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revdep results #3233
Description
Activity
To include on CRAN upload message.
Communication with downstream maintainers has happened in advance :
- behavr Update for data.table v1.12.0: retains attributes rethomics/behavr#40. Update already on CRAN.
- maditr tolerance: expect_identical => expect_equal gdemin/maditr#3 Update already on CRAN.
- rENA maintainer emailed (copied to rownames .SD #3254)
- SpaDES.core Change to pass data.table v1.12.0 please PredictiveEcology/SpaDES.core#85
Already in error/warning on CRAN and unrelated to data.table :
- DeclareDesign I see the same error (
expect_equal(ncol(draw_estimates(des)), 7) did not produce any warnings) locally. Seems unrelated to data.table. - ctsem Passes now locally after installing biber. The warnings and errors on CRAN seem to be system specific and unrelated to data.table
- worrms Fails locally with same error as CRAN (
all(grepl(format(Sys.Date(), "%Y"), aa$modified)) isn't true). Looks unrelated to data.table; e.g. related to 2018 now being 2019.
Current status after full rerun :
Installed data.table to be tested against: 1.11.9 CRAN: ERROR : 2 : DeclareDesign worrms WARNING : 0 : NOTE : 191 OK : 403 TOTAL : 596 / 596 BIOC: ERROR : 6 : GenVisR ImmuneSpaceR LymphoSeq MAST QuartPAC scater WARNING : 18 : bsseq CONFESS CRISPRseek crossmeta eQTL GenoGAM iCNV IrisSpatialFeatures methylPipe minfi MinimumDistance paxtoolsr RiboProfiling rTANDEM S4Vectors SISPA TitanCNA Uniquorn NOTE : 91 OK : 19 TOTAL : 134 / 134 TOTAL : 730Rerun of Bioc fails with CRAN data.table 1.11.8 :
BIOC: ERROR : 5 : GenVisR ImmuneSpaceR LymphoSeq MAST scater WARNING : 18 : bsseq CONFESS CRISPRseek crossmeta eQTL GenoGAM iCNV IrisSpatialFeatures methylPipe minfi MinimumDistance paxtoolsr RiboProfiling rTANDEM S4Vectors SISPA TitanCNA Uniquorn NOTE : 92 OK : 19 TOTAL : 134 / 134So, other than QuartPAC, they're all already in error/warning with CRAN version. This is long-standing on Bioconductor and not receiving attention.
Bioc status diff to investigate :
- QuartPAC When I reran with v1.11.9, it passed fine with just notes. I hadn't kept a log of the previous fail. Sometimes a rerun works if internet access is needed for a package's tests so I'll put it down to that.
Email to 23 Bioconductor package maintainers sent on 4th Jan 2018 :
Dear maintainer of Bioconductor package,
Please could you fix the error or warning status. Your package uses data.table in some way. Since your package is already in error/warning status, it makes it much harder for me to test the impact each data.table update has. In some cases the error/warning status has been left unfixed on Bioconductor for years. In some cases the problem might be local to my machine -- please look at the log attached for your package and let me know.
ERROR : 5 : GenVisR ImmuneSpaceR LymphoSeq MAST scater
WARNING : 18 : bsseq CONFESS CRISPRseek crossmeta eQTL GenoGAM iCNV IrisSpatialFeatures methylPipe minfi MinimumDistance paxtoolsr RiboProfiling rTANDEM S4Vectors SISPA TitanCNA UniquornBest, Matt
I needed to update repo of Bioconductor from 3.7 to 3.8. Thanks to several Bioconductor maintainers for taking a look and letting me know.
After updating to Bioc 3.8 and rerunning, email to 26 Bioc maintainers on 8th Jan 2018 :
Dear maintainer of Bioconductor package,
Please could you fix the error or warning status in the log attached, or let me know how I can fix it locally. Your package uses data.table in some way. Since your package is already in error/warning status with the released version of data.table (1.11.8), it makes it much harder for me to test the impact each data.table update has.
There are no errors or warnings for the 598 packages on CRAN that use data.table :
CRAN: ERROR : 0 : WARNING : 0 : NOTE : 192 OK : 406 TOTAL : 598 / 598There are 26 Bioc packages that use data.table that have error or warning. I don't think these are related to data.table but these make it much harder to spot errors or warnings that data.table has caused when it is updated.
I'm using Bioc 3.8 and session info is at the top of the attached log.BIOC: ERROR : 2 : GENESIS ImmuneSpaceR WARNING : 24 : CEMiTool CONFESS crossmeta dada2 ELMER eQTL flowWorkspace GenoGAM GOTHiC iCNV MAST methylPipe MinimumDistance netSmooth OUTRIDER RiboProfiling rTANDEM S4Vectors SCnorm SISPA TENxBrainData TitanCNA Ularcirc Uniquorn NOTE : 102 OK : 24 TOTAL : 152 / 152Thanks, Matt
- added a commit that references this issue
on Jan 8, 2019 Testing 1.11.9 and looking for diff in status.
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rerun ok for 7 due to resource/internet issues: BiocParallel, MAGeCKFlute, SWATH2stats, GSALightning, RegParallel, TCGAbiolinksGUI, RCAS
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geneXtendeR -- true break caused by data.table in dev: fixed between recycle x too #3264
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checkmate 1.9.0 update today is broken by data.table 1.12.0
Caused by checking a bug isn't fixed but it is now: mllg/checkmate#155Final rerun for #3211 given #3273 (fread colClasses fixes).
- damr
Can't use NULL in colClasses when select or drop is used as well.due to fread colClasses= fixes #3273. Passes ok now with fix in data.table f0bd6e3 - prediction
WARNING Unknown package ‘mnlogit’ in Rd xrefsmnlogit removed from CRAN today "as check issues were not corrected despite reminder." so prediction will need to remove its xref to mnlogit accordingly. - segregation
Error: between + within = total (@test_mutual_total.R#53). New error on CRAN today too (here). I see the same locally. So not due to data.table update. Just coincidence there was a recent change to between() and the messages refer to between. - tosca
GitHub API rate limit exceeded - xlm
Error handling for bad public key.Also on CRAN (new error today) so not due to data.table update. - bsseq
Duplicates detected in dropPR fread drop when NULL in colClasses too #3277
- damr
- added a commit that references this issue
on Jan 12, 2019 GitHub API rate limit exceededmight be client side issue. I am recently getting this when using devtools install_github for dplyr in db-benchmark and I need to wait up to one hour. It seems that gh reduced limit of API calls when not using gh token auth.
Not bad: just 21 out of 586 CRAN revdeps to investigate. Most of the Bioconductor ones are usual suspects: they don't tend to fix warnings on Bioconductor and are usually unrelated to data.table. Still need to be investigated though.
fail.log