* using log directory 'd:/Rcompile/CRANpkg/local/4.6/nosoi.Rcheck'
* using R Under development (unstable) (2025-12-23 r89222 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'nosoi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'nosoi' version '1.1.2'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'nosoi' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s] OK
* checking whether the package can be loaded with stated dependencies ... [0s] OK
* checking whether the package can be unloaded cleanly ... [0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s] OK
* checking whether the namespace can be unloaded cleanly ... [1s] OK
* checking loading without being on the library search path ... [1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [6s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [1s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [38s] ERROR
  Running 'testthat.R' [38s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > if (requireNamespace("testthat", quietly = TRUE)) {
  + 
  +   library(testthat)
  +   library(nosoi)
  + 
  +   test_check("nosoi")
  + 
  + }
  Loading required package: data.table
  
  Attaching package: 'data.table'
  
  The following object is masked from 'package:base':
  
      %notin%
  
  Saving _problems/testTransmissionTree-47.R
  Saving _problems/testTransmissionTree-204.R
  Saving _problems/testTransmissionTree-370.R
  Saving _problems/testTransmissionTree-557.R
  Saving _problems/testTransmissionTree-738.R
  Saving _problems/testTransmissionTree-819.R
  Saving _problems/testTransmissionTree-973.R
  [ FAIL 7 | WARN 2 | SKIP 0 | PASS 477 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('testTransmissionTree.R:47:3'): Single, discrete ─────────────────────
  Error in ``[.data.table`(table.hosts, , `:=`("indNodes", .GRP), by = c("inf.by", "inf.time"))`: attempt access index 11/11 in VECTOR_ELT
  Backtrace:
      ▆
   1. └─nosoi::getTransmissionTree(test.nosoiA) at testTransmissionTree.R:47:3
   2.   ├─table.hosts[, `:=`("indNodes", .GRP), by = c("inf.by", "inf.time")]
   3.   └─data.table:::`[.data.table`(...)
  ── Error ('testTransmissionTree.R:204:3'): Single, continuous ──────────────────
  Error in ``[.data.table`(table.hosts, , `:=`("indNodes", .GRP), by = c("inf.by", "inf.time"))`: attempt access index 15/15 in VECTOR_ELT
  Backtrace:
      ▆
   1. └─nosoi::getTransmissionTree(test.nosoiA) at testTransmissionTree.R:204:3
   2.   ├─table.hosts[, `:=`("indNodes", .GRP), by = c("inf.by", "inf.time")]
   3.   └─data.table:::`[.data.table`(...)
  ── Error ('testTransmissionTree.R:370:3'): Dual, discrete ──────────────────────
  Error in ``[.data.table`(table.hosts, , `:=`("indNodes", .GRP), by = c("inf.by", "inf.time"))`: attempt access index 12/12 in VECTOR_ELT
  Backtrace:
      ▆
   1. └─nosoi::getTransmissionTree(test.nosoiA) at testTransmissionTree.R:370:3
   2.   ├─table.hosts[, `:=`("indNodes", .GRP), by = c("inf.by", "inf.time")]
   3.   └─data.table:::`[.data.table`(...)
  ── Error ('testTransmissionTree.R:557:3'): Dual, continuous ────────────────────
  Error in ``[.data.table`(table.hosts, , `:=`("indNodes", .GRP), by = c("inf.by", "inf.time"))`: attempt access index 16/16 in VECTOR_ELT
  Backtrace:
      ▆
   1. └─nosoi::getTransmissionTree(test.nosoiA) at testTransmissionTree.R:557:3
   2.   ├─table.hosts[, `:=`("indNodes", .GRP), by = c("inf.by", "inf.time")]
   3.   └─data.table:::`[.data.table`(...)
  ── Error ('testTransmissionTree.R:738:3'): Single, discrete, Sink ──────────────
  Error in ``[.data.table`(table.hosts, , `:=`("indNodes", .GRP), by = c("inf.by", "inf.time"))`: attempt access index 12/12 in VECTOR_ELT
  Backtrace:
      ▆
   1. └─nosoi::getTransmissionTree(SimulationSingle) at testTransmissionTree.R:738:3
   2.   ├─table.hosts[, `:=`("indNodes", .GRP), by = c("inf.by", "inf.time")]
   3.   └─data.table:::`[.data.table`(...)
  ── Error ('testTransmissionTree.R:819:3'): Single, none ────────────────────────
  Error in ``[.data.table`(table.hosts, , `:=`("indNodes", .GRP), by = c("inf.by", "inf.time"))`: attempt access index 8/8 in VECTOR_ELT
  Backtrace:
      ▆
   1. └─nosoi::getTransmissionTree(SimulationSingle) at testTransmissionTree.R:819:3
   2.   ├─table.hosts[, `:=`("indNodes", .GRP), by = c("inf.by", "inf.time")]
   3.   └─data.table:::`[.data.table`(...)
  ── Error ('testTransmissionTree.R:973:3'): Dual, none ──────────────────────────
  Error in ``[.data.table`(table.hosts, , `:=`("indNodes", .GRP), by = c("inf.by", "inf.time"))`: attempt access index 9/9 in VECTOR_ELT
  Backtrace:
      ▆
   1. └─nosoi::getTransmissionTree(SimulationDual) at testTransmissionTree.R:973:3
   2.   ├─table.hosts[, `:=`("indNodes", .GRP), by = c("inf.by", "inf.time")]
   3.   └─data.table:::`[.data.table`(...)
  
  [ FAIL 7 | WARN 2 | SKIP 0 | PASS 477 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [49s] ERROR
Error(s) in re-building vignettes:
--- re-building 'continuous.Rmd' using rmarkdown
--- finished re-building 'continuous.Rmd'

--- re-building 'discrete.Rmd' using rmarkdown
--- finished re-building 'discrete.Rmd'

--- re-building 'none.Rmd' using rmarkdown
--- finished re-building 'none.Rmd'

--- re-building 'nosoi.Rmd' using rmarkdown
--- finished re-building 'nosoi.Rmd'

--- re-building 'output.Rmd' using rmarkdown

Quitting from output.Rmd:400-421 [treeA_actual]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 11/11 in VECTOR_ELT
---
Backtrace:
    ▆
 1. └─nosoi::getTransmissionTree(test.nosoiA)
 2.   ├─table.hosts[, `:=`("indNodes", .GRP), by = c("inf.by", "inf.time")]
 3.   └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'output.Rmd' failed with diagnostics:
attempt access index 11/11 in VECTOR_ELT
--- failed re-building 'output.Rmd'

SUMMARY: processing the following file failed:
  'output.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [22s] OK
* checking HTML version of manual ... [14s] OK
* DONE
Status: 2 ERRORs