CRAN Package Check Results for Package NMdata

Last updated on 2025-12-19 12:49:16 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	0.2.2	11.73	141.26	152.99	OK
r-devel-linux-x86_64-debian-gcc	0.2.2	7.26	93.38	100.64	OK
r-devel-linux-x86_64-fedora-clang	0.2.2	19.00	163.42	182.42	ERROR
r-devel-linux-x86_64-fedora-gcc	0.2.2	17.00	154.38	171.38	ERROR
r-devel-windows-x86_64	0.2.2	14.00	157.00	171.00	OK
r-patched-linux-x86_64	0.2.2	11.65	127.76	139.41	OK
r-release-linux-x86_64	0.2.2	10.31	127.90	138.21	OK
r-release-macos-arm64	0.2.2				OK
r-release-macos-x86_64	0.2.2	8.00	128.00	136.00	OK
r-release-windows-x86_64	0.2.2	16.00	143.00	159.00	OK
r-oldrel-macos-arm64	0.2.2				OK
r-oldrel-macos-x86_64	0.2.2	8.00	137.00	145.00	OK
r-oldrel-windows-x86_64	0.2.2	20.00	182.00	202.00	OK

Check Details

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 Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.2.2
Check: tests
Result: ERROR Running ‘spelling.R’ Running ‘testthat.R’ [56s/79s] 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-linux-x86_64-fedora-clang

Version: 0.2.2
Check: tests
Result: ERROR Running ‘spelling.R’ Running ‘testthat.R’ [52s/63s] 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-linux-x86_64-fedora-gcc