• using R Under development (unstable) (2026-09-11 r90528)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 23.1.1     flang version 23.1.1
• running under: Fedora Linux 44 (Server Edition)
• using session charset: UTF-8 * current time: 2026-09-11 21:30:02 UTC
• using option ‘--no-stop-on-test-error’
• checking for file ‘nonmem2rx/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘nonmem2rx’ version ‘0.1.9’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘nonmem2rx’ can be installed ... [25s/41s] OK See the install log for details.
• used C compiler: ‘clang version 23.1.1’
• used C++ compiler: ‘clang version 23.1.1’
• checking installed package size ... INFO   installed size is 7.6Mb   sub-directories of 1Mb or more:     libs 3.3Mb     mods 3.3Mb
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking whether startup messages can be suppressed ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [18s/28s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [47s/69s] ERROR   Running ‘testthat.R’ [47s/69s] 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 5.1.6 using 2 threads (see ?getRxThreads)     no cache: create with `rxCreateCache()`   > setRxThreads(1L)   > library(data.table)      Attaching package: 'data.table'      The following object is masked from 'package:base':          %notin%      > 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 '/data/localhost/ripley/R/packages/tests-clang/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 '/data/localhost/ripley/R/packages/tests-clang/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   i getting information from '/tmp/RtmpbzLC2Y/working_dir/RtmpctJ3zQ/file65a9d30581797.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 $ABBREVITED   i Processing record $gTHETA   i Processing record $OMEGA   i Processing record $SIGMA   i Processing record $PROBLEM   i Processing record $DATA   i Processing record $SUBROUTINES   i Processing record $PK   i Processing record $ERROR   i Processing record $ESTIMATION   i Ignore record $ESTIMATION   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 '/tmp/RtmpbzLC2Y/working_dir/RtmpctJ3zQ/file65a9d6804376b.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 $ABBREVITED   i Processing record $gTHETA   i Processing record $OMEGA   i Processing record $SIGMA   i Processing record $PROBLEM   i Processing record $DATA   i Processing record $SUBROUTINES   i Processing record $PK   i Processing record $ERROR   i Processing record $ESTIMATION   i Ignore record $ESTIMATION   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                  ^   ================================================================================   Saving _problems/test-eta-order-8.R         $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 ------       [32mAll unit tests passed! [m         $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               ^   ================================================================================    [1mlotri syntax error:   ================================================================================= [0m   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,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  [1m:001 [0m: 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 ~ c(1.30441367197642, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1.58844936874363, 4.85473065684898, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.00539049655208395, -0.0748282195029211, 0.0238050759878246, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -0.0346163870505972, -0.0412181533880286, 0.00156764723796178, 0.00761353116573484, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)    [1m================================================================================= [0m   i try to get covariance a different method (slower)   [ FAIL 1 | WARN 2 | SKIP 16 | PASS 766 ]      ══ Skipped tests (16) ══════════════════════════════════════════════════════════   • On CRAN (16): 'test-as-nonmem2rx.R:2:3', 'test-external-models.R:6:5',     'test-full-parsing.R:8:30', 'test-import-numeric.R:6:3', '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-eta-order.R:7:3'): eta order ─────────────────────────────────   Expected `dimnames(f$omega)[[1]]` to equal `c("BSV.KTR", "BSV.Vp", "BSV.BIO", "BSV.Q", "BSV.CLint", "BSV.Vc")`.   Differences:   `actual`: "BSV.CLint" "BSV.Vc" "BSV.KTR" "BSV.Vp" "BSV.BIO" "BSV.Q"   `expected`: "BSV.KTR" "BSV.Vp" "BSV.BIO" "BSV.Q" "BSV.CLint" "BSV.Vc"         [ FAIL 1 | WARN 2 | SKIP 16 | PASS 766 ]   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', and 'vdiff/second-pred-plot.svg'   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [9s/12s] OK
• checking PDF version of manual ... OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR