1.12.4 release checks

[mattdowle]

• Rerun and resolve all revdeps revdep rerun #3581
• CRAN_Release.cmd (e.g. UBSAN, ASAN, rchk, gctorture, win-builder 2*OK)
• win-builder R-devel seems to be stuck; emailed Uwe. r-release and r-oldrel are ok and pass ok.
• CRAN 'additional issues': NoLD fix CRAN noLD note #3515, rchk Pass rchk #3867, and LTO Fixed LTO warnings #3864
• one revdep fail (segregation) caused by removed sole SET_NAMED #3895; tested and filed PR attr<- changed to setattr elbersb/segregation#3; update in v0.3.0 on CRAN 2019-09-20
• one revdep fail (sensobol) caused by := could change calling body and variable in calling scope #3891; just needs publish Application to large scale ODE (PBPK) model arnaldpuy/sensobol#1; update in v0.2.1 on CRAN 2019-09-20
• Revisit test 1294.29 temporarily turned off in PR Coerce 01 #3909
• Final items in milestone
• News item review and tidy
• Codefreeze ba63147
• Repeat win-builder 3*OK
• @renkun-ken go-first run please (last successful run: dc9a32a)
• Final repeat CRAN_Release.cmd
• Final rerun latest revdeps refreshed
• Final repeat win-builder 3*OK
• Submit to CRAN (several opportunities to halt after this)
• CRAN pre-test success email received and OK
• Bump dev version
• Copy and paste revdep.R::status() output as new comment to this issue
• CRAN revdep status impact results email received
• Matt replied to confirm and explain differences to submission note
• CRAN email received to confirm accepted
• Add publish date to v1.12.4 title in NEWS.md
• Update version and date in Installation wiki heading
• Tweet to #rdatatable. https://twitter.com/MattDowle/status/1179833079533203456

Based on 1.12.2 release check list: #3473

[shrektan]

@mattdowle is it possible to merge #3850 #3849 before this CRAN release? Otherwise I can’t use the next CRAN release. Thanks.

[MichaelChirico]

Final low-risk items in milestone

Safe to say anything left on 1.12.4 milestone is targeted for this part? @mattdowle

[mattdowle]

Ideally yes. But that might change. Jan has done a great job postponing a lot already. #3890 is troubling and that's all I'm looking at currently.

[elbersb]

The new version of segregation is on CRAN, so that should be taken care of.

[mattdowle]

Many thanks @elbersb!

@MichaelChirico Just on this 'release checks' issue, please don't edit the ticks. I was waiting to tick these two until they've fed through to my local revdep environment and passed for me locally. Which they have done now. (It's feasible they might not have reached me yet, or passed for me.)

[mattdowle]

@renkun-ken Thanks for testing 4 and 14 days ago and updating the schedule above. I was watching and saw your updates: very useful. I just submitted to CRAN. If you have a chance to do a final go-first test would be great, and tick the box please. If you do find anything I can ask CRAN maintainers to halt the update.

[renkun-ken]

@mattdowle, I'm closely observing the progress and started running the production scripts with latest commit dc9a32a several hours ago. Hopefully, it will finish in a couple of hours.

[renkun-ken]

Everything looks good here.

[mattdowle]

Revdep status on submit. These fails are unrelated to this data.table update.

CRAN:
 ERROR   :   1 : pmpp
 WARNING :   1 : optiSel
 NOTE    : 239
 OK      : 503
 TOTAL   : 744 / 744

BIOC:
 ERROR   :  10 : anamiR chimeraviz contiBAIT ENCODExplorerData GENESIS ImmuneSpaceR
                 ORFik Pviz SparseSignatures TitanCNA
 WARNING :  31 : AUCell BEARscc CellNOptR CONFESS crossmeta CytoML ELMER eQTL
                 flowWorkspace geneXtendeR GenoGAM genomation ggcyto HMMcopy iCNV
                 maftools methylPipe MinimumDistance MMAPPR2 MSnID MSstats netSmooth
                 openCyto pepStat QUALIFIER RegParallel RiboProfiling S4Vectors SISPA
                 TENxBrainData TFutils
 NOTE    : 109
 OK      :  37
 TOTAL   : 187 / 187

TOTAL          : 931

fail.log

Communication with Bioc maintainers in #3581.