 · 2023-12-28T21:43:35Z

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 · 2024-01-12T19:05:26Z

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.

mattfidler mentioned this issue Sep 1, 2022

RcppArmadillo nlmixr2/nlmixr2est#200

Closed

danheck added a commit to danheck/TreeBUGS that referenced this issue Sep 2, 2022

fix deprecated << operator in RcppArmadillo, see RcppCore/RcppArmadil…

b6e8740

…lo#391

eddelbuettel mentioned this issue Sep 4, 2022

Update RcppArmadillo initialization chriscarmona/BNPMIXcluster#3

Merged

eddelbuettel mentioned this issue Sep 4, 2022

Updating RcppArmadillo initialization bpfaff/cccp#3

Merged

eddelbuettel mentioned this issue Sep 5, 2022

Update RcppArmadillo initialization x0range/finity#5

Merged

eddelbuettel mentioned this issue Sep 5, 2022

Updating RcppArmadillo initialization comeetie/greed#23

Merged

eddelbuettel mentioned this issue Sep 5, 2022

Updating RcppArmadillo initialization jacsor/grove#17

Merged

eddelbuettel mentioned this issue Sep 7, 2022

Updating RcppArmadillo initialization CSAFE-ISU/handwriter#10

Merged

eddelbuettel mentioned this issue Sep 8, 2022

Updating RcppArmadillo initialization emilsjoerup/HARModel#5

Merged

eddelbuettel mentioned this issue Sep 9, 2022

Updating RcppArmadillo initialization boennecd/mdgc#1

Merged

boennecd added a commit to boennecd/pedmod that referenced this issue Sep 9, 2022

get rid of deprecated << initialization in Armadillo

f8740ec

see RcppCore/RcppArmadillo#391

eddelbuettel mentioned this issue Sep 10, 2022

Updating RcppArmadillo initialization jacsor/MRS#17

Merged

eddelbuettel mentioned this issue Sep 10, 2022

Updating RcppArmadillo initialization nlmixrdevelopment/nlmixr#620

Open

eddelbuettel mentioned this issue Sep 12, 2022

Updating RcppArmadillo initialization chongma8903/smog#1

Merged

eddelbuettel mentioned this issue Sep 13, 2022

Updating RcppArmadillo initialization wijler/specs#1

Open

eddelbuettel mentioned this issue Sep 13, 2022

Updating RcppArmadillo initialization djpedregal/UComp#1

Open

stephaniereinders mentioned this issue Jan 11, 2023

next time we submit to CRAN CSAFE-ISU/handwriter#74

Closed

eddelbuettel mentioned this issue Nov 1, 2023

Switch to non-deprecated insert_cols sgsokol/r2sundials#2

Merged

eddelbuettel closed this as completed Jan 12, 2024

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