Last updated on 2025-12-28 03:52:14 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| NMcalc | 13 | ||
| NMdata | 1 | 12 | |
| NMsim | 1 | 3 | 9 |
| tracee | 13 |
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, OK: 12
Version: 0.2.2
Check: examples
Result: ERROR
Running examples in 'NMdata-Ex.R' failed
The error most likely occurred in:
> ### Name: NMreadParsText
> ### Title: Read comments to parameter definitions in Nonmem control streams
> ### Aliases: NMreadParsText
>
> ### ** Examples
>
>
> ## setDTthreads() is only needed for CRAN. Users should not do this.
> data.table::setDTthreads(1)
> ## end setDTthreads() for CRAN
>
> ## notice, examples on explicitly stated lines. Most often in
> ## practice, one would use the file argument to automatically
> ## extract the $THETA, $OMEGA and $SIGMA sections from a control
> ## stream.
>
> text <- c("
+
+ $THETA (.1) ;[1]; LTVKA (mL/h)
+ $OMEGA BLOCK(3)
+ 0.126303 ; IIV.CL ; 1 ;IIV ;Between-subject variability on CL;-
+ 0.024 ; IIV.CL.V2.cov ; 1-2 ;IIV ;Covariance of BSV on CL and V2;-
+ 0.127 ; IIV.V2 ; 2 ;IIV ;Between-subject variability on V2;-
+ 0.2 ; IIV.CL.V3.cov ; 1-3 ;IIV ;Covariance of BSV on CL and V3;-
+ 0.2 ; IIV.V2.V3.cov ; 2-3 ;IIV ;Covariance of BSV on V2 and V3;-
+ 0.38 ; IIV.V3 ; 3 ;IIV ;Between-subject variability on V3;-
+ $OMEGA 0 FIX ; IIV.KA ; 4 ;IIV ;Between-subject variability on KA;-
+ $SIGMA 1
+ ")
> lines <- strsplit(text,split="\n")[[1]]
>
> res <- NMreadParsText(lines=lines,
+ format="%init;[%num];%symbol",
+ format.omega="%init; %symbol ; %num ; %type ; %label ; %unit",
+ field.idx="num")
Error in `[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != :
attempt access index 17/17 in VECTOR_ELT
Calls: NMreadParsText ... NMreadInits -> initsToExt -> addSameBlocks -> [ -> [.data.table
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.2.2
Check: tests
Result: ERROR
Running 'spelling.R' [0s]
Running 'testthat.R' [30s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(NMdata)
NMdata 0.2.2. Browse NMdata documentation at
https://NMautoverse.github.io/NMdata/
>
> test_check("NMdata")
Saving _problems/test_NMcheckData-41.R
Saving _problems/test_NMcheckData-52.R
Saving _problems/test_NMcheckData-65.R
Saving _problems/test_NMcheckData-79.R
Saving _problems/test_NMcheckData-96.R
Saving _problems/test_NMcheckData-107.R
Saving _problems/test_NMcheckData-127.R
Saving _problems/test_NMcheckData-139.R
Saving _problems/test_NMcheckData-150.R
Saving _problems/test_NMcheckData-172.R
Saving _problems/test_NMcheckData-189.R
Saving _problems/test_NMcheckData-210.R
Saving _problems/test_NMcheckData-227.R
Saving _problems/test_NMcheckData-241.R
Saving _problems/test_NMcheckData-255.R
Saving _problems/test_NMcheckData-273.R
Saving _problems/test_NMcheckData-292.R
Saving _problems/test_NMcheckData-301.R
Saving _problems/test_NMcheckData-322.R
Saving _problems/test_NMcheckData-338.R
Saving _problems/test_NMcheckData-366.R
Saving _problems/test_NMcheckData-378.R
Saving _problems/test_NMcheckDataFile-47.R
Saving _problems/test_NMdata_utils-15.R
Saving _problems/test_NMgenText-7.R
Saving _problems/test_NMgenText-14.R
Saving _problems/test_NMgenText-21.R
Saving _problems/test_NMgenText-34.R
Saving _problems/test_NMgenText-42.R
Saving _problems/test_NMgenText-49.R
Saving _problems/test_NMgenText-56.R
Saving _problems/test_NMgenText-62.R
Saving _problems/test_NMinfo-6.R
Saving _problems/test_NMreadExt-11.R
Saving _problems/test_NMreadExt-28.R
Saving _problems/test_NMreadExt-47.R
Saving _problems/test_NMreadExt-67.R
Saving _problems/test_NMreadExt-87.R
Saving _problems/test_NMreadExt-115.R
Saving _problems/test_NMreadExt-133.R
Saving _problems/test_NMreadInits-20.R
Saving _problems/test_NMreadInits-58.R
Saving _problems/test_NMreadInits-102.R
Saving _problems/test_NMreadInits-156.R
Saving _problems/test_NMreadInits-191.R
Saving _problems/test_NMreadParText-40.R
Saving _problems/test_NMreadParText-63.R
Saving _problems/test_NMreadParText-107.R
Saving _problems/test_NMreadParText-137.R
Saving _problems/test_NMreadParText-175.R
Saving _problems/test_NMreadParText-205.R
Saving _problems/test_NMreadPhi-8.R
Saving _problems/test_NMreadPhi-18.R
Saving _problems/test_NMreadTab-10.R
Saving _problems/test_NMreadTab-73.R
Saving _problems/test_NMrelate-16.R
Saving _problems/test_NMrelate-27.R
Saving _problems/test_NMrelate-44.R
Saving _problems/test_NMrelate-102.R
Saving _problems/test_NMrelate-130.R
Saving _problems/test_NMscanData-48.R
Saving _problems/test_NMscanData-86.R
Saving _problems/test_NMscanData-114.R
Saving _problems/test_NMscanData-139.R
Saving _problems/test_NMscanData-163.R
Saving _problems/test_NMscanData-184.R
Saving _problems/test_NMscanData-252.R
Saving _problems/test_NMscanData-302.R
Saving _problems/test_NMscanData-335.R
Saving _problems/test_NMscanData-391.R
Saving _problems/test_NMscanData-414.R
Saving _problems/test_NMscanData-435.R
Saving _problems/test_NMscanData-477.R
Saving _problems/test_NMscanData-522.R
Saving _problems/test_NMscanData-547.R
Saving _problems/test_NMscanData-605.R
Saving _problems/test_NMscanData-621.R
Saving _problems/test_NMscanData-679.R
Saving _problems/test_NMscanData-698.R
Saving _problems/test_NMscanData-731.R
Saving _problems/test_NMscanData-765.R
Saving _problems/test_NMscanData-791.R
Saving _problems/test_NMscanData-822.R
Saving _problems/test_NMscanData-885.R
Saving _problems/test_NMscanData-919.R
Saving _problems/test_NMscanData-932.R
Saving _problems/test_NMscanData-958.R
Saving _problems/test_NMscanData-982.R
Saving _problems/test_NMscanData-1002.R
Saving _problems/test_NMscanData-1048.R
Saving _problems/test_NMscanData-1075.R
Saving _problems/test_NMscanData-1092.R
Saving _problems/test_NMscanData-1118.R
Saving _problems/test_NMscanMultiple-43.R
Saving _problems/test_NMscanTables-23.R
Saving _problems/test_NMscanTables-57.R
Saving _problems/test_NMscanTables-75.R
Saving _problems/test_NMscanTables-92.R
Saving _problems/test_NMscanTables-110.R
Saving _problems/test_NMscanTables-138.R
Saving _problems/test_NMscanTables-155.R
Error in `[.data.table`(dt.num.ok, include == TRUE, `:=`(occ.cum, 1:.N), :
attempt access index 5/5 in VECTOR_ELT
Saving _problems/test_NMwriteData-23.R
Error in (function (data, drop, col.flagn, rename, copy, file, dir.data, :
drop cannot contain empty strings and NA's.
Error in `[.data.table`(dt.num.ok, include == TRUE, `:=`(occ.cum, 1:.N), :
attempt access index 5/5 in VECTOR_ELT
Saving _problems/test_NMwriteData-57.R
Error in `[.data.table`(dt.num.ok, include == TRUE, `:=`(occ.cum, 1:.N), :
attempt access index 5/5 in VECTOR_ELT
Error in `[.data.table`(dt.num.ok, include == TRUE, `:=`(occ.cum, 1:.N), :
attempt access index 7/7 in VECTOR_ELT
Saving _problems/test_NMwriteData-124.R
Error in `[.data.table`(dt.num.ok, include == TRUE, `:=`(occ.cum, 1:.N), :
attempt access index 5/5 in VECTOR_ELT
Saving _problems/test_NMwriteData-142.R
Error in `[.data.table`(dt.num.ok, include == TRUE, `:=`(occ.cum, 1:.N), :
attempt access index 5/5 in VECTOR_ELT
Saving _problems/test_NMwriteData-163.R
Error in `[.data.table`(dt.num.ok, include == TRUE, `:=`(occ.cum, 1:.N), :
attempt access index 5/5 in VECTOR_ELT
Saving _problems/test_NMwriteData-186.R
Error in `[.data.table`(dt.num.ok, include == TRUE, `:=`(occ.cum, 1:.N), :
attempt access index 5/5 in VECTOR_ELT
Saving _problems/test_NMwriteData-206.R
Error in `[.data.table`(dt.num.ok, include == TRUE, `:=`(occ.cum, 1:.N), :
attempt access index 5/5 in VECTOR_ELT
Saving _problems/test_NMwriteData-239.R
Error in `[.data.table`(dt.num.ok, include == TRUE, `:=`(occ.cum, 1:.N), :
attempt access index 5/5 in VECTOR_ELT
Saving _problems/test_NMwriteData-262.R
Error in `[.data.table`(dt.num.ok, include == TRUE, `:=`(occ.cum, 1:.N), :
attempt access index 5/5 in VECTOR_ELT
Saving _problems/test_NMwriteData-297.R
Error in `[.data.table`(dt.num.ok, include == TRUE, `:=`(occ.cum, 1:.N), :
attempt access index 5/5 in VECTOR_ELT
Saving _problems/test_NMwriteData-339.R
Saving _problems/test_NMwriteSection-164.R
Saving _problems/test_addCor-9.R
Saving _problems/test_addTAPD-8.R
Saving _problems/test_addTAPD-21.R
Saving _problems/test_addTAPD-32.R
Saving _problems/test_addTAPD-46.R
Saving _problems/test_addTAPD-80.R
Saving _problems/test_addTAPD-96.R
Saving _problems/test_dt2mat-7.R
Saving _problems/test_flags-168.R
Saving _problems/test_print_summary_NMdata-9.R
[ FAIL 123 | WARN 150 | SKIP 1 | PASS 200 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1):
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_NMcheckData.R:41:5'): basic ────────────────────────────────────
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 28/28 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMcheckData(pk, quiet = quiet) at test_NMcheckData.R:41:5
2. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcheckData.R:52:5'): No col.flagn ─────────────────────────────
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 28/28 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMcheckData(pk, col.flagn = FALSE, quiet = quiet) at test_NMcheckData.R:52:5
2. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcheckData.R:65:5'): Misc findings ────────────────────────────
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 28/28 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMcheckData(pk, quiet = quiet) at test_NMcheckData.R:65:5
2. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcheckData.R:79:5'): TIME with characters ─────────────────────
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 28/28 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMcheckData(pk, quiet = quiet) at test_NMcheckData.R:79:5
2. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcheckData.R:96:5'): Misc findings and dup colname ────────────
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 28/28 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(NMcheckData(pk, quiet = quiet)) at test_NMcheckData.R:96:5
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─NMdata::NMcheckData(pk, quiet = quiet)
7. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
8. └─data.table:::`[.data.table`(...)
── Error ('test_NMcheckData.R:107:5'): missing EVID ────────────────────────────
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 27/27 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMcheckData(pk, quiet = quiet) at test_NMcheckData.R:107:5
2. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcheckData.R:127:5'): missing MDV ─────────────────────────────
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 30/30 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMcheckData(pk, quiet = quiet) at test_NMcheckData.R:127:5
2. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcheckData.R:139:5'): With ADDL, no II ────────────────────────
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 29/29 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMcheckData(pk, quiet = quiet) at test_NMcheckData.R:139:5
2. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcheckData.R:150:5'): With II, no ADDL ────────────────────────
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 29/29 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMcheckData(pk, quiet = quiet) at test_NMcheckData.R:150:5
2. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcheckData.R:172:5'): ID and row with leading 0 ───────────────
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 28/28 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMcheckData(pk, quiet = quiet) at test_NMcheckData.R:172:5
2. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcheckData.R:189:5'): One covariate varying within ID ─────────
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 28/28 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMcheckData(...) at test_NMcheckData.R:189:5
2. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcheckData.R:210:5'): with IOV ────────────────────────────────
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 30/30 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMcheckData(...) at test_NMcheckData.R:210:5
2. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcheckData.R:227:5'): covariates within subsets ───────────────
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 31/31 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMcheckData(...) at test_NMcheckData.R:227:5
2. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcheckData.R:241:5'): numerical coded as char and NA as . ─────
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 28/28 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMcheckData(pk, na.strings = NULL, quiet = quiet) at test_NMcheckData.R:241:5
2. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcheckData.R:255:5'): usubjid OK ──────────────────────────────
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 29/29 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMcheckData(pk, col.usubjid = "usubjid", quiet = quiet) at test_NMcheckData.R:255:5
2. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcheckData.R:273:5'): ID not unique ───────────────────────────
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 29/29 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMcheckData(pk, col.usubjid = "usubjid", quiet = quiet) at test_NMcheckData.R:273:5
2. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcheckData.R:292:5'): usubjid not unique ──────────────────────
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 29/29 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMcheckData(pk, col.usubjid = "usubjid", quiet = quiet) at test_NMcheckData.R:292:5
2. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcheckData.R:301:5'): no col.flagn ────────────────────────────
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 28/28 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMcheckData(pk, quiet = quiet) at test_NMcheckData.R:301:5
2. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcheckData.R:322:5'): check data files without cols.dup, but passed with it ──
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 14/14 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMcheckData(dups_data, quiet = quiet) at test_NMcheckData.R:322:5
2. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcheckData.R:338:5'): simulation data ─────────────────────────
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMcheckData(dt.all, quiet = quiet, type.data = "sim") at test_NMcheckData.R:338:5
2. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcheckData.R:366:5'): disable column ──────────────────────────
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 27/27 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMcheckData(pk, quiet = quiet, cols.disable = "CMT") at test_NMcheckData.R:366:5
2. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcheckData.R:378:5'): ID-level ────────────────────────────────
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 28/28 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMcheckData(pk3, quiet = quiet) at test_NMcheckData.R:378:5
2. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcheckDataFile.R:47:5'): Using control stream file ────────────
Error in ``[.data.table`(data, , `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id)`: attempt access index 22/22 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMcheckData(file = file.lst, quiet = TRUE) at test_NMcheckDataFile.R:47:5
2. └─NMdata:::NMcheckDataFile(...)
3. └─NMdata::NMcheckData(...)
4. ├─data[, `:=`(ID.jump, c(0, diff(get(rowint)))), by = col.id]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMdata_utils.R:15:5'): basic ───────────────────────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMdata_utils.R:15:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMgenText.R:7:5'): basic ───────────────────────────────────────
Error in ``[.data.table`(dt.num.ok, include == TRUE, `:=`(occ.cum, 1:.N), by = name.nm)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMgenText(pk, width = 95) at test_NMgenText.R:7:5
2. ├─dt.num.ok[include == TRUE, `:=`(occ.cum, 1:.N), by = name.nm]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMgenText.R:14:5'): df vs dt ───────────────────────────────────
Error in ``[.data.table`(dt.num.ok, include == TRUE, `:=`(occ.cum, 1:.N), by = name.nm)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(NMgenText(pk), NMgenText(pk.df)) at test_NMgenText.R:14:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─NMdata::NMgenText(pk)
5. ├─dt.num.ok[include == TRUE, `:=`(occ.cum, 1:.N), by = name.nm]
6. └─data.table:::`[.data.table`(...)
── Error ('test_NMgenText.R:21:5'): dir.data ───────────────────────────────────
Error in ``[.data.table`(dt.num.ok, include == TRUE, `:=`(occ.cum, 1:.N), by = name.nm)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMgenText(pk, file = "data1.csv") at test_NMgenText.R:21:5
2. ├─dt.num.ok[include == TRUE, `:=`(occ.cum, 1:.N), by = name.nm]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMgenText.R:34:5'): pseudonyms ─────────────────────────────────
Error in ``[.data.table`(dt.num.ok, include == TRUE, `:=`(occ.cum, 1:.N), by = name.nm)`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMgenText(...) at test_NMgenText.R:34:5
2. ├─dt.num.ok[include == TRUE, `:=`(occ.cum, 1:.N), by = name.nm]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMgenText.R:42:5'): rename - same order as in pseudonym syntax ──
Error in ``[.data.table`(dt.num.ok, include == TRUE, `:=`(occ.cum, 1:.N), by = name.nm)`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMgenText(...) at test_NMgenText.R:42:5
2. ├─dt.num.ok[include == TRUE, `:=`(occ.cum, 1:.N), by = name.nm]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMgenText.R:49:5'): drop ───────────────────────────────────────
Error in ``[.data.table`(dt.num.ok, include == TRUE, `:=`(occ.cum, 1:.N), by = name.nm)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMgenText(pk, file = "data1.csv", drop = c("PART"), width = 95) at test_NMgenText.R:49:5
2. ├─dt.num.ok[include == TRUE, `:=`(occ.cum, 1:.N), by = name.nm]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMgenText.R:56:5'): capitalize ─────────────────────────────────
Error in ``[.data.table`(dt.num.ok, include == TRUE, `:=`(occ.cum, 1:.N), by = name.nm)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMgenText(pk, file = "data1.csv", capitalize = T, width = 95) at test_NMgenText.R:56:5
2. ├─dt.num.ok[include == TRUE, `:=`(occ.cum, 1:.N), by = name.nm]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMgenText.R:62:5'): basic - from file ──────────────────────────
Error in ``[.data.table`(dt.num.ok, include == TRUE, `:=`(occ.cum, 1:.N), by = name.nm)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMgenText(pk) at test_NMgenText.R:62:5
2. ├─dt.num.ok[include == TRUE, `:=`(occ.cum, 1:.N), by = name.nm]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMinfo.R:6:5'): basic ──────────────────────────────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMinfo.R:6:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadExt.R:11:5'): basic - pars ───────────────────────────────
Error in ``[.data.table`(pars, get(col.par.type) %in% allpars.mat, `:=`(j, as.integer(sub(pattern = sprintf("%s\\(([0-9]+)\\,([0-9]+)\\)", get(col.par.type)), replacement = "\\2", x = get(col.parameter)))), by = row)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadExt(file = file.ext, as.fun = "data.table") at test_NMreadExt.R:11:5
2. └─NMdata:::addParType(pars)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadExt.R:28:5'): basic - all ────────────────────────────────
Error in ``[.data.table`(pars, get(col.par.type) %in% allpars.mat, `:=`(j, as.integer(sub(pattern = sprintf("%s\\(([0-9]+)\\,([0-9]+)\\)", get(col.par.type)), replacement = "\\2", x = get(col.parameter)))), by = row)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadExt(file = file.ext, as.fun = "data.table", return = "all") at test_NMreadExt.R:28:5
2. └─NMdata:::addParType(pars)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadExt.R:47:5'): basic - all from multiple models ───────────
Error in ``[.data.table`(pars, get(col.par.type) %in% allpars.mat, `:=`(j, as.integer(sub(pattern = sprintf("%s\\(([0-9]+)\\,([0-9]+)\\)", get(col.par.type)), replacement = "\\2", x = get(col.parameter)))), by = row)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadExt(file = file.ext, as.fun = "data.table", return = "all") at test_NMreadExt.R:47:5
2. └─NMdata:::addParType(pars)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadExt.R:67:5'): muref - all ────────────────────────────────
Error in ``[.data.table`(pars, get(col.par.type) %in% allpars.mat, `:=`(j, as.integer(sub(pattern = sprintf("%s\\(([0-9]+)\\,([0-9]+)\\)", get(col.par.type)), replacement = "\\2", x = get(col.parameter)))), by = row)`: attempt access index 14/14 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadExt(file = file.ext, as.fun = "data.table", return = "all") at test_NMreadExt.R:67:5
2. └─NMdata:::addParType(pars)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadExt.R:87:5'): muref SAEM - all ───────────────────────────
Error in ``[.data.table`(pars, get(col.par.type) %in% allpars.mat, `:=`(j, as.integer(sub(pattern = sprintf("%s\\(([0-9]+)\\,([0-9]+)\\)", get(col.par.type)), replacement = "\\2", x = get(col.parameter)))), by = row)`: attempt access index 16/16 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadExt(file = file.ext, as.fun = "data.table", return = "all") at test_NMreadExt.R:87:5
2. └─NMdata:::addParType(pars)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadExt.R:110:5'): muref SAEM - tableno options ──────────────
Error in ``[.data.table`(pars, get(col.par.type) %in% allpars.mat, `:=`(j, as.integer(sub(pattern = sprintf("%s\\(([0-9]+)\\,([0-9]+)\\)", get(col.par.type)), replacement = "\\2", x = get(col.parameter)))), by = row)`: attempt access index 16/16 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadExt(file.ext, tableno = 1, return = "obj") at test_NMreadExt.R:110:5
2. └─NMdata:::addParType(pars)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadExt.R:133:5'): slow ──────────────────────────────────────
Error in ``[.data.table`(pars, get(col.par.type) %in% allpars.mat, `:=`(j, as.integer(sub(pattern = sprintf("%s\\(([0-9]+)\\,([0-9]+)\\)", get(col.par.type)), replacement = "\\2", x = get(col.parameter)))), by = row)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadExt(file = file.ext, as.fun = "data.table") at test_NMreadExt.R:133:5
2. └─NMdata:::addParType(pars)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadInits.R:20:5'): basic ────────────────────────────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadInits(lines = lines, return = "all") at test_NMreadInits.R:20:5
2. └─NMdata:::initsToExt(res)
3. └─NMdata:::addSameBlocks(pars)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadInits.R:58:5'): with OMEGA block ─────────────────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadInits(file = file.mod, return = "all") at test_NMreadInits.R:58:5
2. └─NMdata:::initsToExt(res)
3. └─NMdata:::addSameBlocks(pars)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadInits.R:102:5'): OMEGA SAME ──────────────────────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadInits(lines = text, return = "all") at test_NMreadInits.R:102:5
2. └─NMdata:::initsToExt(res)
3. └─NMdata:::addSameBlocks(pars)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadInits.R:156:5'): OMEGA BLOCK FIX 1 ───────────────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadInits(lines = text1, return = "all", as.fun = "data.table") at test_NMreadInits.R:156:5
2. └─NMdata:::initsToExt(res)
3. └─NMdata:::addSameBlocks(pars)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadInits.R:191:5'): BLOCK(2) SAME ───────────────────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadInits(lines = text, return = "all") at test_NMreadInits.R:191:5
2. └─NMdata:::initsToExt(res)
3. └─NMdata:::addSameBlocks(pars)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadParText.R:40:5'): muref SAEM ─────────────────────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadParsText(file.mod, format = "%init;%symbol") at test_NMreadParText.R:40:5
2. └─NMdata::NMreadInits(...)
3. └─NMdata:::initsToExt(res)
4. └─NMdata:::addSameBlocks(pars)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadParText.R:63:5'): merge with NMreadExt output ────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadParsText(file.mod, format = "%init;%symbol") at test_NMreadParText.R:63:5
2. └─NMdata::NMreadInits(...)
3. └─NMdata:::initsToExt(res)
4. └─NMdata:::addSameBlocks(pars)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadParText.R:107:5'): complex delimiters ────────────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadParsText(lines = lines, format = "%init;[%num2];%symbol") at test_NMreadParText.R:107:5
2. └─NMdata::NMreadInits(...)
3. └─NMdata:::initsToExt(res)
4. └─NMdata:::addSameBlocks(pars)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadParText.R:137:5'): No SIGMA ──────────────────────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadParsText(lines = lines, format = "%init;[%num2];%symbol") at test_NMreadParText.R:137:5
2. └─NMdata::NMreadInits(...)
3. └─NMdata:::initsToExt(res)
4. └─NMdata:::addSameBlocks(pars)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadParText.R:172:5'): Complex OMEGA ─────────────────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadParsText(...) at test_NMreadParText.R:172:5
2. └─NMdata::NMreadInits(...)
3. └─NMdata:::initsToExt(res)
4. └─NMdata:::addSameBlocks(pars)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadParText.R:202:1'): (code run outside of `test_that()`) ───
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadParsText(...) at test_NMreadParText.R:202:1
2. └─NMdata::NMreadInits(...)
3. └─NMdata:::initsToExt(res)
4. └─NMdata:::addSameBlocks(pars)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadPhi.R:8:5'): basic ───────────────────────────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 24/24 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadPhi(file = file.phi, as.fun = "data.table") at test_NMreadPhi.R:8:5
2. └─base::lapply(...)
3. └─NMdata (local) FUN(X[[i]], ...)
4. └─NMdata::NMreadTab(...)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadPhi.R:18:5'): basic - all from multiple models ───────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 24/24 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadPhi(file = file.phi, as.fun = "data.table") at test_NMreadPhi.R:18:5
2. └─base::lapply(...)
3. └─NMdata (local) FUN(X[[i]], ...)
4. └─NMdata::NMreadTab(...)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadTab.R:10:5'): Table with repetitions ─────────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 14/14 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadTab("testData/simulations/xgxr014_testsim1/xgxr014_testsim1.tab") at test_NMreadTab.R:10:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadTab.R:73:5'): table without table title ──────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadTab(file.tab) at test_NMreadTab.R:73:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMrelate.R:10:5'): basic ───────────────────────────────────────
Error in ``[.data.table`(dt.code, var.type %in% cc(ETA, THETA, ERR, EPS), `:=`(i, as.numeric(sub(paste0(".*", var.type, "\\(([1-9][0-9]*)\\)"), "\\1", x = var.name, ignore.case = TRUE))), by = lineno)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata:::NMrelateOne(file = file.mod, par.type = "eta") at test_NMrelate.R:10:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMrelate.R:27:5'): Find all ────────────────────────────────────
Error in ``[.data.table`(dt.code, var.type %in% cc(ETA, THETA, ERR, EPS), `:=`(i, as.numeric(sub(paste0(".*", var.type, "\\(([1-9][0-9]*)\\)"), "\\1", x = var.name, ignore.case = TRUE))), by = lineno)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─NMdata::NMrelate(file = file.mod) at test_NMrelate.R:27:5
2. │ └─base::lapply(...)
3. │ └─NMdata (local) FUN(X[[i]], ...)
4. │ ├─...[]
5. │ └─data.table:::`[.data.table`(...)
6. └─NMdata:::NMrelateOne(lines = text, par.type = tp, as.fun = "data.table")
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test_NMrelate.R:44:5'): merge with NMreadExt results ────────────────
Error in ``[.data.table`(dt.code, var.type %in% cc(ETA, THETA, ERR, EPS), `:=`(i, as.numeric(sub(paste0(".*", var.type, "\\(([1-9][0-9]*)\\)"), "\\1", x = var.name, ignore.case = TRUE))), by = lineno)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─NMdata::NMrelate(file = file.mod) at test_NMrelate.R:44:5
2. │ └─base::lapply(...)
3. │ └─NMdata (local) FUN(X[[i]], ...)
4. │ ├─...[]
5. │ └─data.table:::`[.data.table`(...)
6. └─NMdata:::NMrelateOne(lines = text, par.type = tp, as.fun = "data.table")
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test_NMrelate.R:102:5'): 2 models ───────────────────────────────────
Error in ``[.data.table`(dt.code, var.type %in% cc(ETA, THETA, ERR, EPS), `:=`(i, as.numeric(sub(paste0(".*", var.type, "\\(([1-9][0-9]*)\\)"), "\\1", x = var.name, ignore.case = TRUE))), by = lineno)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─NMdata::NMrelate(file = file.mod[1]) at test_NMrelate.R:102:5
2. │ └─base::lapply(...)
3. │ └─NMdata (local) FUN(X[[i]], ...)
4. │ ├─...[]
5. │ └─data.table:::`[.data.table`(...)
6. └─NMdata:::NMrelateOne(lines = text, par.type = tp, as.fun = "data.table")
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test_NMrelate.R:130:5'): lowercase ──────────────────────────────────
Error in ``[.data.table`(dt.code, var.type %in% cc(ETA, THETA, ERR, EPS), `:=`(i, as.numeric(sub(paste0(".*", var.type, "\\(([1-9][0-9]*)\\)"), "\\1", x = var.name, ignore.case = TRUE))), by = lineno)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─NMdata::NMrelate(file.mod, as.fun = "data.table") at test_NMrelate.R:130:5
2. │ └─base::lapply(...)
3. │ └─NMdata (local) FUN(X[[i]], ...)
4. │ ├─...[]
5. │ └─data.table:::`[.data.table`(...)
6. └─NMdata:::NMrelateOne(lines = text, par.type = tp, as.fun = "data.table")
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:47:5'): basic ─────────────────────────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMscanData.R:47:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:86:5'): Modifications to column names in $INPUT ───
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMscanData.R:86:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:114:5'): No translation of column names in $INPUT ──
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMscanData.R:114:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:139:5'): Multiple output table formats ────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMscanData.R:139:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:163:5'): Interpret IGNORE statement ───────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMscanData.R:163:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:184:5'): List of ACCEPT statements and vs separate statements ──
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMscanData.R:184:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:249:5'): Only a firstonly without ID but with ROW ──
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test_NMscanData.R:249:5
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─NMdata::NMscanData(...)
7. └─NMdata::NMscanTables(...)
8. └─NMdata::NMreadTab(...)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:300:5'): FO and row-level output. No ID, no row. ──
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 7/7 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test_NMscanData.R:300:5
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─NMdata::NMscanData(file = file.lst, check.time = FALSE, quiet = T)
7. └─NMdata::NMscanTables(...)
8. └─NMdata::NMreadTab(...)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:333:5'): FO and row-level output. No ID, no row. cbind.by.filters=T ──
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 7/7 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test_NMscanData.R:333:5
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─NMdata::NMscanData(...)
7. └─NMdata::NMscanTables(...)
8. └─NMdata::NMreadTab(...)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:389:5'): Only a firstonly without ID but with ROW. Using merge.by.row=TRUE. ──
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test_NMscanData.R:389:5
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─NMdata::NMscanData(...)
7. └─NMdata::NMscanTables(...)
8. └─NMdata::NMreadTab(...)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:414:5'): recoverRows without a row identifier ─────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMscanData.R:414:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:435:5'): use as.fun to get a data.frame ───────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMscanData.R:435:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:477:5'): use as.fun to get a tibble ───────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMscanData.R:477:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:522:5'): dir structure with input.txt/output.txt ──
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMscanData.R:522:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:547:5'): input.txt/output.txt - unset modelname ───
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMscanData.R:547:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:605:5'): output.txt, file.mod=identity - NMinfo file.mod=output.txt? ──
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMscanData.R:605:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:619:5'): Duplicate columns in input data ──────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test_NMscanData.R:619:5
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─NMdata::NMscanData(...)
7. └─NMdata::NMscanTables(...)
8. └─NMdata::NMreadTab(...)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:679:5'): merge.by.row=ifAvailable when available ──
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMscanData.R:679:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:698:5'): merge.by.row=ifAvailable when not available ──
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMscanData.R:698:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:728:5'): col.row does not exist, but merge.by.row==TRUE ──
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test_NMscanData.R:728:5
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─NMdata::NMscanData(...)
7. └─NMdata::NMscanTables(...)
8. └─NMdata::NMreadTab(...)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:765:5'): A filter without operator ────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMscanData.R:765:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:791:5'): Including a redundant output table ───────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMscanData.R:791:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:820:5'): redundant output ─────────────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_message(NMscanData(file = file.lst, quiet = T)) at test_NMscanData.R:820:5
2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─NMdata::NMscanData(file = file.lst, quiet = T)
7. └─NMdata::NMscanTables(...)
8. └─NMdata::NMreadTab(...)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:885:5'): $INPUT copy ──────────────────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(file.lst.1, quiet = T) at test_NMscanData.R:885:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:919:5'): only firstonly. Has col.id, no col.row. ──
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(file.lst, quiet = TRUE) at test_NMscanData.R:919:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:932:5'): Two firstonly, one full-length ───────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(file = file.lst, check.time = F, quiet = T) at test_NMscanData.R:932:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:958:5'): Two firstonly, one full-length with col.nmrep ──
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMscanData.R:958:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:982:5'): Input data as character ──────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMscanData.R:982:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:1002:5'): Input control stream missing ────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(file = file.lst, use.input = F, quiet = T) at test_NMscanData.R:1002:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:1048:5'): simulation model with subproblems ───────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 14/14 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMscanData.R:1048:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:1075:5'): csv vs rds vs fst ───────────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMscanData.R:1075:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:1092:5'): inside lappy ────────────────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_NMscanData.R:1092:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanData.R:1118:5'): NMtran seems to treat NA as zero ────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_message(...) at test_NMscanData.R:1118:5
2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─NMdata::NMscanData("testData/nonmem/xgxr054.mod", merge.by.row = F)
7. └─NMdata::NMscanTables(...)
8. └─NMdata::NMreadTab(...)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanMultiple.R:43:5'): basic ─────────────────────────────────
Error in `NMscanMultiple(lsts, check.time = FALSE, quiet = TRUE)`: No models were succesfully read.
Backtrace:
▆
1. └─NMdata::NMscanMultiple(lsts, check.time = FALSE, quiet = TRUE) at test_NMscanMultiple.R:43:5
── Error ('test_NMscanTables.R:23:5'): Multiple output table formats ───────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanTables(...) at test_NMscanTables.R:23:5
2. └─NMdata::NMreadTab(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanTables.R:57:5'): Details table ───────────────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanTables(...) at test_NMscanTables.R:57:5
2. └─NMdata::NMreadTab(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanTables.R:75:5'): $TABLE header options ───────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanTables(...) at test_NMscanTables.R:75:5
2. └─NMdata::NMreadTab(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanTables.R:91:5'): Two firstonly, one full-length ──────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanTables(...) at test_NMscanTables.R:91:5
2. └─NMdata::NMreadTab(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanTables.R:110:5'): Commented output table ─────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 7/7 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanTables(file.lst) at test_NMscanTables.R:110:5
2. └─NMdata::NMreadTab(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanTables.R:138:5'): Table with repetitions ─────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanTables("testData/nonmem/xgxr014.lst") at test_NMscanTables.R:138:5
2. └─NMdata::NMreadTab(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_NMscanTables.R:155:5'): more tab formats ───────────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanTables("testData/nonmem/xgxr035.lst") at test_NMscanTables.R:155:5
2. └─NMdata::NMreadTab(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_NMwriteData.R:22:5'): basic ────────────────────────────────────
Error in `NMwriteData(pk, file = "testOutput/NMwriteData1.csv", formats = cc(csv), nmdir.data = "/example")`: NMgenText failed.
Backtrace:
▆
1. └─NMdata::NMwriteData(...) at test_NMwriteData.R:22:5
── Error ('test_NMwriteData.R:53:5'): Dropping a column in Nonmem ──────────────
Error in `NMwriteData(pk, file = "testOutput/NMwriteDataTmp.csv", save = FALSE, nm.drop = "PART", genText = TRUE, nmdir.data = "/example")`: NMgenText failed.
Backtrace:
▆
1. └─NMdata::NMwriteData(...) at test_NMwriteData.R:53:5
── Error ('test_NMwriteData.R:119:5'): nm.copy, nm.rename, drop ────────────────
Error in `NMwriteData(pk, file = "testOutput/NMwriteDataTmp.csv", write.csv = FALSE, genText = TRUE, args.NMgenText = list(dir.data = "../derived", drop = "PROFDAY", copy = c(CONC = "DV"), rename = c(BBW = "WEIGHTB"), capitalize = TRUE, width = 80), args.rds = list(version = 2))`: NMgenText failed.
Backtrace:
▆
1. └─NMdata::NMwriteData(...) at test_NMwriteData.R:119:5
── Error ('test_NMwriteData.R:134:5'): nm.copy, nm.rename, drop ────────────────
Error in `NMwriteData(pk, file = "testOutput/pk.csv", write.csv = TRUE, write.rds = TRUE, write.RData = TRUE, args.rds = list(version = 2), , args.RData = list(version = 2), args.NMgenText = list(width = 95))`: NMgenText failed.
Backtrace:
▆
1. └─NMdata::NMwriteData(...) at test_NMwriteData.R:134:5
── Error ('test_NMwriteData.R:160:5'): with stamp ──────────────────────────────
Error in `NMwriteData(pk, file = NULL, save = FALSE, genText = T, nmdir.data = "/example", script = "A simple test")`: NMgenText failed.
Backtrace:
▆
1. └─NMdata::NMwriteData(...) at test_NMwriteData.R:160:5
── Error ('test_NMwriteData.R:182:5'): with stamp on csv ───────────────────────
Error in `NMwriteData(pk, file = outfile, script = "A simple test", write.rds = TRUE, args.stamp = list(time = as.POSIXct("2021-11-21 11:00:00")), args.rds = list(version = 2))`: NMgenText failed.
Backtrace:
▆
1. └─NMdata::NMwriteData(...) at test_NMwriteData.R:182:5
── Error ('test_NMwriteData.R:203:5'): Quiet but get text for NM ───────────────
Error in `NMwriteData(pk, file = outfile, script = "A simple test", write.rds = FALSE, args.stamp = list(time = as.POSIXct("2021-11-21 11:00:00")), quiet = T)`: NMgenText failed.
Backtrace:
▆
1. └─NMdata::NMwriteData(...) at test_NMwriteData.R:203:5
── Error ('test_NMwriteData.R:238:5'): script=NULL ─────────────────────────────
Error in `NMwriteData(pk, file = "testOutput/NMwriteData10.csv", write.rds = T, write.csv = T, nmdir.data = "/example", script = NULL, args.rds = list(version = 2))`: NMgenText failed.
Backtrace:
▆
1. └─NMdata::NMwriteData(...) at test_NMwriteData.R:238:5
── Error ('test_NMwriteData.R:260:5'): csv.trunc.as.nm ─────────────────────────
Error in `NMtext$INPUT`: $ operator is invalid for atomic vectors
Backtrace:
▆
1. └─NMdata::NMwriteData(...) at test_NMwriteData.R:260:5
2. ├─base::sub(" *\\$INPUT *", "", paste(NMtext$INPUT, collapse = " "))
3. │ └─base::is.factor(x)
4. └─base::paste(NMtext$INPUT, collapse = " ")
── Error ('test_NMwriteData.R:295:5'): save csv and fst ────────────────────────
Error in `NMwriteData(pk, file = outfile, script = "A simple test", formats = cc(csv, fst), args.stamp = list(time = "2021-11-21 11:00:00"))`: NMgenText failed.
Backtrace:
▆
1. └─NMdata::NMwriteData(...) at test_NMwriteData.R:295:5
── Error ('test_NMwriteData.R:337:5'): Non-numeric DATE and TIME ───────────────
Error in `NMwriteData(pk, file = outfile, script = "DATE and TIME as char", formats = cc(csv), args.stamp = list(time = "2021-11-21 11:00:00"))`: NMgenText failed.
Backtrace:
▆
1. └─NMdata::NMwriteData(...) at test_NMwriteData.R:337:5
── Error ('test_NMwriteSection.R:164:5'): update INPUT based on NMgenText ──────
Error in ``[.data.table`(dt.num.ok, include == TRUE, `:=`(occ.cum, 1:.N), by = name.nm)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMgenText(...) at test_NMwriteSection.R:164:5
2. ├─dt.num.ok[include == TRUE, `:=`(occ.cum, 1:.N), by = name.nm]
3. └─data.table:::`[.data.table`(...)
── Error ('test_addCor.R:9:5'): basic ──────────────────────────────────────────
Error in ``[.data.table`(pars, get(col.par.type) %in% allpars.mat, `:=`(j, as.integer(sub(pattern = sprintf("%s\\(([0-9]+)\\,([0-9]+)\\)", get(col.par.type)), replacement = "\\2", x = get(col.parameter)))), by = row)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadExt(file.mod) at test_addCor.R:9:5
2. └─NMdata:::addParType(pars)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_addTAPD.R:8:5'): basic ─────────────────────────────────────────
Error in ``[.data.table`(data, !is.na(get(col.time)), `:=`((col.doscumn), cumsum(get(col.event) == TRUE)), by = by)`: attempt access index 28/28 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::addTAPD(data = dat) at test_addTAPD.R:8:5
2. └─NMdata (local) addVars(data2)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_addTAPD.R:21:5'): repeated dosing data ─────────────────────────
Error in ``[.data.table`(data, !is.na(get(col.time)), `:=`((col.doscumn), cumsum(get(col.event) == TRUE)), by = by)`: attempt access index 25/25 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::addTAPD(data = dat, as.fun = "data.table") at test_addTAPD.R:21:5
2. └─NMdata (local) addVars(data2)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_addTAPD.R:32:5'): Custom names and discard one ─────────────────
Error in ``[.data.table`(data, !is.na(get(col.time)), `:=`((col.doscumn), cumsum(get(col.event) == TRUE)), by = by)`: attempt access index 25/25 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::addTAPD(data = dat, as.fun = "data.table") at test_addTAPD.R:32:5
2. └─NMdata (local) addVars(data2)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_addTAPD.R:46:5'): SDOSE ────────────────────────────────────────
Error in ``[.data.table`(data, !is.na(get(col.time)), `:=`((col.doscumn), cumsum(get(col.event) == TRUE)), by = by)`: attempt access index 28/28 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::addTAPD(data = dat) at test_addTAPD.R:46:5
2. └─NMdata (local) addVars(data2)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_addTAPD.R:80:5'): Repeated doses without samples ───────────────
Error in ``[.data.table`(data, !is.na(get(col.time)), `:=`((col.doscumn), cumsum(get(col.event) == TRUE)), by = by)`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::addTAPD(dat.all[EVID == 1]) at test_addTAPD.R:80:5
2. └─NMdata (local) addVars(data2)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_addTAPD.R:96:5'): Subjects without doses ───────────────────────
Error in ``[.data.table`(data, !is.na(get(col.time)), `:=`((col.doscumn), cumsum(get(col.event) == TRUE)), by = by)`: attempt access index 28/28 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::addTAPD(data = dat, as.fun = "data.table") at test_addTAPD.R:96:5
2. └─NMdata (local) addVars(data2)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_dt2mat.R:7:5'): basic ──────────────────────────────────────────
Error in ``[.data.table`(pars, get(col.par.type) %in% allpars.mat, `:=`(j, as.integer(sub(pattern = sprintf("%s\\(([0-9]+)\\,([0-9]+)\\)", get(col.par.type)), replacement = "\\2", x = get(col.parameter)))), by = row)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadExt("testData/nonmem/xgxr021.mod", as.fun = "data.table") at test_dt2mat.R:7:5
2. └─NMdata:::addParType(pars)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_flags.R:168:5'): count by ──────────────────────────────────────
Error in ``[.data.table`(allres, , `:=`(N.discard, c(NA, -diff(N.left))), by = by)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::flagsCount(...) at test_flags.R:168:5
2. ├─allres[, `:=`(N.discard, c(NA, -diff(N.left))), by = by]
3. └─data.table:::`[.data.table`(...)
── Error ('test_print_summary_NMdata.R:9:5'): basic ────────────────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(...) at test_print_summary_NMdata.R:9:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
[ FAIL 123 | WARN 150 | SKIP 1 | PASS 200 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-windows-x86_64
Current CRAN status: ERROR: 1, NOTE: 3, OK: 9
Version: 0.2.6
Check: examples
Result: ERROR
Running examples in 'NMsim-Ex.R' failed
The error most likely occurred in:
> ### Name: NMaddSamples
> ### Title: Add simulation (sample) records to dosing records
> ### Aliases: NMaddSamples
>
> ### ** Examples
>
> (doses1 <- NMcreateDoses(TIME=c(0,12,24,36),AMT=c(2,1)))
Error in `[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row) :
attempt access index 1/1 in VECTOR_ELT
Calls: NMcreateDoses -> [ -> [.data.table
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.2.6
Check: tests
Result: ERROR
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(NMsim)
NMsim 0.2.6. Browse NMsim documentation at
https://NMautoverse.github.io/NMsim/
>
> test_check("NMsim")
Saving _problems/test_NMaddSamples-10.R
Saving _problems/test_NMaddSamples-29.R
Saving _problems/test_NMaddSamples-51.R
Saving _problems/test_NMaddSamples-74.R
Saving _problems/test_NMaddSamples-93.R
Saving _problems/test_NMaddSamples-117.R
Saving _problems/test_NMaddSamples-134.R
Saving _problems/test_NMaddSamples-153.R
Saving _problems/test_NMaddSamples-171.R
Saving _problems/test_NMaddSamples-199.R
Saving _problems/test_NMaddSamples-218.R
Saving _problems/test_NMaddSamples-230.R
Saving _problems/test_NMaddSamples-240.R
Saving _problems/test_NMaddSamples-248.R
Saving _problems/test_NMaddSamples-258.R
Saving _problems/test_NMaddSamples-268.R
Saving _problems/test_NMaddSamples-277.R
Saving _problems/test_NMaddSamples-289.R
Saving _problems/test_NMaddSamples-316.R
Saving _problems/test_NMaddSamples-340.R
Saving _problems/test_NMaddSamples-378.R
Saving _problems/test_NMaddSamples-397.R
Saving _problems/test_NMaddSamples-425.R
Saving _problems/test_NMcreateDoses-13.R
Saving _problems/test_NMcreateDoses-20.R
Saving _problems/test_NMcreateDoses-29.R
Saving _problems/test_NMcreateDoses-45.R
Saving _problems/test_NMcreateDoses-56.R
Saving _problems/test_NMcreateDoses-67.R
Saving _problems/test_NMcreateDoses-100.R
Saving _problems/test_NMcreateDoses-113.R
Saving _problems/test_NMcreateDoses-130.R
Saving _problems/test_NMcreateDoses-137.R
Saving _problems/test_NMcreateDoses-147.R
Saving _problems/test_NMcreateDoses-162.R
Saving _problems/test_NMcreateDoses-171.R
Saving _problems/test_NMcreateDoses-197.R
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Saving _problems/test_NMcreateDoses-277.R
Saving _problems/test_NMcreateDoses-287.R
Saving _problems/test_NMcreateMatLines-14.R
Saving _problems/test_NMcreateMatLines-40.R
Saving _problems/test_NMreadParsWide-16.R
Saving _problems/test_NMreadSim-30.R
Saving _problems/test_NMseed-13.R
Saving _problems/test_NMseed-31.R
Saving _problems/test_NMseed-44.R
Saving _problems/test_NMseed-62.R
Saving _problems/test_NMsim-23.R
Saving _problems/test_NMsim_NWPRI-41.R
Saving _problems/test_NMsim_VarCov-23.R
Saving _problems/test_NMwriteInits-25.R
Saving _problems/test_NMwriteInits-50.R
Saving _problems/test_NMwriteInits-75.R
Saving _problems/test_NMwriteInits-103.R
Saving _problems/test_NMwriteInits-125.R
Saving _problems/test_NMwriteInits-155.R
Saving _problems/test_NMwriteInits-186.R
Saving _problems/test_NMwriteInits-219.R
Saving _problems/test_NMwriteInits-264.R
Saving _problems/test_NMwriteInits-285.R
Saving _problems/test_NMwriteInits-311.R
Saving _problems/test_addEVID2-10.R
Saving _problems/test_addEVID2-29.R
Saving _problems/test_addEVID2-51.R
Saving _problems/test_addEVID2-74.R
Saving _problems/test_addEVID2-93.R
Saving _problems/test_addEVID2-119.R
Saving _problems/test_addEVID2-136.R
Saving _problems/test_addEVID2-155.R
Saving _problems/test_addEVID2-173.R
Saving _problems/test_addEVID2-201.R
Saving _problems/test_addEVID2-220.R
Saving _problems/test_addEVID2-232.R
Saving _problems/test_addEVID2-242.R
Saving _problems/test_addEVID2-250.R
Saving _problems/test_addEVID2-260.R
Saving _problems/test_addEVID2-270.R
Saving _problems/test_addEVID2-279.R
Saving _problems/test_addEVID2-291.R
Saving _problems/test_addEVID2-317.R
Saving _problems/test_addEVID2-343.R
Saving _problems/test_addEVID2-369.R
Saving _problems/test_expandCovLists-9.R
Saving _problems/test_expandCovLists-29.R
Saving _problems/test_expandCovLists-50.R
Saving _problems/test_expandCovLists-73.R
Saving _problems/test_genPhiFile-15.R
Saving _problems/test_sampleCovs-10.R
Saving _problems/test_simPopEtas-20.R
Saving _problems/test_summarizeCovs-54.R
Saving _problems/test_summarizeCovs-81.R
Saving _problems/test_typicalize-10.R
Saving _problems/test_typicalize-31.R
Saving _problems/test_typicalize-56.R
[ FAIL 99 | WARN 0 | SKIP 6 | PASS 28 ]
══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• empty test (6): , , , , ,
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_NMaddSamples.R:10:5'): Basic ───────────────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = c(0, 12), AMT = 10, CMT = 2) at test_NMaddSamples.R:10:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMaddSamples.R:29:5'): Multiple compartments ───────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = c(0, 12), AMT = 10, CMT = 1) at test_NMaddSamples.R:29:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMaddSamples.R:51:5'): compartments with covariates ────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = c(0, 12), AMT = 10, CMT = 1) at test_NMaddSamples.R:51:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMaddSamples.R:74:5'): data.frame CMT ──────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = c(0, 12), AMT = 10, CMT = 1, as.fun = as.data.frame) at test_NMaddSamples.R:74:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMaddSamples.R:93:5'): time with covariates ────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMaddSamples.R:93:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMaddSamples.R:117:5'): EVID=0 ─────────────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = c(0, 12), AMT = 10, CMT = 2) at test_NMaddSamples.R:117:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMaddSamples.R:134:5'): time after dose ────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = c(0, 12), AMT = 10, CMT = 1) at test_NMaddSamples.R:134:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMaddSamples.R:153:5'): TIME and TAPD ──────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = c(0, 12), AMT = 10, CMT = 1) at test_NMaddSamples.R:153:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMaddSamples.R:171:5'): TAPD with ADDL/II ──────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMaddSamples.R:171:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMaddSamples.R:199:5'): simple, more than one id ───────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMaddSamples.R:199:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMaddSamples.R:218:5'): TAPD - covariates on dosing data, not on TAPD ──
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMaddSamples.R:218:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMaddSamples.R:230:5'): TAPD - covariates on dosing data, and on TAPD ──
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMaddSamples.R:230:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMaddSamples.R:240:5'): all subjects covered ───────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMaddSamples.R:240:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMaddSamples.R:248:5'): sampling schemes overlapping into next doses ──
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMaddSamples.R:248:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMaddSamples.R:258:5'): sampling at time of doses ──────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMaddSamples.R:258:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMaddSamples.R:268:5'): sampling times not unique ──────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMaddSamples.R:268:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMaddSamples.R:277:5'): No CMT column ──────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMaddSamples.R:277:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMaddSamples.R:289:5'): Providing DV ───────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMaddSamples.R:289:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMaddSamples.R:316:5'): default - common columns are not merged by ──
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMaddSamples.R:316:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMaddSamples.R:340:5'): by unmatched (covariates) ──────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMaddSamples.R:340:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMaddSamples.R:378:5'): Unmatched covariates not in by ─────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMaddSamples.R:378:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMaddSamples.R:397:5'): Unmatched are not covs ─────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMaddSamples.R:397:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMaddSamples.R:425:5'): MDV missing on doses ───────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = c(0), AMT = 10, CMT = 2, as.fun = "data.table") at test_NMaddSamples.R:425:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateDoses.R:13:5'): Basic ──────────────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = 0, AMT = 10) at test_NMcreateDoses.R:13:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateDoses.R:20:5'): custom CMT value ───────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = 0, AMT = 10) at test_NMcreateDoses.R:20:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateDoses.R:29:5'): Expand columns ─────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = c(0, 12), AMT = 10, CMT = 2) at test_NMcreateDoses.R:29:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateDoses.R:45:5'): non-unique AMT ─────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMcreateDoses.R:45:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateDoses.R:56:5'): II/ADDL ────────────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMcreateDoses.R:56:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateDoses.R:67:5'): ADDL and II one by one ─────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMcreateDoses.R:67:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateDoses.R:100:5'): II and ADDL of length=1 ───────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMcreateDoses.R:100:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateDoses.R:113:5'): NA columns ────────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMcreateDoses.R:113:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateDoses.R:130:5'): covariates basics ─────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMcreateDoses.R:130:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateDoses.R:137:5'): covariates basics 2 ───────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMcreateDoses.R:137:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateDoses.R:147:5'): covariates not spanning same covariate values ──
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMcreateDoses.R:147:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateDoses.R:162:5'): covariates spanning same covariate values ──
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMcreateDoses.R:162:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateDoses.R:171:5'): covariates spanning same covariate values - addl ──
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMcreateDoses.R:171:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateDoses.R:197:5'): Expanding AMT within a covariate ──────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMcreateDoses.R:197:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateDoses.R:206:5'): as.fun ────────────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = 0, AMT = 10) at test_NMcreateDoses.R:206:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateDoses.R:219:5'): data.frames accepted ──────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_NMcreateDoses.R:219:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateDoses.R:227:5'): col.id ────────────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = 0, AMT = 10, col.id = "NOOOO") at test_NMcreateDoses.R:227:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateDoses.R:242:5'): covs in multiple arguments ────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = dt.time, AMT = dt.amt) at test_NMcreateDoses.R:242:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateDoses.R:267:5'): Suppress EVID ─────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = 0, AMT = 1, EVID = NULL) at test_NMcreateDoses.R:267:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateDoses.R:277:5'): length(TIME)=3 and length(ADDL)=1 ─────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = c(0, 2, 4), AMT = 1, ADDL = 4, II = 12) at test_NMcreateDoses.R:277:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateDoses.R:287:5'): Basic with N>1 ────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = 0, AMT = 10, N = 3) at test_NMcreateDoses.R:287:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateMatLines.R:14:5'): basic ───────────────────────────────
Error in ``[.data.table`(pars, get(col.par.type) %in% allpars.mat, `:=`(j, as.integer(sub(pattern = sprintf("%s\\(([0-9]+)\\,([0-9]+)\\)", get(col.par.type)), replacement = "\\2", x = get(col.parameter)))), by = row)`: attempt access index 16/16 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadExt(file.mod) at test_NMcreateMatLines.R:14:5
2. └─NMdata:::addParType(pars)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_NMcreateMatLines.R:40:5'): Fixed block ─────────────────────────
Error in ``[.data.table`(pars, get(col.par.type) %in% allpars.mat, `:=`(j, as.integer(sub(pattern = sprintf("%s\\(([0-9]+)\\,([0-9]+)\\)", get(col.par.type)), replacement = "\\2", x = get(col.parameter)))), by = row)`: attempt access index 16/16 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadExt(file.mod, as.fun = "data.table") at test_NMcreateMatLines.R:40:5
2. └─NMdata:::addParType(pars)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadParsWide.R:16:5'): basic ─────────────────────────────────
Error in ``[.data.table`(pars.l, , `:=`((c("i", "j")), deriveCols(name.wide, n = 2)), by = c(col.model, col.model.sim, "name.wide"))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::readParsWide(parsWide) at test_NMreadParsWide.R:16:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMreadSim.R:30:1'): (code run outside of `test_that()`) ────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = 0, AMT = dt.amt, as.fun = "data.table") at test_NMreadSim.R:30:1
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMseed.R:13:5'): basic ─────────────────────────────────────────
Error in ``[.data.table`(values, , `:=`(string, paste(paste0("(", unlist(.SD), " ", dist, ")"), collapse = " ")), by = .(nsim))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim:::NMseed(...) at test_NMseed.R:13:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMseed.R:31:5'): manually provided values ──────────────────────
Error in ``[.data.table`(values, , `:=`(string, paste(paste0("(", unlist(.SD), " ", dist, ")"), collapse = " ")), by = .(nsim))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim:::NMseed(...) at test_NMseed.R:31:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMseed.R:44:5'): Only one value per source ─────────────────────
Error in ``[.data.table`(values, , `:=`(string, paste(paste0("(", unlist(.SD), " ", dist, ")"), collapse = " ")), by = .(nsim))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim:::NMseed(...) at test_NMseed.R:44:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMseed.R:62:5'): basic ─────────────────────────────────────────
Error in ``[.data.table`(values, , `:=`(string, paste(paste0("(", unlist(.SD), " ", dist, ")"), collapse = " ")), by = .(nsim))`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim:::NMseed(models = data.table(1), values = 2) at test_NMseed.R:62:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMsim.R:23:1'): (code run outside of `test_that()`) ────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = 0, AMT = dt.amt, as.fun = "data.table") at test_NMsim.R:23:1
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMsim_NWPRI.R:41:1'): (code run outside of `test_that()`) ──────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = 0, AMT = dt.amt, as.fun = "data.table") at test_NMsim_NWPRI.R:41:1
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMsim_VarCov.R:23:1'): (code run outside of `test_that()`) ─────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = 0, AMT = dt.amt, as.fun = "data.table") at test_NMsim_VarCov.R:23:1
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_NMwriteInits.R:25:5'): Basic ───────────────────────────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMwriteInits(file.mod, `THETA(1)` = list(init = 3), update = FALSE) at test_NMwriteInits.R:25:5
2. └─NMsim:::NMreadInits(...)
3. └─NMsim:::initsToExt(res)
4. └─NMsim:::addSameBlocks(pars)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_NMwriteInits.R:50:5'): Update + value ──────────────────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMwriteInits(file.mod, `THETA(1)` = list(init = 3), update = TRUE) at test_NMwriteInits.R:50:5
2. └─NMsim:::NMreadInits(...)
3. └─NMsim:::initsToExt(res)
4. └─NMsim:::addSameBlocks(pars)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_NMwriteInits.R:75:5'): unfix ───────────────────────────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMwriteInits(file.mod, `OMEGA(1,1)` = list(fix = 0), update = F) at test_NMwriteInits.R:75:5
2. └─NMsim:::NMreadInits(...)
3. └─NMsim:::initsToExt(res)
4. └─NMsim:::addSameBlocks(pars)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_NMwriteInits.R:103:5'): fix a block ────────────────────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMwriteInits(file.mod, `OMEGA(2,2)` = list(fix = 1), update = FALSE) at test_NMwriteInits.R:103:5
2. └─NMsim:::NMreadInits(...)
3. └─NMsim:::initsToExt(res)
4. └─NMsim:::addSameBlocks(pars)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_NMwriteInits.R:125:5'): modify omega in a block ───────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMwriteInits(file.mod, `OMEGA(2,2)` = list(init = 1)) at test_NMwriteInits.R:125:5
2. └─NMsim:::NMreadInits(...)
3. └─NMsim:::initsToExt(res)
4. └─NMsim:::addSameBlocks(pars)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_NMwriteInits.R:155:5'): comments on parameters ─────────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMwriteInits(...) at test_NMwriteInits.R:155:5
2. └─NMsim:::NMreadInits(...)
3. └─NMsim:::initsToExt(res)
4. └─NMsim:::addSameBlocks(pars)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_NMwriteInits.R:186:5'): multiple named lists ───────────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMwriteInits(...) at test_NMwriteInits.R:186:5
2. └─NMsim:::NMreadInits(...)
3. └─NMsim:::initsToExt(res)
4. └─NMsim:::addSameBlocks(pars)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_NMwriteInits.R:219:5'): An ext object ──────────────────────────
Error in ``[.data.table`(pars, get(col.par.type) %in% allpars.mat, `:=`(j, as.integer(sub(pattern = sprintf("%s\\(([0-9]+)\\,([0-9]+)\\)", get(col.par.type)), replacement = "\\2", x = get(col.parameter)))), by = row)`: attempt access index 16/16 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadExt(file.mod, as.fun = "data.table") at test_NMwriteInits.R:219:5
2. └─NMdata:::addParType(pars)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_NMwriteInits.R:263:5'): an inits.tab object ────────────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMwriteInits(file.mod, update = FALSE, inits.tab = inits.tab) at test_NMwriteInits.R:263:5
2. └─NMsim:::NMreadInits(...)
3. └─NMsim:::initsToExt(res)
4. └─NMsim:::addSameBlocks(pars)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_NMwriteInits.R:283:5'): fix multiple ───────────────────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMwriteInits(...) at test_NMwriteInits.R:283:5
2. └─NMsim:::NMreadInits(...)
3. └─NMsim:::initsToExt(res)
4. └─NMsim:::addSameBlocks(pars)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_NMwriteInits.R:311:5'): IOV with SAME ──────────────────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMwriteInits(file.mod, update = TRUE) at test_NMwriteInits.R:311:5
2. └─NMsim:::NMreadInits(...)
3. └─NMsim:::initsToExt(res)
4. └─NMsim:::addSameBlocks(pars)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_addEVID2.R:10:5'): Basic ───────────────────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = c(0, 12), AMT = 10, CMT = 2) at test_addEVID2.R:10:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_addEVID2.R:29:5'): Multiple compartments ───────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = c(0, 12), AMT = 10, CMT = 1) at test_addEVID2.R:29:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_addEVID2.R:51:5'): compartments with covariates ────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = c(0, 12), AMT = 10, CMT = 1) at test_addEVID2.R:51:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_addEVID2.R:74:5'): data.frame CMT ──────────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = c(0, 12), AMT = 10, CMT = 1, as.fun = as.data.frame) at test_addEVID2.R:74:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_addEVID2.R:93:5'): time with covariates ────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_addEVID2.R:93:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_addEVID2.R:119:5'): EVID=0 ─────────────────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = c(0, 12), AMT = 10, CMT = 2) at test_addEVID2.R:119:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_addEVID2.R:136:5'): time after dose ────────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = c(0, 12), AMT = 10, CMT = 1) at test_addEVID2.R:136:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_addEVID2.R:155:5'): TIME and TAPD ──────────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(TIME = c(0, 12), AMT = 10, CMT = 1) at test_addEVID2.R:155:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_addEVID2.R:173:5'): TAPD with ADDL/II ──────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 1/1 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_addEVID2.R:173:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_addEVID2.R:201:5'): simple, more than one id ───────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_addEVID2.R:201:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_addEVID2.R:220:5'): TAPD - covariates on dosing data, not on TAPD ──
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_addEVID2.R:220:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_addEVID2.R:232:5'): TAPD - covariates on dosing data, and on TAPD ──
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_addEVID2.R:232:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_addEVID2.R:242:5'): all subjects covered ───────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_addEVID2.R:242:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_addEVID2.R:250:5'): sampling schemes overlapping into next doses ──
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_addEVID2.R:250:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_addEVID2.R:260:5'): sampling at time of doses ──────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_addEVID2.R:260:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_addEVID2.R:270:5'): sampling times not unique ──────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_addEVID2.R:270:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_addEVID2.R:279:5'): No CMT column ──────────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_addEVID2.R:279:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_addEVID2.R:291:5'): Providing DV ───────────────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_addEVID2.R:291:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_addEVID2.R:317:5'): Unmatched covariates ───────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_addEVID2.R:317:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_addEVID2.R:343:5'): Unmatched covariates ───────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_addEVID2.R:343:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_addEVID2.R:369:5'): Unmatched are not covs ─────────────────────
Error in ``[.data.table`(combs, , `:=`(Nna, sum(is.na(.SD))), by = col.row)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMcreateDoses(...) at test_addEVID2.R:369:5
2. ├─combs[, `:=`(Nna, sum(is.na(.SD))), by = col.row]
3. └─data.table:::`[.data.table`(...)
── Error ('test_expandCovLists.R:9:5'): basic ──────────────────────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(file.mod, quiet = TRUE) at test_expandCovLists.R:9:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_expandCovLists.R:29:5'): with categorical ──────────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(file.mod, quiet = TRUE) at test_expandCovLists.R:29:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_expandCovLists.R:50:5'): labeling ──────────────────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(file.mod, quiet = TRUE) at test_expandCovLists.R:50:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_expandCovLists.R:73:5'): keep all refs ─────────────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData(file.mod, quiet = TRUE) at test_expandCovLists.R:73:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_genPhiFile.R:15:5'): Basic ─────────────────────────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMreadPhi(file.phi) at test_genPhiFile.R:15:5
2. └─base::lapply(...)
3. └─NMdata (local) FUN(X[[i]], ...)
4. └─NMdata::NMreadTab(...)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_sampleCovs.R:10:5'): basic ─────────────────────────────────────
Error in ``[.data.table`(dt1, grep("^TABLE", as.character(get(cnames[1])), perl = TRUE), `:=`((col.table.name.text), mypaste(.SD)), by = col.row.tmp)`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. └─NMdata::NMscanData("testData/nonmem/xgxr134.mod", quiet = TRUE) at test_sampleCovs.R:10:5
2. └─NMdata::NMscanTables(...)
3. └─NMdata::NMreadTab(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_simPopEtas.R:20:5'): Basic ─────────────────────────────────────
Error in ``[.data.table`(pars, get(col.par.type) %in% allpars.mat, `:=`(j, as.integer(sub(pattern = sprintf("%s\\(([0-9]+)\\,([0-9]+)\\)", get(col.par.type)), replacement = "\\2", x = get(col.parameter)))), by = row)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::simPopEtas(file.mod, N = 10, seed = 4) at test_simPopEtas.R:20:5
2. └─NMdata::NMreadExt(...)
3. └─NMdata:::addParType(pars)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_summarizeCovs.R:54:5'): basic ──────────────────────────────────
Error in ``[.data.table`(modtab, , `:=`(path.lst.read, { if (is.null(dir.sims)) { dirSims <- file.path(dirname(path.rds.read), pathSimsFromRes) } else { dirSims <- dir.sims } simplePath(file.path(dirSims, relative_path(path.sim.lst, dirSims))) }), by = .(ROWTMP))`: attempt access index 35/35 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMreadSim("testData/simres/xgxr134_forest1_MetaData.rds") at test_summarizeCovs.R:54:5
2. └─NMsim:::NMreadSimModTab(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_summarizeCovs.R:81:5'): zero refs ──────────────────────────────
Error in ``[.data.table`(modtab, , `:=`(path.lst.read, { if (is.null(dir.sims)) { dirSims <- file.path(dirname(path.rds.read), pathSimsFromRes) } else { dirSims <- dir.sims } simplePath(file.path(dirSims, relative_path(path.sim.lst, dirSims))) }), by = .(ROWTMP))`: attempt access index 35/35 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim::NMreadSim("testData/simres/xgxr134_forest1_MetaData.rds") at test_summarizeCovs.R:81:5
2. └─NMsim:::NMreadSimModTab(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_typicalize.R:10:5'): basic ─────────────────────────────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim:::typicalize(lines = lines.in) at test_typicalize.R:10:5
2. └─NMsim:::NMreadInits(lines = lines, as.fun = "data.table", section = section)
3. └─NMsim:::initsToExt(res)
4. └─NMsim:::addSameBlocks(pars)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_typicalize.R:31:5'): Priors ────────────────────────────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim:::typicalize(file.mod) at test_typicalize.R:31:5
2. └─NMsim:::NMreadInits(lines = lines, as.fun = "data.table", section = section)
3. └─NMsim:::initsToExt(res)
4. └─NMsim:::addSameBlocks(pars)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_typicalize.R:56:5'): zero sigma ────────────────────────────────
Error in ``[.data.table`(df, , `:=`(Nsameblock, ifelse(any(sameblock != 0), .N - 1, 0)), by = sameblock)`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. └─NMsim:::typicalize(lines = lines.in, section = c("omega", "sigma")) at test_typicalize.R:56:5
2. └─NMsim:::NMreadInits(lines = lines, as.fun = "data.table", section = section)
3. └─NMsim:::initsToExt(res)
4. └─NMsim:::addSameBlocks(pars)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
[ FAIL 99 | WARN 0 | SKIP 6 | PASS 28 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.2.6
Check: package dependencies
Result: NOTE
Package which this enhances but not available for checking: ‘simpar’
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: OK: 13
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