==1186447== Memcheck, a memory error detector ==1186447== Copyright (C) 2002-2026, and GNU GPL'd, by Julian Seward et al. ==1186447== Using Valgrind-3.27.1 and LibVEX; rerun with -h for copyright info ==1186447== Command: /data/localhost/ripley/R/R-devel-vg/bin/exec/R -f testthat.R --restore --save --no-readline --vanilla ==1186447== R Under development (unstable) (2026-09-22 r90584) -- "Unsuffered Consequences" Copyright (C) 2026 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # 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) --1186447-- Warning: zero subprog, missing DW_AT_abstract_origin in DW_TAG_inlined_subroutine in /data/localhost/ripley/R/test-dev/rxode2/libs/rxode2.so > library(rxode2) rxode2 5.1.7 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: 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-vg/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-vg/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/RtmpgQkg9p/file121a8f7c7ea04a.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 save model and validation i done i getting information from '/tmp/RtmpgQkg9p/file121a8f39cbb6b0.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 save model and validation i done i $DATA format (3F10.0,2(1X,F5.0)) ignored; data read as delimited i $DATA NOOPEN: data file is not opened by NM-TRAN i $DATA PRED_IGNORE_DATA is not applied when reading input data $DATA syntax error: :001: file.csv IGNORE=(A-EQ-1) ^ ================================================================================ $DATA syntax error: :001: file.csv ACCEPT=(A.EQ.1) (3F10.0) ^ ================================================================================ i $DATA format (3F10.0, 2F5.0) ignored; data read as delimited $DATA syntax error: :001: matt.csv matt=.csv ^ ================================================================================ ==1186447== Invalid read of size 1 ==1186447== at 0x484B7A6: strlen (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/memcheck/../shared/vg_replace_strmem.c:506) ==1186447== by 0x569C3B9: printf_positional (/usr/src/debug/glibc-2.43-8.fc44.x86_64/stdio-common/vfprintf-process-arg.c:443) ==1186447== by 0x569D341: __printf_buffer (/usr/src/debug/glibc-2.43-8.fc44.x86_64/stdio-common/vfprintf-internal.c:1040) ==1186447== by 0x569FAD4: __vfprintf_internal (/usr/src/debug/glibc-2.43-8.fc44.x86_64/stdio-common/vfprintf-internal.c:1563) ==1186447== by 0x56288A: Rvprintf (/data/localhost/ripley/R/svn/R-devel/src/main/printutils.c:993) ==1186447== by 0x56295B: Rprintf (/data/localhost/ripley/R/svn/R-devel/src/main/printutils.c:906) ==1186447== by 0x1A0F787B: nonmem2rx_printErrorInfo (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/parseSyntaxErrors.h:130) ==1186447== by 0x1A0F787B: nonmem2rxSyntaxError (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/parseSyntaxErrors.h:340) ==1186447== by 0x18A6BBCD: error_recovery (/tmp/RtmpN6Ja0E/R.INSTALL23c8dc4391138b/dparser/src/parse.c:1736) ==1186447== by 0x18A6BBCD: exhaustive_parse (/tmp/RtmpN6Ja0E/R.INSTALL23c8dc4391138b/dparser/src/parse.c:1906) ==1186447== by 0x18A6C239: dparse (/tmp/RtmpN6Ja0E/R.INSTALL23c8dc4391138b/dparser/src/parse.c:2142) ==1186447== by 0x1A0F81A0: trans_lst (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/lst.c:166) ==1186447== by 0x1A0F841C: _nonmem2rx_trans_lst (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/lst.c:184) ==1186447== by 0x497029: R_doDotCall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:757) ==1186447== Address 0x1bfd3704 is 2,052 bytes inside a block of size 48,000 free'd ==1186447== at 0x4844D73: free (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/coregrind/m_replacemalloc/vg_replace_malloc.c:950) ==1186447== by 0x1A101170: lineFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/sbuf.c:91) ==1186447== by 0x1A0F843E: nonmem2rx_full_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:42) ==1186447== by 0x1A0F86DA: _nonmem2rx_r_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:102) ==1186447== by 0x497051: R_doDotCall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:751) ==1186447== by 0x497583: do_dotcall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:1437) ==1186447== by 0x4E4D1D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1258) ==1186447== by 0x4E81B3: do_begin (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3001) ==1186447== by 0x4E4A8D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1230) ==1186447== by 0x47D235: Rf_endcontext (/data/localhost/ripley/R/svn/R-devel/src/main/context.c:315) ==1186447== by 0x4E6510: R_execClosure (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2401) ==1186447== by 0x4E72FF: applyClosure_core (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2314) ==1186447== Block was alloc'd at ==1186447== at 0x484962B: calloc (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/coregrind/m_replacemalloc/vg_replace_malloc.c:1616) ==1186447== by 0x521710: R_chk_calloc (/data/localhost/ripley/R/svn/R-devel/src/main/memory.c:3550) ==1186447== by 0x1A101076: lineIni (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/sbuf.c:72) ==1186447== by 0x1A0F85FF: nonmem2rx_full_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:67) ==1186447== by 0x1A0F86DA: _nonmem2rx_r_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:102) ==1186447== by 0x497051: R_doDotCall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:751) ==1186447== by 0x497583: do_dotcall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:1437) ==1186447== by 0x4E4D1D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1258) ==1186447== by 0x4E81B3: do_begin (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3001) ==1186447== by 0x4E4A8D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1230) ==1186447== by 0x47D235: Rf_endcontext (/data/localhost/ripley/R/svn/R-devel/src/main/context.c:315) ==1186447== by 0x4E6510: R_execClosure (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2401) ==1186447== ==1186447== Invalid read of size 1 ==1186447== at 0x484B7B4: strlen (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/memcheck/../shared/vg_replace_strmem.c:506) ==1186447== by 0x569C3B9: printf_positional (/usr/src/debug/glibc-2.43-8.fc44.x86_64/stdio-common/vfprintf-process-arg.c:443) ==1186447== by 0x569D341: __printf_buffer (/usr/src/debug/glibc-2.43-8.fc44.x86_64/stdio-common/vfprintf-internal.c:1040) ==1186447== by 0x569FAD4: __vfprintf_internal (/usr/src/debug/glibc-2.43-8.fc44.x86_64/stdio-common/vfprintf-internal.c:1563) ==1186447== by 0x56288A: Rvprintf (/data/localhost/ripley/R/svn/R-devel/src/main/printutils.c:993) ==1186447== by 0x56295B: Rprintf (/data/localhost/ripley/R/svn/R-devel/src/main/printutils.c:906) ==1186447== by 0x1A0F787B: nonmem2rx_printErrorInfo (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/parseSyntaxErrors.h:130) ==1186447== by 0x1A0F787B: nonmem2rxSyntaxError (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/parseSyntaxErrors.h:340) ==1186447== by 0x18A6BBCD: error_recovery (/tmp/RtmpN6Ja0E/R.INSTALL23c8dc4391138b/dparser/src/parse.c:1736) ==1186447== by 0x18A6BBCD: exhaustive_parse (/tmp/RtmpN6Ja0E/R.INSTALL23c8dc4391138b/dparser/src/parse.c:1906) ==1186447== by 0x18A6C239: dparse (/tmp/RtmpN6Ja0E/R.INSTALL23c8dc4391138b/dparser/src/parse.c:2142) ==1186447== by 0x1A0F81A0: trans_lst (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/lst.c:166) ==1186447== by 0x1A0F841C: _nonmem2rx_trans_lst (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/lst.c:184) ==1186447== by 0x497029: R_doDotCall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:757) ==1186447== Address 0x1bfd3705 is 2,053 bytes inside a block of size 48,000 free'd ==1186447== at 0x4844D73: free (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/coregrind/m_replacemalloc/vg_replace_malloc.c:950) ==1186447== by 0x1A101170: lineFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/sbuf.c:91) ==1186447== by 0x1A0F843E: nonmem2rx_full_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:42) ==1186447== by 0x1A0F86DA: _nonmem2rx_r_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:102) ==1186447== by 0x497051: R_doDotCall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:751) ==1186447== by 0x497583: do_dotcall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:1437) ==1186447== by 0x4E4D1D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1258) ==1186447== by 0x4E81B3: do_begin (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3001) ==1186447== by 0x4E4A8D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1230) ==1186447== by 0x47D235: Rf_endcontext (/data/localhost/ripley/R/svn/R-devel/src/main/context.c:315) ==1186447== by 0x4E6510: R_execClosure (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2401) ==1186447== by 0x4E72FF: applyClosure_core (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2314) ==1186447== Block was alloc'd at ==1186447== at 0x484962B: calloc (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/coregrind/m_replacemalloc/vg_replace_malloc.c:1616) ==1186447== by 0x521710: R_chk_calloc (/data/localhost/ripley/R/svn/R-devel/src/main/memory.c:3550) ==1186447== by 0x1A101076: lineIni (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/sbuf.c:72) ==1186447== by 0x1A0F85FF: nonmem2rx_full_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:67) ==1186447== by 0x1A0F86DA: _nonmem2rx_r_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:102) ==1186447== by 0x497051: R_doDotCall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:751) ==1186447== by 0x497583: do_dotcall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:1437) ==1186447== by 0x4E4D1D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1258) ==1186447== by 0x4E81B3: do_begin (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3001) ==1186447== by 0x4E4A8D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1230) ==1186447== by 0x47D235: Rf_endcontext (/data/localhost/ripley/R/svn/R-devel/src/main/context.c:315) ==1186447== by 0x4E6510: R_execClosure (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2401) ==1186447== ==1186447== Invalid read of size 2 ==1186447== at 0x48501B0: memmove (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/memcheck/../shared/vg_replace_strmem.c:1429) ==1186447== by 0x56943F7: memcpy (/usr/src/debug/glibc-2.43-8.fc44.x86_64/stdio-common/../string/bits/string_fortified.h:29) ==1186447== by 0x56943F7: __printf_buffer_write (/usr/src/debug/glibc-2.43-8.fc44.x86_64/stdio-common/Xprintf_buffer_write.c:39) ==1186447== by 0x569B656: printf_positional (/usr/src/debug/glibc-2.43-8.fc44.x86_64/stdio-common/vfprintf-process-arg.c:471) ==1186447== by 0x569D341: __printf_buffer (/usr/src/debug/glibc-2.43-8.fc44.x86_64/stdio-common/vfprintf-internal.c:1040) ==1186447== by 0x569FAD4: __vfprintf_internal (/usr/src/debug/glibc-2.43-8.fc44.x86_64/stdio-common/vfprintf-internal.c:1563) ==1186447== by 0x56288A: Rvprintf (/data/localhost/ripley/R/svn/R-devel/src/main/printutils.c:993) ==1186447== by 0x56295B: Rprintf (/data/localhost/ripley/R/svn/R-devel/src/main/printutils.c:906) ==1186447== by 0x1A0F787B: nonmem2rx_printErrorInfo (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/parseSyntaxErrors.h:130) ==1186447== by 0x1A0F787B: nonmem2rxSyntaxError (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/parseSyntaxErrors.h:340) ==1186447== by 0x18A6BBCD: error_recovery (/tmp/RtmpN6Ja0E/R.INSTALL23c8dc4391138b/dparser/src/parse.c:1736) ==1186447== by 0x18A6BBCD: exhaustive_parse (/tmp/RtmpN6Ja0E/R.INSTALL23c8dc4391138b/dparser/src/parse.c:1906) ==1186447== by 0x18A6C239: dparse (/tmp/RtmpN6Ja0E/R.INSTALL23c8dc4391138b/dparser/src/parse.c:2142) ==1186447== by 0x1A0F81A0: trans_lst (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/lst.c:166) ==1186447== by 0x1A0F841C: _nonmem2rx_trans_lst (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/lst.c:184) ==1186447== Address 0x1bfd3704 is 2,052 bytes inside a block of size 48,000 free'd ==1186447== at 0x4844D73: free (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/coregrind/m_replacemalloc/vg_replace_malloc.c:950) ==1186447== by 0x1A101170: lineFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/sbuf.c:91) ==1186447== by 0x1A0F843E: nonmem2rx_full_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:42) ==1186447== by 0x1A0F86DA: _nonmem2rx_r_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:102) ==1186447== by 0x497051: R_doDotCall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:751) ==1186447== by 0x497583: do_dotcall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:1437) ==1186447== by 0x4E4D1D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1258) ==1186447== by 0x4E81B3: do_begin (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3001) ==1186447== by 0x4E4A8D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1230) ==1186447== by 0x47D235: Rf_endcontext (/data/localhost/ripley/R/svn/R-devel/src/main/context.c:315) ==1186447== by 0x4E6510: R_execClosure (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2401) ==1186447== by 0x4E72FF: applyClosure_core (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2314) ==1186447== Block was alloc'd at ==1186447== at 0x484962B: calloc (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/coregrind/m_replacemalloc/vg_replace_malloc.c:1616) ==1186447== by 0x521710: R_chk_calloc (/data/localhost/ripley/R/svn/R-devel/src/main/memory.c:3550) ==1186447== by 0x1A101076: lineIni (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/sbuf.c:72) ==1186447== by 0x1A0F85FF: nonmem2rx_full_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:67) ==1186447== by 0x1A0F86DA: _nonmem2rx_r_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:102) ==1186447== by 0x497051: R_doDotCall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:751) ==1186447== by 0x497583: do_dotcall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:1437) ==1186447== by 0x4E4D1D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1258) ==1186447== by 0x4E81B3: do_begin (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3001) ==1186447== by 0x4E4A8D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1230) ==1186447== by 0x47D235: Rf_endcontext (/data/localhost/ripley/R/svn/R-devel/src/main/context.c:315) ==1186447== by 0x4E6510: R_execClosure (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2401) ==1186447== ==1186447== Invalid read of size 2 ==1186447== at 0x48501BE: memmove (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/memcheck/../shared/vg_replace_strmem.c:1429) ==1186447== by 0x56943F7: memcpy (/usr/src/debug/glibc-2.43-8.fc44.x86_64/stdio-common/../string/bits/string_fortified.h:29) ==1186447== by 0x56943F7: __printf_buffer_write (/usr/src/debug/glibc-2.43-8.fc44.x86_64/stdio-common/Xprintf_buffer_write.c:39) ==1186447== by 0x569B656: printf_positional (/usr/src/debug/glibc-2.43-8.fc44.x86_64/stdio-common/vfprintf-process-arg.c:471) ==1186447== by 0x569D341: __printf_buffer (/usr/src/debug/glibc-2.43-8.fc44.x86_64/stdio-common/vfprintf-internal.c:1040) ==1186447== by 0x569FAD4: __vfprintf_internal (/usr/src/debug/glibc-2.43-8.fc44.x86_64/stdio-common/vfprintf-internal.c:1563) ==1186447== by 0x56288A: Rvprintf (/data/localhost/ripley/R/svn/R-devel/src/main/printutils.c:993) ==1186447== by 0x56295B: Rprintf (/data/localhost/ripley/R/svn/R-devel/src/main/printutils.c:906) ==1186447== by 0x1A0F787B: nonmem2rx_printErrorInfo (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/parseSyntaxErrors.h:130) ==1186447== by 0x1A0F787B: nonmem2rxSyntaxError (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/parseSyntaxErrors.h:340) ==1186447== by 0x18A6BBCD: error_recovery (/tmp/RtmpN6Ja0E/R.INSTALL23c8dc4391138b/dparser/src/parse.c:1736) ==1186447== by 0x18A6BBCD: exhaustive_parse (/tmp/RtmpN6Ja0E/R.INSTALL23c8dc4391138b/dparser/src/parse.c:1906) ==1186447== by 0x18A6C239: dparse (/tmp/RtmpN6Ja0E/R.INSTALL23c8dc4391138b/dparser/src/parse.c:2142) ==1186447== by 0x1A0F81A0: trans_lst (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/lst.c:166) ==1186447== by 0x1A0F841C: _nonmem2rx_trans_lst (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/lst.c:184) ==1186447== Address 0x1bfd3708 is 2,056 bytes inside a block of size 48,000 free'd ==1186447== at 0x4844D73: free (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/coregrind/m_replacemalloc/vg_replace_malloc.c:950) ==1186447== by 0x1A101170: lineFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/sbuf.c:91) ==1186447== by 0x1A0F843E: nonmem2rx_full_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:42) ==1186447== by 0x1A0F86DA: _nonmem2rx_r_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:102) ==1186447== by 0x497051: R_doDotCall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:751) ==1186447== by 0x497583: do_dotcall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:1437) ==1186447== by 0x4E4D1D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1258) ==1186447== by 0x4E81B3: do_begin (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3001) ==1186447== by 0x4E4A8D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1230) ==1186447== by 0x47D235: Rf_endcontext (/data/localhost/ripley/R/svn/R-devel/src/main/context.c:315) ==1186447== by 0x4E6510: R_execClosure (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2401) ==1186447== by 0x4E72FF: applyClosure_core (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2314) ==1186447== Block was alloc'd at ==1186447== at 0x484962B: calloc (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/coregrind/m_replacemalloc/vg_replace_malloc.c:1616) ==1186447== by 0x521710: R_chk_calloc (/data/localhost/ripley/R/svn/R-devel/src/main/memory.c:3550) ==1186447== by 0x1A101076: lineIni (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/sbuf.c:72) ==1186447== by 0x1A0F85FF: nonmem2rx_full_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:67) ==1186447== by 0x1A0F86DA: _nonmem2rx_r_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:102) ==1186447== by 0x497051: R_doDotCall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:751) ==1186447== by 0x497583: do_dotcall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:1437) ==1186447== by 0x4E4D1D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1258) ==1186447== by 0x4E81B3: do_begin (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3001) ==1186447== by 0x4E4A8D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1230) ==1186447== by 0x47D235: Rf_endcontext (/data/localhost/ripley/R/svn/R-devel/src/main/context.c:315) ==1186447== by 0x4E6510: R_execClosure (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2401) ==1186447== $TABLE syntax error: ==1186447== Invalid read of size 1 ==1186447== at 0x484B7A6: strlen (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/memcheck/../shared/vg_replace_strmem.c:506) ==1186447== by 0x569C3B9: printf_positional (/usr/src/debug/glibc-2.43-8.fc44.x86_64/stdio-common/vfprintf-process-arg.c:443) ==1186447== by 0x569D341: __printf_buffer (/usr/src/debug/glibc-2.43-8.fc44.x86_64/stdio-common/vfprintf-internal.c:1040) ==1186447== by 0x56C3F38: __vsnprintf_internal (/usr/src/debug/glibc-2.43-8.fc44.x86_64/libio/vsnprintf.c:96) ==1186447== by 0x56C3F38: vsnprintf (/usr/src/debug/glibc-2.43-8.fc44.x86_64/libio/vsnprintf.c:103) ==1186447== by 0x1A100F9B: sAppend (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/sbuf.c:54) ==1186447== by 0x1A0F7924: nonmem2rx_printErrorInfo (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/parseSyntaxErrors.h:133) ==1186447== by 0x1A0F7924: nonmem2rxSyntaxError (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/parseSyntaxErrors.h:340) ==1186447== by 0x18A6BBCD: error_recovery (/tmp/RtmpN6Ja0E/R.INSTALL23c8dc4391138b/dparser/src/parse.c:1736) ==1186447== by 0x18A6BBCD: exhaustive_parse (/tmp/RtmpN6Ja0E/R.INSTALL23c8dc4391138b/dparser/src/parse.c:1906) ==1186447== by 0x18A6C239: dparse (/tmp/RtmpN6Ja0E/R.INSTALL23c8dc4391138b/dparser/src/parse.c:2142) ==1186447== by 0x1A0F81A0: trans_lst (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/lst.c:166) ==1186447== by 0x1A0F841C: _nonmem2rx_trans_lst (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/lst.c:184) ==1186447== by 0x497029: R_doDotCall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:757) ==1186447== by 0x497583: do_dotcall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:1437) ==1186447== Address 0x1bfd3704 is 2,052 bytes inside a block of size 48,000 free'd ==1186447== at 0x4844D73: free (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/coregrind/m_replacemalloc/vg_replace_malloc.c:950) ==1186447== by 0x1A101170: lineFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/sbuf.c:91) ==1186447== by 0x1A0F843E: nonmem2rx_full_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:42) ==1186447== by 0x1A0F86DA: _nonmem2rx_r_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:102) ==1186447== by 0x497051: R_doDotCall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:751) ==1186447== by 0x497583: do_dotcall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:1437) ==1186447== by 0x4E4D1D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1258) ==1186447== by 0x4E81B3: do_begin (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3001) ==1186447== by 0x4E4A8D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1230) ==1186447== by 0x47D235: Rf_endcontext (/data/localhost/ripley/R/svn/R-devel/src/main/context.c:315) ==1186447== by 0x4E6510: R_execClosure (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2401) ==1186447== by 0x4E72FF: applyClosure_core (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2314) ==1186447== Block was alloc'd at ==1186447== at 0x484962B: calloc (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/coregrind/m_replacemalloc/vg_replace_malloc.c:1616) ==1186447== by 0x521710: R_chk_calloc (/data/localhost/ripley/R/svn/R-devel/src/main/memory.c:3550) ==1186447== by 0x1A101076: lineIni (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/sbuf.c:72) ==1186447== by 0x1A0F85FF: nonmem2rx_full_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:67) ==1186447== by 0x1A0F86DA: _nonmem2rx_r_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:102) ==1186447== by 0x497051: R_doDotCall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:751) ==1186447== by 0x497583: do_dotcall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:1437) ==1186447== by 0x4E4D1D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1258) ==1186447== by 0x4E81B3: do_begin (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3001) ==1186447== by 0x4E4A8D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1230) ==1186447== by 0x47D235: Rf_endcontext (/data/localhost/ripley/R/svn/R-devel/src/main/context.c:315) ==1186447== by 0x4E6510: R_execClosure (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2401) ==1186447== ==1186447== Invalid read of size 1 ==1186447== at 0x484B7B4: strlen (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/memcheck/../shared/vg_replace_strmem.c:506) ==1186447== by 0x569C3B9: printf_positional (/usr/src/debug/glibc-2.43-8.fc44.x86_64/stdio-common/vfprintf-process-arg.c:443) ==1186447== by 0x569D341: __printf_buffer (/usr/src/debug/glibc-2.43-8.fc44.x86_64/stdio-common/vfprintf-internal.c:1040) ==1186447== by 0x56C3F38: __vsnprintf_internal (/usr/src/debug/glibc-2.43-8.fc44.x86_64/libio/vsnprintf.c:96) ==1186447== by 0x56C3F38: vsnprintf (/usr/src/debug/glibc-2.43-8.fc44.x86_64/libio/vsnprintf.c:103) ==1186447== by 0x1A100F9B: sAppend (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/sbuf.c:54) ==1186447== by 0x1A0F7924: nonmem2rx_printErrorInfo (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/parseSyntaxErrors.h:133) ==1186447== by 0x1A0F7924: nonmem2rxSyntaxError (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/parseSyntaxErrors.h:340) ==1186447== by 0x18A6BBCD: error_recovery (/tmp/RtmpN6Ja0E/R.INSTALL23c8dc4391138b/dparser/src/parse.c:1736) ==1186447== by 0x18A6BBCD: exhaustive_parse (/tmp/RtmpN6Ja0E/R.INSTALL23c8dc4391138b/dparser/src/parse.c:1906) ==1186447== by 0x18A6C239: dparse (/tmp/RtmpN6Ja0E/R.INSTALL23c8dc4391138b/dparser/src/parse.c:2142) ==1186447== by 0x1A0F81A0: trans_lst (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/lst.c:166) ==1186447== by 0x1A0F841C: _nonmem2rx_trans_lst (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/lst.c:184) ==1186447== by 0x497029: R_doDotCall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:757) ==1186447== by 0x497583: do_dotcall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:1437) ==1186447== Address 0x1bfd3705 is 2,053 bytes inside a block of size 48,000 free'd ==1186447== at 0x4844D73: free (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/coregrind/m_replacemalloc/vg_replace_malloc.c:950) ==1186447== by 0x1A101170: lineFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/sbuf.c:91) ==1186447== by 0x1A0F843E: nonmem2rx_full_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:42) ==1186447== by 0x1A0F86DA: _nonmem2rx_r_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:102) ==1186447== by 0x497051: R_doDotCall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:751) ==1186447== by 0x497583: do_dotcall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:1437) ==1186447== by 0x4E4D1D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1258) ==1186447== by 0x4E81B3: do_begin (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3001) ==1186447== by 0x4E4A8D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1230) ==1186447== by 0x47D235: Rf_endcontext (/data/localhost/ripley/R/svn/R-devel/src/main/context.c:315) ==1186447== by 0x4E6510: R_execClosure (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2401) ==1186447== by 0x4E72FF: applyClosure_core (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2314) ==1186447== Block was alloc'd at ==1186447== at 0x484962B: calloc (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/coregrind/m_replacemalloc/vg_replace_malloc.c:1616) ==1186447== by 0x521710: R_chk_calloc (/data/localhost/ripley/R/svn/R-devel/src/main/memory.c:3550) ==1186447== by 0x1A101076: lineIni (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/sbuf.c:72) ==1186447== by 0x1A0F85FF: nonmem2rx_full_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:67) ==1186447== by 0x1A0F86DA: _nonmem2rx_r_parseFree (/data/localhost/ripley/R/packages/tests-vg/nonmem2rx/src/mem.c:102) ==1186447== by 0x497051: R_doDotCall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:751) ==1186447== by 0x497583: do_dotcall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:1437) ==1186447== by 0x4E4D1D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1258) ==1186447== by 0x4E81B3: do_begin (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3001) ==1186447== by 0x4E4A8D: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1230) ==1186447== by 0x47D235: Rf_endcontext (/data/localhost/ripley/R/svn/R-devel/src/main/context.c:315) ==1186447== by 0x4E6510: R_execClosure (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2401) ==1186447== :001: + :001: + 3.0000E+00 4.0000E+00 ================================================================================ i getting information from '/tmp/RtmpgQkg9p/file121a8f11ca390f.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 $MODEL 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 $DES i Processing record $ERROR i Processing record $ESTIMATION i Ignore record $ESTIMATION i final parameters not updated, will skip validation i changing most variables to lower case i done i replace theta names i done (no labels) i replace eta names i done (no labels) i renaming compartments i done $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 ^ ================================================================================ i read in nonmem input data (for model validation): /tmp/RtmpgQkg9p/file121a8f10ed4392/data.csv i applying names specified by $INPUT i renaming 'ytype' to 'nmytype' i renaming 'dur' to 'rxDur' i done :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 0 | WARN 10 | SKIP 32 | PASS 1000 ] ══ Skipped tests (32) ══════════════════════════════════════════════════════════ • On CRAN (29): 'test-advan5.R:152:3', 'test-as-nonmem2rx.R:2:3', 'test-dde.R:187:5', 'test-dde.R:201:5', 'test-dde.R:217:5', 'test-dde.R:229:5', 'test-dde.R:262:5', 'test-external-models.R:6:5', 'test-full-parsing.R:8:30', 'test-grammar-scaling.R:14:3', 'test-import-numeric.R:6:3', 'test-linCmt.R:2:3', 'test-mix.R:63:3', 'test-mix.R:88:3', 'test-model-load.R:7:5', 'test-nm75.R:7:5', 'test-piping.R:7:5', 'test-piping.R:46:5', 'test-print.R:2:3', 'test-read-nonmemData.R:3:5', 'test-read-nonmemData.R:19:5', 'test-read-nonmemData.R:49:5', 'test-rename.R:7:5', 'test-rxsolve.R:11:5', 'test-sim-iwres.R:2:3', 'test-sim-iwres.R:62:3', 'test-tad-alias.R:30:3', 'test-vdiff.R:2:3', 'test-vdiff.R:51:3' • Requires ~2.5GB RAM to construct a 2.147 GB identifier string that triggers integer overflow in buffer size calculation (1): 'test-mem-sbuf-overflow.R:2:3' • Requires ~2GB free RAM to construct a >INT_MAX-byte input string (1): 'test-mem-rc-dup-str.R:17:3' • Requires ~3GB free RAM; fix pending dparser-R udparse() CRAN release (1): 'test-mem-dparse-int-cast.R:22:3' [ FAIL 0 | WARN 10 | SKIP 32 | PASS 1000 ] Deleting unused snapshots: 'vdiff/first-plot.svg', 'vdiff/first-pred-plot.svg', 'vdiff/multiple-endpoint-page-plot.svg', 'vdiff/multiple-endpoint-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' > > proc.time() user system elapsed 4398.723 33.005 4472.397 ==1186447== ==1186447== HEAP SUMMARY: ==1186447== in use at exit: 316,964,274 bytes in 104,117 blocks ==1186447== total heap usage: 311,344,605 allocs, 311,240,488 frees, 28,740,135,305 bytes allocated ==1186447== ==1186447== 112 bytes in 1 blocks are definitely lost in loss record 154 of 5,313 ==1186447== at 0x484962B: calloc (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/coregrind/m_replacemalloc/vg_replace_malloc.c:1616) ==1186447== by 0x197C9A17: ensureRworkPool (/tmp/RtmpOsDzHZ/R.INSTALL2c970161310284/rxode2/src/par_solve.cpp:157) ==1186447== by 0x199BB68E: rxSolve_(Rcpp::RObject_Impl const&, Rcpp::Vector<19, Rcpp::PreserveStorage> const&, Rcpp::Nullable > const&, Rcpp::Nullable > const&, Rcpp::RObject_Impl const&, Rcpp::RObject_Impl const&, Rcpp::RObject_Impl const&, int) (/tmp/RtmpOsDzHZ/R.INSTALL2c970161310284/rxode2/src/rxData.cpp:6893) ==1186447== by 0x199C51E9: rxSolveSEXP(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*) (/tmp/RtmpOsDzHZ/R.INSTALL2c970161310284/rxode2/src/rxData.cpp:7904) ==1186447== by 0x1936C66F: _rxode2_rxSolveSEXP_try(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*) (/tmp/RtmpOsDzHZ/R.INSTALL2c970161310284/rxode2/src/RcppExports.cpp:1557) ==1186447== by 0x1936C7EA: _rxode2_rxSolveSEXP (/tmp/RtmpOsDzHZ/R.INSTALL2c970161310284/rxode2/src/RcppExports.cpp:1565) ==1186447== by 0x496F67: R_doDotCall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:780) ==1186447== by 0x4D4E5A: bcEval_loop (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8704) ==1186447== by 0x4E4301: bcEval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7533) ==1186447== by 0x4E4301: bcEval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7518) ==1186447== by 0x4E46CA: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167) ==1186447== by 0x4E6566: R_execClosure (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2398) ==1186447== by 0x4E72FF: applyClosure_core (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2314) ==1186447== ==1186447== 1,080 bytes in 1 blocks are definitely lost in loss record 581 of 5,313 ==1186447== at 0x484962B: calloc (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/coregrind/m_replacemalloc/vg_replace_malloc.c:1616) ==1186447== by 0x197C99DF: ensureRworkPool (/tmp/RtmpOsDzHZ/R.INSTALL2c970161310284/rxode2/src/par_solve.cpp:144) ==1186447== by 0x199BB68E: rxSolve_(Rcpp::RObject_Impl const&, Rcpp::Vector<19, Rcpp::PreserveStorage> const&, Rcpp::Nullable > const&, Rcpp::Nullable > const&, Rcpp::RObject_Impl const&, Rcpp::RObject_Impl const&, Rcpp::RObject_Impl const&, int) (/tmp/RtmpOsDzHZ/R.INSTALL2c970161310284/rxode2/src/rxData.cpp:6893) ==1186447== by 0x199C51E9: rxSolveSEXP(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*) (/tmp/RtmpOsDzHZ/R.INSTALL2c970161310284/rxode2/src/rxData.cpp:7904) ==1186447== by 0x1936C66F: _rxode2_rxSolveSEXP_try(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*) (/tmp/RtmpOsDzHZ/R.INSTALL2c970161310284/rxode2/src/RcppExports.cpp:1557) ==1186447== by 0x1936C7EA: _rxode2_rxSolveSEXP (/tmp/RtmpOsDzHZ/R.INSTALL2c970161310284/rxode2/src/RcppExports.cpp:1565) ==1186447== by 0x496F67: R_doDotCall (/data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:780) ==1186447== by 0x4D4E5A: bcEval_loop (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8704) ==1186447== by 0x4E4301: bcEval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7533) ==1186447== by 0x4E4301: bcEval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7518) ==1186447== by 0x4E46CA: Rf_eval (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167) ==1186447== by 0x4E6566: R_execClosure (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2398) ==1186447== by 0x4E72FF: applyClosure_core (/data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2314) ==1186447== ==1186447== 4,040 (2,232 direct, 1,808 indirect) bytes in 1 blocks are definitely lost in loss record 770 of 5,313 ==1186447== at 0x484962B: calloc (/builddir/build/BUILD/valgrind-3.27.1-build/valgrind-3.27.1/coregrind/m_replacemalloc/vg_replace_malloc.c:1616) ==1186447== by 0x1970F666: lsoda_prepare (/tmp/RtmpOsDzHZ/R.INSTALL2c970161310284/rxode2/src/lsoda.c:469) ==1186447== by 0x19820076: ind_liblsoda0 (/tmp/RtmpOsDzHZ/R.INSTALL2c970161310284/rxode2/src/par_solve.cpp:4731) ==1186447== by 0x19820A18: par_liblsoda._omp_fn.0 (/tmp/RtmpOsDzHZ/R.INSTALL2c970161310284/rxode2/src/par_solve.cpp:5133) ==1186447== by 0x560D2F5: GOMP_parallel (/usr/src/debug/gcc-16.2.1-2.fc44.x86_64/obj-x86_64-redhat-linux/x86_64-redhat-linux/libgomp/../../../libgomp/parallel.c:178) ==1186447== by 0x197B028A: par_liblsoda (/tmp/RtmpOsDzHZ/R.INSTALL2c970161310284/rxode2/src/par_solve.cpp:5122) ==1186447== by 0x198EBAE8: par_solve (/tmp/RtmpOsDzHZ/R.INSTALL2c970161310284/rxode2/src/par_solve.cpp:8103) ==1186447== by 0x1999CD91: rxSolve_finalize(Rcpp::RObject_Impl const&, Rcpp::Vector<19, Rcpp::PreserveStorage> const&, Rcpp::Nullable > const&, Rcpp::Nullable > const&, Rcpp::RObject_Impl const&, Rcpp::RObject_Impl const&, Rcpp::RObject_Impl const&, rxSolve_t*) (/tmp/RtmpOsDzHZ/R.INSTALL2c970161310284/rxode2/src/rxData.cpp:5965) ==1186447== by 0x199BDBA4: rxSolve_(Rcpp::RObject_Impl const&, Rcpp::Vector<19, Rcpp::PreserveStorage> const&, Rcpp::Nullable > const&, Rcpp::Nullable > const&, Rcpp::RObject_Impl const&, Rcpp::RObject_Impl const&, Rcpp::RObject_Impl const&, int) (/tmp/RtmpOsDzHZ/R.INSTALL2c970161310284/rxode2/src/rxData.cpp:7385) ==1186447== by 0x199C51E9: rxSolveSEXP(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*) (/tmp/RtmpOsDzHZ/R.INSTALL2c970161310284/rxode2/src/rxData.cpp:7904) ==1186447== by 0x1936C66F: _rxode2_rxSolveSEXP_try(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*) (/tmp/RtmpOsDzHZ/R.INSTALL2c970161310284/rxode2/src/RcppExports.cpp:1557) ==1186447== by 0x1936C7EA: _rxode2_rxSolveSEXP (/tmp/RtmpOsDzHZ/R.INSTALL2c970161310284/rxode2/src/RcppExports.cpp:1565) ==1186447== ==1186447== LEAK SUMMARY: ==1186447== definitely lost: 3,424 bytes in 3 blocks ==1186447== indirectly lost: 1,808 bytes in 1 blocks ==1186447== possibly lost: 0 bytes in 0 blocks ==1186447== still reachable: 316,959,042 bytes in 104,113 blocks ==1186447== suppressed: 0 bytes in 0 blocks ==1186447== Reachable blocks (those to which a pointer was found) are not shown. ==1186447== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==1186447== ==1186447== For lists of detected and suppressed errors, rerun with: -s ==1186447== ERROR SUMMARY: 33 errors from 9 contexts (suppressed: 0 from 0)