Package check result: OK Changes to worse in reverse depends: Package: babelmixr2 Check: package dependencies Old result: NOTE Package suggested but not available for checking: ‘lixoftConnectors’ New result: ERROR Packages required but not available: 'nlmixr2', 'nlmixr2est' Package suggested but not available for checking: ‘lixoftConnectors’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Package: nlmixr2 Check: package dependencies New result: ERROR Packages required but not available: 'nlmixr2est', 'nlmixr2extra', 'nlmixr2plot' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Package: nlmixr2est Check: whether package can be installed New result: ERROR Installation failed. Package: nlmixr2extra Check: package dependencies New result: ERROR Package required but not available: ‘nlmixr2est’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Package: nlmixr2lib Check: package dependencies New result: ERROR Package required but not available: ‘nlmixr2est’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Package: nlmixr2plot Check: package dependencies New result: ERROR Packages required but not available: 'nlmixr2est', 'nlmixr2extra' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Package: nlmixr2rpt Check: package dependencies New result: ERROR Packages required but not available: 'nlmixr2', 'nlmixr2extra', 'xpose.nlmixr2' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Package: nonmem2rx Check: tests New result: ERROR Running ‘testthat.R’ [42s/42s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(nonmem2rx) > library(rxode2) rxode2 3.0.0 using 3 threads (see ?getRxThreads) no cache: create with `rxCreateCache()` > setRxThreads(1L) > library(data.table) > setDTthreads(1L) > > > test_check("nonmem2rx") $ABBREV record syntax error error: ================================================================================ :ERR: will not change var type from 'EPS' to 'THETA': :001: REPLACE EPS(ECL)=THETA(4) ================================================================================ :ERR: will not change var type from 'THETA' to 'ETA': :001: REPLACE THETA(CL,V1,Q,V2)=ETA(1,2,3,4) ================================================================================ :ERR: 'MOD' function not supported in translation: :001: CL = MOD(C) ================================================================================ :ERR: 'INT' function not supported in translation: :001: CL = INT(C) ================================================================================ :ERR: 'A#' NONMEM reserved variable is not translated: :001: CL = A12345 ================================================================================ :ERR: 'C#' NONMEM reserved variable is not translated: :001: CL = C12345 ================================================================================ :ERR: 'COMACT' NONMEM reserved variable is not translated: :001: A = COMACT ================================================================================ :ERR: 'COMSAV' NONMEM reserved variable is not translated: :001: A = COMSAV ================================================================================ :ERR: 'CALL PASS(MODE)' statements not supported in translation: :001: CALL PASS(MODE) ================================================================================ :ERR: 'CALL SUPP(# , #)' statements not supported in translation: :001: CALL SUPP(0 , 1) ================================================================================ :ERR: DT(#) not supported in translation: :001: C=DT(3) ================================================================================ :ERR: MNEXT(#) not supported in translation: :001: C=MNEXT(3) ================================================================================ :ERR: COM(#) not supported in translation: :001: C=COM(3) ================================================================================ :ERR: PCMT(#) not supported in translation: :001: C=PCMT(3) ================================================================================ :ERR: DA(#, #) not supported in translation: :001: DA(1, 2) = -KEL*A(1) ================================================================================ :ERR: DP(#, #) not supported in translation: :001: DP(1, 2) = -KEL*A(1) ================================================================================ :ERR: 'TSCALE' NONMEM reserved variable is not translated: :001: TSCALE = 4 ================================================================================ :ERR: 'XSCALE' NONMEM reserved variable is not translated: :001: XSCALE = 4 ================================================================================ :ERR: 'CALL GETETA(ETA)' not supported in translation: :001: CALL GETETA(ETA) ================================================================================ $PRED syntax error: :001: , ^ ================================================================================ :ERR: can only request depot and central compartments for solved systems in rxode2 translations: :001: f3=1 ================================================================================ :ERR: can only request depot and central compartments for solved systems in rxode2 translations: :001: f3=1 ================================================================================ :ERR: F0/FO is not supported in translation: :001: F0=3 ================================================================================ i getting information from '/home/hornik/tmp/CRAN_recheck/nonmem2rx.Rcheck/nonmem2rx/TheopdExt.ctl' i reading in lst file i seeing if file argument is actually lst file i not list file, control stream i done i splitting control stream by records i done i Processing record $INPUT i Processing record $gTHETA i Processing record $OMEGA i Processing record $SIGMA i Processing record $PROBLEM i Processing record $DATA i Processing record $ESTIMATION i Ignore record $ESTIMATION i Processing record $COVARIANCE i Ignore record $COVARIANCE i Processing record $PRED i Processing record $TABLE i final parameters not updated, will skip validation i changing most variables to lower case i done i replace theta names i done i replace eta names i done i getting information from '/home/hornik/tmp/CRAN_recheck/nonmem2rx.Rcheck/nonmem2rx/Theopd.ctl' i reading in lst file i seeing if file argument is actually lst file i not list file, control stream i done i splitting control stream by records i done i Processing record $INPUT i Processing record $gTHETA i Processing record $OMEGA i Processing record $SIGMA i Processing record $PROBLEM i Processing record $DATA i Processing record $ESTIMATION i Ignore record $ESTIMATION i Processing record $COVARIANCE i Ignore record $COVARIANCE i Processing record $PRED i Processing record $TABLE i final parameters not updated, will skip validation i changing most variables to lower case i done i replace theta names i done i replace eta names i done $DATA syntax error: :001: matt.csv matt=.csv ^ ================================================================================ $INPUT syntax error: :001: matt~1 ^ ================================================================================ $MODEL syntax error: :001: malformed ^ ================================================================================ :ERR: $OMEGA or $SIGMA BLOCK(N) does not have enough elements: :001: BLOCK(3) 6. .005 .3 .0002 .006 ================================================================================ :ERR: $OMEGA or $SIGMA BLOCK(N) has too many elements: :001: BLOCK(3) 6. .005 .3 .0002 .006 .4 .4 ================================================================================ :ERR: (FIXED/UNINT .4) is not supported in an $OMEGA or $SIGMA BLOCK: :001: BLOCK(3) 6. .005 .3 .0002 .006 (fix .4) ================================================================================ $OMEGA syntax error: :001: garbage ^ ================================================================================ :ERR: REPLACE requesting data item replacement for 'NOINP' which is not defined in the $INPUT record: :001: REPLACE ETA(NOINP)=ETA(0,2,3) ================================================================================ ----------------------- String Comparison Tests ----------------------- INTENTIONAL UNIT TEST FAILURE to show what a unit test failure looks like! FAILED at line 210 in function _nonmem2rx_parse_strncmpci! strncmpci("hey", "HEY", 3) != 'h' - 'H' a: strncmpci("hey", "HEY", 3) is 0 b: 'h' - 'H' is 32 ------ beginning ------ All unit tests passed! $SUB syntax error: :001: tranvan1 ^ ================================================================================ :ERR: $SUBROUTINES 'INFN' unsupported for translation: :001: INFN=matt.f ================================================================================ :ERR: $SUBROUTINES 'TOL' subroutine from external fortran unsupported for translation: :001: TOL=matt.f ================================================================================ :ERR: $SUBROUTINES 'ATOL' subroutine from external fortran unsupported for translation: :001: ATOL=matt.f ================================================================================ :ERR: $SUBROUTINES 'SSATOL' subroutine from external fortran unsupported for translation: :001: SSATOL=matt.f ================================================================================ $TAB syntax error: :001: fun=funny.csv ^ ================================================================================ :ERR: the NAMES() statement named more parameters than present in this $THETA block, error in translation: :001: NAMES(V1,CL,Q,V2) (0.0,7.0) (0.0,7.0) (0.0,7.0) ================================================================================ $THETA syntax error: :001: garbage ^ ================================================================================ lotri syntax error: ================================================================================= lotri error: lower triangular matrix not correct size did you mean something like: theta1 + theta2 + theta3 + theta4 + theta5 + theta6 + theta7 + theta8 + theta9 + theta10 + theta11 + theta12 + theta13 + eta1 + omega.1.2 + omega.1.3 + omega.1.4 + omega.1.5 + omega.1.6 + omega.1.7 + omega.1.8 + omega.1.9 + omega.1.10 + omega.1.11 + omega.1.12 + eta2 + omega.2.3 + omega.2.4 + omega.2.5 + omega.2.6 + omega.2.7 + omega.2.8 + omega.2.9 + omega.2.10 + omega.2.11 + omega.2.12 + eta3 + omega.3.4 + omega.3.5 + omega.3.6 + omega.3.7 + omega.3.8 + omega.3.9 + omega.3.10 + omega.3.11 + omega.3.12 + eta4 + omega.4.5 + omega.4.6 + omega.4.7 + omega.4.8 + omega.4.9 + omega.4.10 + omega.4.11 + omega.4.12 + eta5 + omega.5.6 + omega.5.7 + omega.5.8 + omega.5.9 + omega.5.10 + omega.5.11 + omega.5.12 + eta6 + omega.6.7 + omega.6.8 + omega.6.9 + omega.6.10 + omega.6.11 + omega.6.12 + eta7 + omega.7.8 + omega.7.9 + omega.7.10 + omega.7.11 + omega.7.12 + eta8 + omega.8.9 + omega.8.10 + omega.8.11 + omega.8.12 + eta9 + omega.9.10 + omega.9.11 + omega.9.12 + eta10 + omega.10.11 + omega.10.12 + eta11 + omega.11.12 + eta12 + eps1+v1+v2+v3+v4+v5+v6+v7+v8+v9+v10+v11+v12+v13+v14+v15+v16+v17+v18+v19+v20+v21+v22+v23+v24+v25+v26+v27~c(1.30441367197642, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, :001: theta1 + theta2 + theta3 + theta4 + theta5 + theta6 + theta7 + theta8 + theta9 + theta10 + theta11 + theta12 + theta13 + eta1 + omega.1.2 + omega.1.3 + omega.1.4 + omega.1.5 + omega.1.6 + omega.1.7 + omega.1.8 + omega.1.9 + omega.1.10 + omega.1.11 + omega.1.12 + eta2 + omega.2.3 + omega.2.4 + omega.2.5 + omega.2.6 + omega.2.7 + omega.2.8 + omega.2.9 + omega.2.10 + omega.2.11 + omega.2.12 + eta3 + omega.3.4 + omega.3.5 + omega.3.6 + omega.3.7 + omega.3.8 + omega.3.9 + omega.3.10 + omega.3.11 + omega.3.12 + eta4 + omega.4.5 + omega.4.6 + omega.4.7 + omega.4.8 + omega.4.9 + omega.4.10 + omega.4.11 + omega.4.12 + eta5 + omega.5.6 + omega.5.7 + omega.5.8 + omega.5.9 + omega.5.10 + omega.5.11 + omega.5.12 + eta6 + omega.6.7 + omega.6.8 + omega.6.9 + omega.6.10 + omega.6.11 + omega.6.12 + eta7 + omega.7.8 + omega.7.9 + omega.7.10 + omega.7.11 + omega.7.12 + eta8 + omega.8.9 + omega.8.10 + omega.8.11 + omega.8.12 + eta9 + omega.9.10 + omega.9.11 + omega.9.12 + eta10 + omega.10.11 + omega.10.12 + eta11 + omega.11.12 + 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================================================================================= i try to get covariance a different method (slower) [ FAIL 8 | WARN 2 | SKIP 15 | PASS 751 ] ══ Skipped tests (15) ══════════════════════════════════════════════════════════ • On CRAN (15): 'test-as-nonmem2rx.R:2:3', 'test-external-models.R:6:5', 'test-full-parsing.R:8:30', 'test-linCmt.R:2:3', 'test-model-load.R:7:5', 'test-nm75.R:7:5', 'test-piping.R:7:5', 'test-print.R:2:3', 'test-read-nonmemData.R:3:5', 'test-read-nonmemData.R:19:5', 'test-rename.R:7:5', 'test-rxsolve.R:11:5', 'test-sim-iwres.R:2:3', 'test-sim-iwres.R:62:3', 'test-vdiff.R:2:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-omega.R:12:5'): test omega ─────────────────────────────────── .nonmem2rx$ini (`actual`) not equal to `eq` (`expected`). actual vs expected - "eta1 ~ fix(0.09)" - "eta2 ~ fix(1e-04, 0.09)" - "eta3 ~ fix(1e-04, 1e-04, 0.09)" + "eta1 + eta2 + eta3 ~ fix(0.09, 1e-04, 0.09, 1e-04, 1e-04, 0.09)" Backtrace: ▆ 1. └─nonmem2rx (local) .o(...) at test-omega.R:94:3 2. └─testthat::expect_equal(.nonmem2rx$ini, eq) at test-omega.R:12:5 ── Failure ('test-omega.R:12:5'): test omega ─────────────────────────────────── .nonmem2rx$ini (`actual`) not equal to `eq` (`expected`). actual vs expected - "eta1 ~ fix(0.09)" - "eta2 ~ fix(1e-04, 0.09)" - "eta3 ~ fix(1e-04, 1e-04, 0.09)" + "eta1 + eta2 + eta3 ~ fix(0.09, 1e-04, 0.09, 1e-04, 1e-04, 0.09)" Backtrace: ▆ 1. └─nonmem2rx (local) .o(...) at test-omega.R:103:3 2. └─testthat::expect_equal(.nonmem2rx$ini, eq) at test-omega.R:12:5 ── Failure ('test-omega.R:12:5'): test omega ─────────────────────────────────── .nonmem2rx$ini (`actual`) not equal to `eq` (`expected`). actual vs expected - "eta1 ~ c(eta1 = 0.1)" - "eta2 ~ c(eta1 = 0.01, eta2 = 0.1)" - "eta3 ~ c(eta1 = 0.01, eta2 = 0.01, eta3 = 0.1)" - "eta4 ~ c(eta1 = 0.01, eta2 = 0.01, eta3 = 0.01, eta4 = 0.1)" - "eta5 ~ c(eta1 = 0.01, eta2 = 0.01, eta3 = 0.01, eta4 = 0.01, eta5 = 0.1)" - "eta6 ~ c(eta1 = 0.01, eta2 = 0.01, eta3 = 0.01, eta4 = 0.01, eta5 = 0.01, eta6 = 0.1)" + "eta1 + eta2 + eta3 + eta4 + eta5 + eta6 ~ c(0.1, 0.01, 0.1, 0.01, 0.01, 0.1, 0.01, 0.01, 0.01, 0.1, 0.01, 0.01, 0.01, 0.01, 0.1, 0.01, 0.01, 0.01, 0.01, 0.01, 0.1)" Backtrace: ▆ 1. └─nonmem2rx (local) .o(...) at test-omega.R:107:3 2. └─testthat::expect_equal(.nonmem2rx$ini, eq) at test-omega.R:12:5 ── Failure ('test-omega.R:12:5'): test omega ─────────────────────────────────── .nonmem2rx$ini (`actual`) not equal to `eq` (`expected`). actual vs expected - "eta1 ~ c(eta1 = 0.1)" - "eta2 ~ c(eta1 = 0.01, eta2 = 0.1)" - "eta3 ~ c(eta1 = 0.01, eta2 = 0.01, eta3 = 0.1)" - "eta4 ~ c(eta1 = 0.01, eta2 = 0.01, eta3 = 0.01, eta4 = 0.1)" - "eta5 ~ c(eta1 = 0.01, eta2 = 0.01, eta3 = 0.01, eta4 = 0.01, eta5 = 0.1)" - "eta6 ~ c(eta1 = 0.01, eta2 = 0.01, eta3 = 0.01, eta4 = 0.01, eta5 = 0.01, eta6 = 0.1)" + "eta1 + eta2 + eta3 + eta4 + eta5 + eta6 ~ c(0.1, 0.01, 0.1, 0.01, 0.01, 0.1, 0.01, 0.01, 0.01, 0.1, 0.01, 0.01, 0.01, 0.01, 0.1, 0.01, 0.01, 0.01, 0.01, 0.01, 0.1)" "eta7 ~ 0.02" Backtrace: ▆ 1. └─nonmem2rx (local) .o(...) at test-omega.R:110:3 2. └─testthat::expect_equal(.nonmem2rx$ini, eq) at test-omega.R:12:5 ── Failure ('test-omega.R:12:5'): test omega ─────────────────────────────────── .nonmem2rx$ini (`actual`) not equal to `eq` (`expected`). actual vs expected - "eta1 ~ 0.03" - "eta2 ~ c(0.01, 0.03)" - "eta3 ~ c(0.01, 0.01, 0.03)" - "eta4 ~ c(0.01, 0.01, 0.01, 0.03)" + "eta1 + eta2 + eta3 + eta4 ~ c(0.03, 0.01, 0.03, 0.01, 0.01, 0.03, 0.01, 0.01, 0.01, 0.03)" Backtrace: ▆ 1. └─nonmem2rx (local) .o(...) at test-omega.R:170:3 2. └─testthat::expect_equal(.nonmem2rx$ini, eq) at test-omega.R:12:5 ── Failure ('test-omega.R:12:5'): test omega ─────────────────────────────────── .nonmem2rx$ini (`actual`) not equal to `eq` (`expected`). actual vs expected - "eta1 ~ fix(0.03)" - "eta2 ~ fix(0.01, 0.03)" - "eta3 ~ fix(0.01, 0.01, 0.03)" - "eta4 ~ fix(0.01, 0.01, 0.01, 0.03)" + "eta1 + eta2 + eta3 + eta4 ~ fix(0.03, 0.01, 0.03, 0.01, 0.01, 0.03, 0.01, 0.01, 0.01, 0.03)" Backtrace: ▆ 1. └─nonmem2rx (local) .o(...) at test-omega.R:173:3 2. └─testthat::expect_equal(.nonmem2rx$ini, eq) at test-omega.R:12:5 ── Failure ('test-omega.R:12:5'): test omega ─────────────────────────────────── .nonmem2rx$ini (`actual`) not equal to `eq` (`expected`). actual vs expected - "eta1 ~ fix(0.03)" - "eta2 ~ fix(0.01, 0.03)" - "eta3 ~ fix(0.01, 0.01, 0.03)" - "eta4 ~ fix(0.01, 0.01, 0.01, 0.03)" + "eta1 + eta2 + eta3 + eta4 ~ fix(0.03, 0.01, 0.03, 0.01, 0.01, 0.03, 0.01, 0.01, 0.01, 0.03)" Backtrace: ▆ 1. └─nonmem2rx (local) .o(...) at test-omega.R:176:3 2. └─testthat::expect_equal(.nonmem2rx$ini, eq) at test-omega.R:12:5 ── Failure ('test-omega.R:12:5'): test omega ─────────────────────────────────── .nonmem2rx$ini (`actual`) not equal to `eq` (`expected`). actual vs expected - "eta1 ~ fix(0.03)" - "eta2 ~ fix(0.01, 0.03)" - "eta3 ~ fix(0.01, 0.01, 0.03)" - "eta4 ~ fix(0.01, 0.01, 0.01, 0.03)" + "eta1 + eta2 + eta3 + eta4 ~ fix(0.03, 0.01, 0.03, 0.01, 0.01, 0.03, 0.01, 0.01, 0.01, 0.03)" Backtrace: ▆ 1. └─nonmem2rx (local) .o(...) at test-omega.R:179:3 2. └─testthat::expect_equal(.nonmem2rx$ini, eq) at test-omega.R:12:5 [ FAIL 8 | WARN 2 | SKIP 15 | PASS 751 ] Deleting unused snapshots: • vdiff/first-plot.svg • vdiff/first-pred-plot.svg • vdiff/second-plot-gg-logxy.svg • vdiff/second-plot-gg.svg • vdiff/second-plot-logxy.svg • vdiff/second-plot.svg • vdiff/second-pred-plot-gg-logxy.svg • vdiff/second-pred-plot-gg.svg • vdiff/second-pred-plot-logxy.svg • vdiff/second-pred-plot.svg Error: Test failures Execution halted Package: ruminate Check: package dependencies New result: NOTE Package suggested but not available for checking: ‘nlmixr2lib’