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The RPM package version of Flint fails to produce simulation output on CentOS 7.
For example, I could not render the line graph of the simulation result with test/models/lorenz.phml.

https://www.wxwidgets.org/news/2022/09/wxwidgets-3.2.1-released/

Issue opened as part of the JOSS review (openjournals/joss-reviews#2331)

Here are a few issues I noticed in the user manual:

• The user manual does not seem to mention the parameter fitting functionality
• It seems that the command-line interface has less functionality than the GUI. This should be clearly stated in the user manual and elsewhere (e.g. the github README currently states: "It provides graphical user interface on top of command-line interface")
• 3.4.7 (p.11): "accepts a formula (in an infix notation)" – this is a bit odd, would a user expect e.g. postfix notation? Also, formula here just refers to an arithmetic expression, and not to arbitrary formulas (using exp, sqrt, ...) I imagine? If there is support for a power operation, does it use "^" or another symbol?
• 3.4.7. (p.11): The documentation talks about "value-sets" but it seems that in the application they are actually called "parameter sets". Also, the software asks whether to create a "parameter", "product", or "zip" after selecting "Define parameter set" – the documentation only talks about the "parameter" functionality, as far as I can see.
• The installation creates additional command-line binaries (flint-cli, flint-run, flint-tr, ...), but these are not mentioned in the user manual and only have very brief README files. Are these only meant for internal use?

Minor issues/typos:

• 1.1 (p.3): "...via an external program such as gnuplot" – I think gnuplot is the only program that is directly supported?
• 2.2 (p.5): broken link to Figure
• 3.4.1 (p.9): "simulatoin" → "simulation"
• 3.4.6 (p.10): "matching its properties, such as name" – what other properties can be matched? Is using a pattern the only way to specify the outputs, or can you also select them directly in the GUI?
• 3.6.2 (p.13): "these operation" → "this operation"
• 3.10.2 (p.15): at least on Linux, it does not seem to be necessary to specify the path to gnuplot

Exporting one result is OK.

This is a to-do.

See the attached figure. It is annoying as the Run button turns off after the error and cannot be re-enabled. The cause is a bug of the formula parser.
A workaround is to put spaces between "+" and the following number, like "x+ 1".

Reproducible by loading test/models/gaussian.isml. Other variates such as lognormal, weibull, etc. are OK.

This is a to-do.

... not only in PDF. Suggested in openjournals/joss-reviews#2331 (comment).

Suggested in openjournals/joss-reviews#2331 (comment).
wxWidgets' wxUIActionSimulator may help.

This is a to-do.

See the report:
flint.log

It's 100% reproducible on macOS High Sierra:

1. load a model and go to "Parameters" tab
2. Click "Edit parameter set"
3. Add a parameter and focus on the name part, as in the following screenshot.
4. Click the "-" button (then a dialog appears)
5. Confirm "Yes" on the dialog

Irreproducible on Windows and Linux.

This is another TODO.

... instead of reinterpret_cast, once we migrate C++20 or later.
Reference: https://eel.is/c++draft/bit.cast

This is a to-do.

GCC 10 fails to build SOSlib.

/usr/bin/ld: options.o:/home/abe/rpmbuild/BUILD/flint-soslib-1.9.0/odeSolver/options.h:61: multiple definition of `Opt'; commandLine.o:/home/abe/rpmbuild/BUILD/flint-soslib-1.9.0/odeSolver/options.h:61: first defined here

/usr/bin/ld: printModel.o:/home/abe/rpmbuild/BUILD/flint-soslib-1.9.0/odeSolver/options.h:61: multiple definition of `Opt'; commandLine.o:/home/abe/rpmbuild/BUILD/flint-soslib-1.9.0/odeSolver/options.h:61: first defined here

/usr/bin/ld: interactive.o:/home/abe/rpmbuild/BUILD/flint-soslib-1.9.0/odeSolver/options.h:61: multiple definition of `Opt'; commandLine.o:/home/abe/rpmbuild/BUILD/flint-soslib-1.9.0/odeSolver/options.h:61: first defined here

collect2: error: ld returned 1 exit status

make[2]: *** [Makefile:449: odeSolver] Error 1

make[2]: Leaving directory '/home/abe/rpmbuild/BUILD/flint-soslib-1.9.0/odeSolver'

make[1]: *** [Makefile:459: all-recursive] Error 1

make[1]: Leaving directory '/home/abe/rpmbuild/BUILD/flint-soslib-1.9.0'

error: Bad exit status from /var/tmp/rpm-tmp.6iSiUV (%build)





RPM build errors:

    Bad exit status from /var/tmp/rpm-tmp.6iSiUV (%build)

make: *** [Makefile:179: /home/abe/rpmbuild/RPMS/x86_64/flint-soslib-1.9.0-1.fc32.x86_64.rpm] Error 1

Check if

• building Flint works,
• make check passes, and
• the program runs as expected.

Check if

• building Flint works,
• make check passes, and
• the program runs as expected.

We wait for fix of https://trac.wxwidgets.org/ticket/16116.

The installed binary fails to launch with the following error:

Process: flint [27882]
Path: /Applications/Flint.app/Contents/MacOS/flint
Identifier: jp.physiome.flint
Version: 2.1.0 (2.1.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: flint [27882]
User ID: 504

Date/Time: 2019-02-01 17:42:03.855 +0900
OS Version: Mac OS X 10.12.6 (16G1510)
Report Version: 12
Anonymous UUID: BC62780F-AD78-90AB-749C-FED6EBE2C461

Time Awake Since Boot: 6400000 seconds

System Integrity Protection: enabled

Crashed Thread: 0

Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFY

Termination Reason: DYLD, [0x1] Library missing

Application Specific Information:
dyld: launch, loading dependent libraries

Dyld Error Message:
Library not loaded: /opt/local/lib/libuuid.16.dylib
Referenced from: /Applications/Flint.app/Contents/MacOS/flint
Reason: image not found

Binary Images:
0x10a4af000 - 0x10a5feff7 +jp.physiome.flint (2.1.0 - 2.1.0) /Applications/Flint.app/Contents/MacOS/flint
0x10a730000 - 0x10acdcff7 +libflintxx.0.dylib (0) <82D39042-F5D0-3143-BFF8-6EAA33228FF8> /Applications/Flint.app/Contents/Frameworks/libflintxx.0.dylib
0x10ba58000 - 0x10ba59ff3 +libflint.0.dylib (0) /Applications/Flint.app/Contents/Frameworks/libflint.0.dylib
0x10ba62000 - 0x10ba94ffb +libODES.0.dylib (0) <65424862-5DA3-3B40-9505-E39277E4F059> /Applications/Flint.app/Contents/Frameworks/libODES.0.dylib
0x10baa6000 - 0x10c0bafff +libsbml.5.17.0.dylib (0) /Applications/Flint.app/Contents/Frameworks/libsbml.5.17.0.dylib
0x10c276000 - 0x10c2b1fff +libsundials_arkode.1.dylib (0) <02103D80-2F0E-3188-91F1-8CCF279C6983> /Applications/Flint.app/Contents/Frameworks/libsundials_arkode.1.dylib
0x10c2bf000 - 0x10c2e1ffb +libsundials_cvode.2.dylib (0) <5414D37F-C785-3817-AE77-4D6A383FB3EF> /Applications/Flint.app/Contents/Frameworks/libsundials_cvode.2.dylib
0x10c2eb000 - 0x10c329fff +libsundials_cvodes.2.dylib (0) <480C892D-2890-3BA1-9C9F-D92A683578B3> /Applications/Flint.app/Contents/Frameworks/libsundials_cvodes.2.dylib
0x10c337000 - 0x10c358ff3 +libsundials_ida.2.dylib (0) /Applications/Flint.app/Contents/Frameworks/libsundials_ida.2.dylib
0x10c35f000 - 0x10c37bff7 +libsundials_kinsol.2.dylib (0) <88F135D0-676F-34C2-BE3E-B6641536971C> /Applications/Flint.app/Contents/Frameworks/libsundials_kinsol.2.dylib
0x10c382000 - 0x10c385fff +libsundials_nvecserial.2.dylib (0) /Applications/Flint.app/Contents/Frameworks/libsundials_nvecserial.2.dylib
0x10c38f000 - 0x10c39fffb +libsedml.0.dylib (0) <9A54CC57-09DC-38BE-B8D7-0DA007945504> /Applications/Flint.app/Contents/Frameworks/libsedml.0.dylib
0x10c3a4000 - 0x10c41effb +libczmq.4.dylib (0) /Applications/Flint.app/Contents/Frameworks/libczmq.4.dylib
0x1112c0000 - 0x1112fddc7 dyld (433.5) <322C06B7-8878-311D-888C-C8FD2CA96FF3> /usr/lib/dyld

Model: MacPro6,1, BootROM MP61.0124.B00, 8 processors, 8-Core Intel Xeon E5, 3 GHz, 64 GB, SMC 2.20f18
Graphics: AMD FirePro D500, AMD FirePro D500, PCIe, 3072 MB
Graphics: AMD FirePro D500, AMD FirePro D500, PCIe, 3072 MB
Memory Module: DIMM1, 16 GB, DDR3 ECC, 1866 MHz, 0x80AD, 0x484D54343247523742465234432D52442020
Memory Module: DIMM2, 16 GB, DDR3 ECC, 1866 MHz, 0x80AD, 0x484D54343247523742465234432D52442020
Memory Module: DIMM3, 16 GB, DDR3 ECC, 1866 MHz, 0x80AD, 0x484D54343247523742465234432D52442020
Memory Module: DIMM4, 16 GB, DDR3 ECC, 1866 MHz, 0x80AD, 0x484D54343247523742465234432D52442020
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x135), Broadcom BCM43xx 1.0 (7.21.171.133.1a2)
Bluetooth: Version 5.0.5f3, 3 services, 27 devices, 1 incoming serial ports
Network Service: Ethernet 1, Ethernet, en0
PCI Card: AMD FirePro D500, Display Controller, Slot-1
PCI Card: AMD FirePro D500, Display Controller, Slot-2
PCI Card: pci1b4b,9220, AHCI Controller, Thunderbolt@236,0,0
Serial ATA Device: APPLE SSD SM0512G, 500.28 GB
Serial ATA Device: LaCie 2big v2 THB USB3 Raid 1, 4 TB
Serial ATA Device: MARVELL VIRTUAL
USB Device: USB 2.0 Bus
USB Device: Hub
USB Device: BRCM20702 Hub
USB Device: Bluetooth USB Host Controller
USB Device: USB 3.0 Bus
USB Device: Hub
USB Device: USB Keyboard
Thunderbolt Bus: Mac Pro, Apple Inc., 19.2
Thunderbolt Bus: Mac Pro, Apple Inc., 19.2
Thunderbolt Bus: Mac Pro, Apple Inc., 19.2
Thunderbolt Device: 2big TBT2 USB3, LaCie, 1, 22.1

This is a to-do.

Issue opened as part of the JOSS review (openjournals/joss-reviews#2331)

I was able to compile the software from source given the instructions in INSTALL.org on Ubuntu 18.04.

I think this document should also mention how to run the test suite (if I am not mistaken, running make check in posix/var/sequential-version/test will do it).

As a minor suggestion: I think it should more clearly mention that before running the build commands, you have to install the prerequisites for your platform. Currently it reads a bit odd: "This is the command to build it: .... Before running the above command, you have to do this: ..."

It occurred at linking SOSlib to libSBML.

Environment:
macOS 11.4; MacBook Pro (13-inch, M1, 2020)
Xcode 12.5.1

mv -f .deps/sensSolver.Tpo .deps/sensSolver.Plo
/bin/sh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I/Users/abe/src/Flint/xcode/usr/include -I/Users/abe/src/Flint/xcode/usr/include -Wno-unknown-pragmas -Wall -Wextra -ansi -std=iso9899:1990 -arch x86_64 -mmacosx-version-min=10.11 -O2 -g -MT solverError.lo -MD -MP -MF .deps/solverError.Tpo -c -o solverError.lo solverError.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -I/Users/abe/src/Flint/xcode/usr/include -I/Users/abe/src/Flint/xcode/usr/include -Wno-unknown-pragmas -Wall -Wextra -ansi -std=iso9899:1990 -arch x86_64 -mmacosx-version-min=10.11 -O2 -g -MT solverError.lo -MD -MP -MF .deps/solverError.Tpo -c solverError.c -fno-common -DPIC -o .libs/solverError.o
mv -f .deps/solverError.Tpo .deps/solverError.Plo
/bin/sh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I/Users/abe/src/Flint/xcode/usr/include -I/Users/abe/src/Flint/xcode/usr/include -Wno-unknown-pragmas -Wall -Wextra -ansi -std=iso9899:1990 -arch x86_64 -mmacosx-version-min=10.11 -O2 -g -MT util.lo -MD -MP -MF .deps/util.Tpo -c -o util.lo util.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -I/Users/abe/src/Flint/xcode/usr/include -I/Users/abe/src/Flint/xcode/usr/include -Wno-unknown-pragmas -Wall -Wextra -ansi -std=iso9899:1990 -arch x86_64 -mmacosx-version-min=10.11 -O2 -g -MT util.lo -MD -MP -MF .deps/util.Tpo -c util.c -fno-common -DPIC -o .libs/util.o
mv -f .deps/util.Tpo .deps/util.Plo
/bin/sh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I/Users/abe/src/Flint/xcode/usr/include -I/Users/abe/src/Flint/xcode/usr/include -Wno-unknown-pragmas -Wall -Wextra -ansi -std=iso9899:1990 -arch x86_64 -mmacosx-version-min=10.11 -O2 -g -MT data.lo -MD -MP -MF .deps/data.Tpo -c -o data.lo test -f 'private/data.c' || echo './'private/data.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -I/Users/abe/src/Flint/xcode/usr/include -I/Users/abe/src/Flint/xcode/usr/include -Wno-unknown-pragmas -Wall -Wextra -ansi -std=iso9899:1990 -arch x86_64 -mmacosx-version-min=10.11 -O2 -g -MT data.lo -MD -MP -MF .deps/data.Tpo -c private/data.c -fno-common -DPIC -o .libs/data.o
mv -f .deps/data.Tpo .deps/data.Plo
/bin/sh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I/Users/abe/src/Flint/xcode/usr/include -I/Users/abe/src/Flint/xcode/usr/include -Wno-unknown-pragmas -Wall -Wextra -ansi -std=iso9899:1990 -arch x86_64 -mmacosx-version-min=10.11 -O2 -g -MT error.lo -MD -MP -MF .deps/error.Tpo -c -o error.lo test -f 'private/error.c' || echo './'private/error.c
libtool: compile: clang -DHAVE_CONFIG_H -I. -I/Users/abe/src/Flint/xcode/usr/include -I/Users/abe/src/Flint/xcode/usr/include -Wno-unknown-pragmas -Wall -Wextra -ansi -std=iso9899:1990 -arch x86_64 -mmacosx-version-min=10.11 -O2 -g -MT error.lo -MD -MP -MF .deps/error.Tpo -c private/error.c -fno-common -DPIC -o .libs/error.o
mv -f .deps/error.Tpo .deps/error.Plo
/bin/sh ../libtool --tag=CC --mode=link clang -Wno-unknown-pragmas -Wall -Wextra -ansi -std=iso9899:1990 -arch x86_64 -mmacosx-version-min=10.11 -O2 -g -no-undefined -L/Users/abe/src/Flint/xcode/usr/lib -L/usr/lib -L/Users/abe/src/Flint/xcode/usr/lib -arch x86_64 -mmacosx-version-min=10.11 -headerpad_max_install_names -o libODES.la -rpath /Users/abe/src/Flint/xcode/usr/lib ASTIndexNameNode.lo arithmeticCompiler.lo charBuffer.lo compiler.lo cvodeData.lo cvodeSolver.lo daeSolver.lo drawGraph.lo evaluateAST.lo integratorInstance.lo integratorSettings.lo interpol.lo modelSimplify.lo nullSolver.lo odeConstruct.lo odeModel.lo odeSolver.lo processAST.lo sbml.lo sbmlResults.lo sensSolver.lo solverError.lo util.lo data.lo error.lo -lsbml -lxml2 -lsundials_ida -lsundials_kinsol -lsundials_cvodes -lsundials_nvecserial -lm -lm
libtool: link: clang -dynamiclib -o .libs/libODES.0.dylib .libs/ASTIndexNameNode.o .libs/arithmeticCompiler.o .libs/charBuffer.o .libs/compiler.o .libs/cvodeData.o .libs/cvodeSolver.o .libs/daeSolver.o .libs/drawGraph.o .libs/evaluateAST.o .libs/integratorInstance.o .libs/integratorSettings.o .libs/interpol.o .libs/modelSimplify.o .libs/nullSolver.o .libs/odeConstruct.o .libs/odeModel.o .libs/odeSolver.o .libs/processAST.o .libs/sbml.o .libs/sbmlResults.o .libs/sensSolver.o .libs/solverError.o .libs/util.o .libs/data.o .libs/error.o -L/Users/abe/src/Flint/xcode/usr/lib -L/usr/lib /Users/abe/src/Flint/xcode/usr/lib/libsbml.dylib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/lib -lz -lpthread -licucore -lc++ -lxml2 -lsundials_ida -lsundials_kinsol -lsundials_cvodes -lsundials_nvecserial -lm -arch x86_64 -mmacosx-version-min=10.11 -O2 -g -arch x86_64 -mmacosx-version-min=10.11 -install_name /Users/abe/src/Flint/xcode/usr/lib/libODES.0.dylib -compatibility_version 1 -current_version 1.0 -Wl,-single_module
Undefined symbols for architecture x86_64:
"_ASTNode_addChild", referenced from:
_AST_replaceNameByFormula in modelSimplify.o
_Species_odeFromReactions in odeConstruct.o
_differentiateAST in processAST.o
_simplifyAST in processAST.o
_determinantNAST in processAST.o
_indexAST in processAST.o
_copyRevertDataAST in sensSolver.o
...
"_ASTNode_create", referenced from:
_Species_odeFromReactions in odeConstruct.o
_differentiateAST in processAST.o
_simplifyAST in processAST.o
_determinantNAST in processAST.o
_indexAST in processAST.o
_copyRevertDataAST in sensSolver.o
(maybe you meant: _ASTNode_createIndexName)
"_ASTNode_createWithType", referenced from:
_ASTNode_createIndexName in ASTIndexNameNode.o
_Species_odeFromReactions in odeConstruct.o
"_ASTNode_deepCopy", referenced from:
_copyAST in processAST.o
_differentiateAST in processAST.o
_simplifyAST in processAST.o
_determinantNAST in processAST.o
"_ASTNode_free", referenced from:
_AST_replaceFunctionDefinition in modelSimplify.o
_Model_reduceToOdes in odeConstruct.o
_Species_odeFromReactions in odeConstruct.o
_ODEModel_freeDiscontinuities in odeModel.o
_ODEModel_free in odeModel.o
_ODEModel_freeJacobian in odeModel.o
_ODEModel_constructJacobian in odeModel.o
...
"_ASTNode_getChild", referenced from:
_evaluateAST in evaluateAST.o
_AST_replaceNameByFormula in modelSimplify.o
_AST_replaceFunctionDefinition in modelSimplify.o
_Species_odeFromReactions in odeConstruct.o
_differentiateAST in processAST.o
_simplifyAST in processAST.o
_determinantNAST in processAST.o
...
"_ASTNode_getInteger", referenced from:
_evaluateAST in evaluateAST.o
_AST_replaceNameByFormula in modelSimplify.o
_AST_replaceFunctionDefinition in modelSimplify.o
_Model_reduceToOdes in odeConstruct.o
_ODEModel_constructJacobian in odeModel.o
_ODESense_create in odeModel.o
_ODEModel_compileCVODEFunctions in odeModel.o
...
"_ASTNode_getLeftChild", referenced from:
_simplifyAST in processAST.o
"_ASTNode_getListOfNodes", referenced from:
_AST_replaceNameByName in modelSimplify.o
_AST_replaceNameByValue in modelSimplify.o
_AST_replaceNameByParameters in modelSimplify.o
_AST_replaceNameByFormula in modelSimplify.o
_AST_replaceFunctionDefinition in modelSimplify.o
_ODEModel_constructJacobian in odeModel.o
_ODESense_create in odeModel.o
...
"_ASTNode_getName", referenced from:
_evaluateAST in evaluateAST.o
_AST_replaceNameByName in modelSimplify.o
_AST_replaceNameByValue in modelSimplify.o
_AST_replaceNameByParameters in modelSimplify.o
_AST_replaceNameByFormula in modelSimplify.o
_AST_replaceFunctionDefinition in modelSimplify.o
_ODEModel_constructJacobian in odeModel.o
...
"_ASTNode_getNumChildren", referenced from:
_evaluateAST in evaluateAST.o
_AST_replaceNameByFormula in modelSimplify.o
_AST_replaceFunctionDefinition in modelSimplify.o
_differentiateAST in processAST.o
_simplifyAST in processAST.o
_indexAST in processAST.o
_ASTNode_getIndices in processAST.o
...
"_ASTNode_getReal", referenced from:
_evaluateAST in evaluateAST.o
_AST_replaceNameByFormula in modelSimplify.o
_AST_replaceFunctionDefinition in modelSimplify.o
_Model_reduceToOdes in odeConstruct.o
_ODEModel_constructJacobian in odeModel.o
_ODESense_create in odeModel.o
_ODEModel_compileCVODEFunctions in odeModel.o
...
"_ASTNode_getRightChild", referenced from:
_AST_replaceFunctionDefinition in modelSimplify.o
_simplifyAST in processAST.o
"_ASTNode_getType", referenced from:
_ASTNode_getIndex in ASTIndexNameNode.o
_ASTNode_setIndex in ASTIndexNameNode.o
_ASTNode_isIndexName in ASTIndexNameNode.o
_ASTNode_isSetIndex in ASTIndexNameNode.o
_ASTNode_isSetData in ASTIndexNameNode.o
_ASTNode_setData in ASTIndexNameNode.o
_evaluateAST in evaluateAST.o
...
"_ASTNode_getUserData", referenced from:
_ASTNode_getIndex in ASTIndexNameNode.o
_ASTNode_setIndex in ASTIndexNameNode.o
_ASTNode_isIndexName in ASTIndexNameNode.o
_ASTNode_isSetIndex in ASTIndexNameNode.o
_ASTNode_isSetData in ASTIndexNameNode.o
_ASTNode_setData in ASTIndexNameNode.o
"_ASTNode_isFunction", referenced from:
_AST_replaceFunctionDefinition in modelSimplify.o
_differentiateAST in processAST.o
"_ASTNode_isInteger", referenced from:
_AST_replaceNameByFormula in modelSimplify.o
_AST_replaceFunctionDefinition in modelSimplify.o
_ODEModel_constructJacobian in odeModel.o
_ODESense_create in odeModel.o
_ODEModel_compileCVODEFunctions in odeModel.o
_ODESense_compileCVODESenseFunctions in odeModel.o
_simplifyAST in processAST.o
...
"_ASTNode_isLogical", referenced from:
_differentiateAST in processAST.o
"_ASTNode_isName", referenced from:
_AST_replaceNameByName in modelSimplify.o
_AST_replaceNameByValue in modelSimplify.o
_AST_replaceNameByParameters in modelSimplify.o
_AST_replaceNameByFormula in modelSimplify.o
_AST_replaceFunctionDefinition in modelSimplify.o
_ODEModel_constructJacobian in odeModel.o
_ODESense_create in odeModel.o
...
"_ASTNode_isOperator", referenced from:
_differentiateAST in processAST.o
_simplifyAST in processAST.o
"_ASTNode_isReal", referenced from:
_AST_replaceNameByFormula in modelSimplify.o
_AST_replaceFunctionDefinition in modelSimplify.o
_ODEModel_constructJacobian in odeModel.o
_ODESense_create in odeModel.o
_ODEModel_compileCVODEFunctions in odeModel.o
_ODESense_compileCVODESenseFunctions in odeModel.o
_simplifyAST in processAST.o
...
"_ASTNode_isRelational", referenced from:
_differentiateAST in processAST.o
"_ASTNode_isUMinus", referenced from:
_simplifyAST in processAST.o
"_ASTNode_isUnknown", referenced from:
_evaluateAST in evaluateAST.o
_differentiateAST in processAST.o
"_ASTNode_setCharacter", referenced from:
_Species_odeFromReactions in odeConstruct.o
"_ASTNode_setInteger", referenced from:
_AST_replaceNameByFormula in modelSimplify.o
_AST_replaceFunctionDefinition in modelSimplify.o
_Species_odeFromReactions in odeConstruct.o
_differentiateAST in processAST.o
_simplifyAST in processAST.o
_indexAST in processAST.o
_copyRevertDataAST in sensSolver.o
...
"_ASTNode_setName", referenced from:
_AST_replaceNameByName in modelSimplify.o
_AST_replaceNameByFormula in modelSimplify.o
_AST_replaceFunctionDefinition in modelSimplify.o
_Species_odeFromReactions in odeConstruct.o
_differentiateAST in processAST.o
_simplifyAST in processAST.o
_indexAST in processAST.o
...
"_ASTNode_setReal", referenced from:
_AST_replaceNameByValue in modelSimplify.o
_AST_replaceNameByParameters in modelSimplify.o
_AST_replaceNameByFormula in modelSimplify.o
_AST_replaceFunctionDefinition in modelSimplify.o
_Species_odeFromReactions in odeConstruct.o
_differentiateAST in processAST.o
_simplifyAST in processAST.o
...
"_ASTNode_setType", referenced from:
_AST_replaceNameByFormula in modelSimplify.o
_AST_replaceFunctionDefinition in modelSimplify.o
_differentiateAST in processAST.o
_simplifyAST in processAST.o
_determinantNAST in processAST.o
_indexAST in processAST.o
_copyRevertDataAST in sensSolver.o
...
"_ASTNode_setUserData", referenced from:
_ASTNode_createIndexName in ASTIndexNameNode.o
_ASTNode_setIndex in ASTIndexNameNode.o
_ASTNode_setData in ASTIndexNameNode.o
"_ASTNode_swapChildren", referenced from:
_AST_replaceFunctionDefinition in modelSimplify.o
"_List_add", referenced from:
_topoSort in odeModel.o
_ODEModel_constructJacobian in odeModel.o
_ODESense_create in odeModel.o
_ASTNode_getIndices in processAST.o
_SolverError_error in solverError.o
"_List_create", referenced from:
_topoSort in odeModel.o
_ODEModel_constructJacobian in odeModel.o
_ODESense_create in odeModel.o
_ASTNode_getIndexArray in processAST.o
_SolverError_error in solverError.o
"_List_free", referenced from:
_AST_replaceNameByName in modelSimplify.o
_AST_replaceNameByValue in modelSimplify.o
_AST_replaceNameByParameters in modelSimplify.o
_AST_replaceNameByFormula in modelSimplify.o
_AST_replaceFunctionDefinition in modelSimplify.o
_ODEModel_topologicalRuleSort in odeModel.o
_topoSort in odeModel.o
...
"_List_get", referenced from:
_AST_replaceNameByName in modelSimplify.o
_AST_replaceNameByValue in modelSimplify.o
_AST_replaceNameByParameters in modelSimplify.o
_AST_replaceNameByFormula in modelSimplify.o
_AST_replaceFunctionDefinition in modelSimplify.o
_ODEModel_topologicalRuleSort in odeModel.o
_ODEModel_constructJacobian in odeModel.o
...
"_List_remove", referenced from:
_ODEModel_topologicalRuleSort in odeModel.o
_topoSort in odeModel.o
_ASTNode_getIndexArray in processAST.o
_SolverError_clear in solverError.o
"_List_size", referenced from:
_AST_replaceNameByName in modelSimplify.o
_AST_replaceNameByValue in modelSimplify.o
_AST_replaceNameByParameters in modelSimplify.o
_AST_replaceNameByFormula in modelSimplify.o
_AST_replaceFunctionDefinition in modelSimplify.o
_ODEModel_topologicalRuleSort in odeModel.o
_topoSort in odeModel.o
...
"_SBML_formulaToString", referenced from:
_drawModel in drawGraph.o
_IntegratorInstance_updateData in integratorInstance.o
_IntegratorInstance_checkTrigger in integratorInstance.o
_AST_dump in processAST.o
_IntegratorInstance_printQuad in sensSolver.o
"_SBML_parseFormula", referenced from:
_IntegratorInstance_setLinearObjectiveFunction in sensSolver.o
_IntegratorInstance_setObjectiveFunction in sensSolver.o
_IntegratorInstance_setObjectiveFunctionFromString in sensSolver.o
"_XMLError_getErrorId", referenced from:
_parseModel in sbml.o
_convertModel in sbml.o
"_XMLError_getMessage", referenced from:
_parseModel in sbml.o
_convertModel in sbml.o
"_XMLError_getSeverity", referenced from:
_parseModel in sbml.o
_convertModel in sbml.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[3]: *** [libODES.la] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [tmp/SBML_odeSolver-1.9.0.installed] Error 2

It would be helpful for potential contributors to have Flint's community guidelines in the official site and in documentation.
Suggested in openjournals/joss-reviews#2331 (comment).

... as follows:

See https://ci.appveyor.com/project/tabe/flint/builds/33192152, which is due to protocolbuffers/protobuf#7567.