statnet / networkDynamic

Dynamic Extensions for Network Objects
10 stars 1 forks source link

CRAN takedown warning: CRAN packages with 'length > 1 in coercion to logical' reports #12

Closed skyebend closed 2 years ago

skyebend commented 2 years ago

That is

Data2LD EHR FastKM ForeCA LearnPCA MLVSBM MRPC PRSim PTXQC RAT RFCCA RevGadgets bayestestR bucky causalCmprsk cdcatR cheatR countytimezones dmacs drtmle easySdcTable eixport epiR expstudy ffbase gdalUtils ggvoronoi hesim idm iheiddown isotracer mstDIF networkDynamic neurobase nmaINLA onlineforecast ordinalNet pROC peacesciencer penalizedclr psychotools randnet rapportools scDIFtest semTools tableone tiledb traineR vortexR

(and some others reported separately). NEWS for R-devel has

 • Calling && or || with either argument of length greater than one
   now gives a warning (which it is intended will become an error).

and checks with this made into a fatal error can be seen at

https://www.stats.ox.ac.uk/pub/bdr/LENGTH1/

with reproduction instructions in the 00README.txt file. (As this was made a fatal error, only the first error will be shown so please do run those instructions before re-submission.)

The problems are occurring in a different package and there is a table of which in that 00README.txt, In some cases this is from misuse but you may need to contact the maintainer of the other package -- packages

kableExtra pracma tidygraph

have already been contacted but ignored us.

Please correct before 2022-04-04 to safely retain your package on CRAN.

skyebend commented 2 years ago

I think this might be some logic in the test: https://www.stats.ox.ac.uk/pub/bdr/LENGTH1/networkDynamic.out

> # a network with a point-activated edge
  > cnet7 <- network.initialize(2)
  > cnet7[1,2]<-1
  > activate.edges(cnet7,at=1)
  > check7<-network.dynamic.check(cnet7)
  > c7 <- (check7$vertex.checks==c(T,T) &&
  +        check7$edge.checks==T &&
  +        check7$dyad.checks==T)
   ----------- FAILURE REPORT -------------- 
   --- failure: length > 1 in coercion to logical ---
   --- srcref --- 
  : 
   --- package (from environment) --- 
  testthat
   --- call from context --- 
  NULL
   --- call from argument --- 
  check7$vertex.checks == c(T, T) && check7$edge.checks == T
   --- R stacktrace ---

   --- value of length: 2 type: logical ---
  [1] TRUE TRUE
   --- function from context --- 
   --- function search by body ---
   ----------- END OF FAILURE REPORT -------------- 
  Fatal error: length > 1 in coercion to logical
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [18s/45s] OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-LENGTH1/networkDynamic.Rcheck/00check.log’
for details.
gvegayon commented 2 years ago

This problem affects netdiffuseR as well. I think it suffices with using all() around the vector checks, or better,

with(check7, all(c(vertex.checks, edge.checks, dyad.checks)))
skyebend commented 2 years ago

Working on this today:

Dear maintainers,

This concerns the CRAN packages

EpiModel ITNr PAFit ndtv netdiffuseR networkDynamic networkDynamicData statnet tergm tergmLite tsna

maintained by one of you:

George Vega Yon g.vegayon@gmail.com: netdiffuseR Martina Morris morrism@uw.edu: statnet Matthew Smith matt_smith.90@hotmail.co.uk: ITNr Pavel N. Krivitsky pavel+tergm@unsw.edu.au: tergm Samuel Jenness samuel.m.jenness@emory.edu: EpiModel Samuel M. Jenness samuel.m.jenness@emory.edu: tergmLite Skye Bender-deMoll skyebend@uw.edu: networkDynamic ndtv networkDynamicData tsna Thong Pham thongphamthe@gmail.com: PAFit

We have asked for an update fixing the check problems shown at one of https://www.stats.ox.ac.uk/pub/bdr/LENGTH1_self/networkDynamic.out https://www.stats.ox.ac.uk/pub/bdr/LENGTH1/networkDynamic.out with no update from the maintainer thus far.

Thus, package 'networkDynamic' is now scheduled for archival on 2022-04-18, and archiving this will necessitate also archiving its CRAN strong reverse dependencies.

Please negotiate the necessary actions.

skyebend commented 2 years ago

Note: error only reproduced when running Sys.setenv(_R_CHECK_LENGTH_1_LOGIC2_="true")`

skyebend commented 2 years ago

pushed fixed version to CRAN, awaiting revdep checks etc

skyebend commented 2 years ago

v0.1.11 on cran!