RcppArmadillo
RcppArmadillo copied to clipboard
RcppCore
Deprecating old initialization code in packages using RcppArmadillo
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 not throw deprecation warnings as Armadillo upstream activated those.
CRAN of course frowns on this so we temporarily disabled the warning in RcppArmadillo. Going forward we should aim to patch this in all affected packages, and we will try to provide PRs. This affects these packages:
- [x] ACEt (at https://r-forge.r-project.org/R/?group_id=2167) (patch created, tested and emailed 2022-09-01) (heard back 2022-09-04: "within a few weeks") (version 1.8.2 on CRAN 2022-09-26)
- [x] autostsm (at https://bitbucket.org/ajhubb/autostsm.git) (pull request made 2022-09-01) (version 3.0.2 at CRAN)
- [x] BAMBI (at https://github.com/c7rishi/BAMBI/) (already addressed by upstream) (version 2.3.4 on CRAN)
- [ ] BayesPPD (no known repo) (patch created, tested, and emailed 2022-09-04)
- [ ] BNPMIXcluster (at https://github.com/chriscarmona/BNPMIXcluster) (PR created 2022-09-04) (merged 2022-09-09)
- [x] cccp (at https://github.com/bpfaff/cccp) (PR created 2022-09-04) (merged 2022-09-06) (version 0.2-9 on CRAN 2022-09-09)
- [ ] finity (at https://github.com/x0range/finity) (PR created 2022-09-05)
- [x] greed (at https://github.com/comeetie/greed) (PR created 2022-09-05) (heard back 2022-09-06 'within days') (merged 2022-09-07) (version 0.6.1 on CRAN 2022-10-03)
- [ ] grove (at https://github.com/jacsor/grove) (PR created 2022-08-05)
- [ ] handwriter (at https://github.com/CSAFE-ISU/handwriter) (PR created 2022-09-06) (merged 2022-09-09)
- [ ] HARModel (at https://github.com/emilsjoerup/HARModel) (PR created 2022-09-07)
- [x] mdgc (at https://github.com/boennecd/mdgc) (PR create 2022-09-08) (merged 2022-09-08) (version 0.1.6 on CRAN 2022-09-10)
- [ ] minimaxdesign (no known repo) (patch created, tested and emailed 2022-09-10) (heard back 2022-09-12, "in the coming months")
- [ ] MRS (at https://github.com/jacsor/MRS) (PR created 2022-09-10) (merged 2022-10-07)
- [x] 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/nlmixrdevelopment/nlmixr) (fix created and merged by upstream 2022-09-01)
- [x] pedmod (at https://github.com/boennecd/pedmod) (committed upstream 2022-09-08) (new version 0.2.4 on CRAN 2022-09-11)
- [ ] smog (at https://github.com/chongma8903/smog) (PR made 2022-09-11) (merged 2022-09-12)
- [ ] SparseFactorAnalysis (no known repo) (patch created, tested and emailed 2022-09-12)
- [x] spBFA (at https://github.com/berchuck/spBFA) (committed upstream 2022-09-04, on CRAN as 1.2, 2022-09-04)
- [x] spCP (at https://github.com/berchuck/spCP) (committed upstream 2022-09-04, on CRAN as 1.3, 2022-09-05)
- [ ] specs (at https://github.com/wijler/specs) (PR made 2022-09-12)
- [x] 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)
- [x] womblR (at https://github.com/berchuck/womblR) (committed upstream 2022-09-04, on CRAN as 1.0.5, 2022-09-05)
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!)
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
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
>
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
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
>
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
>
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
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.
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
>
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
>
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
>
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.
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
>
RcppArmadillo release 0.12.6.6.1 is now on CRAN, and no longer defines ARMA_IGNORE_DEPRECATED_MARKER.
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
>
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.
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
>
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.