installation difficulty on Ventura 13

Maya Kaul

unread,

Jan 16, 2023, 7:16:17 PM1/16/23

to Morpheus users

Hi,

I tried to install morpheus and it looks like it's installed but when I run morpheus-gui, or open it from my applications folder, it closes immediately. Sometimes I get a message from apple saying "morpheus-gui quit unexpectedly"

It worked fine on a 2017 mac, so I think this is a Ventura problem. If anyone has any fixes, I'd be grateful!

thank you so much.

here's the full report, if at all useful

-------------------------------------
Translated Report (Full Report Below)
-------------------------------------

Process: morpheus-gui [37075]
Path: /usr/local/Cellar/morpheus/2.3.3/Morpheus.app/Contents/MacOS/morpheus-gui
Identifier: de.tu-dresden.Morpheus
Version: 2.3 (2.3.3)
Code Type: X86-64 (Translated)
Parent Process: launchd [1]
User ID: 501

Date/Time: 2023-01-16 17:59:02.6220 -0500
OS Version: macOS 13.0 (22A380)
Report Version: 12
Anonymous UUID: 8667EAC0-720D-2827-7064-39955DB634D5

Sleep/Wake UUID: 7E2A83FD-08BA-40C5-9362-31B4BA015BFA

Time Awake Since Boot: 51000 seconds
Time Since Wake: 310 seconds

System Integrity Protection: enabled

Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Exception Type: EXC_BAD_INSTRUCTION (SIGILL)
Exception Codes: 0x0000000000000001, 0x0000000000000000

Termination Reason: Namespace SIGNAL, Code 4 Illegal instruction: 4
Terminating Process: exc handler [37075]

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 morpheus-gui 0x10297351c _GLOBAL__sub_I_mocs_compilation.cpp + 4
1 dyld 0x203112618 invocation function for block in dyld4::Loader::findAndRunAllInitializers(dyld4::RuntimeState&) const + 172
2 dyld 0x203151c4d invocation function for block in dyld3::MachOAnalyzer::forEachInitializer(Diagnostics&, dyld3::MachOAnalyzer::VMAddrConverter const&, void (unsigned int) block_pointer, void const*) const + 132
3 dyld 0x203145ef7 invocation function for block in dyld3::MachOFile::forEachSection(void (dyld3::MachOFile::SectionInfo const&, bool, bool&) block_pointer) const + 557
4 dyld 0x2030f80b7 dyld3::MachOFile::forEachLoadCommand(Diagnostics&, void (load_command const*, bool&) block_pointer) const + 245
5 dyld 0x2031450a7 dyld3::MachOFile::forEachSection(void (dyld3::MachOFile::SectionInfo const&, bool, bool&) block_pointer) const + 175
6 dyld 0x2031477ea dyld3::MachOFile::forEachInitializerPointerSection(Diagnostics&, void (unsigned int, unsigned int, bool&) block_pointer) const + 116
7 dyld 0x203151882 dyld3::MachOAnalyzer::forEachInitializer(Diagnostics&, dyld3::MachOAnalyzer::VMAddrConverter const&, void (unsigned int) block_pointer, void const*) const + 390
8 dyld 0x2031124f6 dyld4::Loader::findAndRunAllInitializers(dyld4::RuntimeState&) const + 150
9 dyld 0x203112750 dyld4::Loader::runInitializersBottomUp(dyld4::RuntimeState&, dyld3::Array<dyld4::Loader const*>&) const + 178
10 dyld 0x20311282c dyld4::Loader::runInitializersBottomUpPlusUpwardLinks(dyld4::RuntimeState&) const + 164
11 dyld 0x203132117 dyld4::APIs::runAllInitializersForMain() + 337
12 dyld 0x2030fd369 dyld4::prepare(dyld4::APIs&, dyld3::MachOAnalyzer const*) + 3743
13 dyld 0x2030fc281 start + 2289

Thread 1:: com.apple.rosetta.exceptionserver
0 runtime 0x7ff7ffd44750 0x7ff7ffd40000 + 18256
1 runtime 0x7ff7ffd5066c 0x7ff7ffd40000 + 67180
2 runtime 0x7ff7ffd5206c 0x7ff7ffd40000 + 73836

Thread 2:
0 runtime 0x7ff7ffd6287c 0x7ff7ffd40000 + 141436

Thread 3:
0 runtime 0x7ff7ffd6287c 0x7ff7ffd40000 + 141436

Thread 4:
0 runtime 0x7ff7ffd6287c 0x7ff7ffd40000 + 141436

Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x000000010baa0c40 rbx: 0x00000003099909f8 rcx: 0x00000003099979e8 rdx: 0x00000003099978e0
rdi: 0x0000000000000001 rsi: 0x00000003099978d0 rbp: 0x00000003099909e0 rsp: 0x00000003099909e0
r8: 0x00007ff842208510 r9: 0x0000000000000000 r10: 0x00007ff843d844a0 r11: 0x0000000000003fff
r12: 0x0000000102e2bc80 r13: 0x00000001027aa418 r14: 0x0000000102973518 r15: 0x0000000309990ee8
rip: <unavailable> rfl: 0x0000000000000202
tmp0: 0x000000010297351c tmp1: 0x0511f8c5c057f8c5 tmp2: 0x00358d48004f4410

Binary Images:
0x1027aa000 - 0x102e29fff de.tu-dresden.Morpheus (2.3) <f069301c-2d4d-3a10-9c4f-2a6ae161b565> /usr/local/Cellar/morpheus/2.3.3/Morpheus.app/Contents/MacOS/morpheus-gui
0x2030f6000 - 0x20318dfff dyld (*) <0f050705-2258-3d40-b7bc-f3b35a44bbea> /usr/lib/dyld
0x7ff7ffd40000 - 0x7ff7ffd6ffff runtime (*) <6f797d84-b330-3656-9a0d-7b3dbd3f8a07> /usr/libexec/rosetta/runtime

External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 0
thread_create: 0
thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=897.1M resident=0K(0%) swapped_out_or_unallocated=897.1M(100%)
Writable regions: Total=691.6M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=691.6M(100%)

VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Activity Tracing 256K 1
Kernel Alloc Once 8K 1
MALLOC 146.1M 13
MALLOC guard page 96K 5
MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)
Rosetta Arena 4096K 2
Rosetta Generic 1016K 251
Rosetta IndirectBranch 192K 2
Rosetta JIT 128.0M 1
Rosetta Return Stack 60K 6
Rosetta Thread Context 60K 6
STACK GUARD 12K 3
Stack 9772K 4
Stack Guard 56.0M 1
VM_ALLOCATE 7384K 18
VM_ALLOCATE (reserved) 72K 11 reserved VM address space (unallocated)
__CTF 756 1
__DATA 39.9M 587
__DATA_CONST 38.6M 368
__DATA_DIRTY 1815K 220
__FONT_DATA 2352 1
__LINKEDIT 174.2M 33
__OBJC_RO 65.1M 1
__OBJC_RW 1980K 2
__TEXT 722.9M 606
dyld private memory 512K 2
mapped file 4.2G 1308
shared memory 64K 4
unshared pmap 8768K 6
=========== ======= =======
TOTAL 6.0G 3465
TOTAL, minus reserved VM space 5.6G 3465

-----------
Full Report
-----------

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"legacyInfo" : {
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"factorPackIds" : {
"SIRI_UNDERSTANDING_ASR_ASSISTANT" : "6348ad0234d9d80ede80aabb",
"SIRI_UNDERSTANDING_MORPHUN" : "62ec7220c682040ba94e6a20"
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Model: MacBookAir10,1, BootROM 8419.41.10, proc 8:4:4 processors, 16 GB, SMC
Graphics: Apple M1, Apple M1, Built-In
Display: Color LCD, 2560 x 1600 Retina, Main, MirrorOff, Online
Memory Module: LPDDR4, Hynix
AirPort: spairport_wireless_card_type_wifi (0x14E4, 0x4378), wl0: Sep 3 2022 03:37:22 version 18.20.379.4.7.8.143 FWID 01-e3c71b50
Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial ports
Network Service: Wi-Fi, AirPort, en0
USB Device: USB31Bus
USB Device: USB31Bus
Thunderbolt Bus: MacBook Air, Apple Inc.
Thunderbolt Bus: MacBook Air, Apple Inc.

Diego Jahn

unread,

Jan 17, 2023, 7:34:57 AM1/17/23

to Morpheus users

Hi Maya,

yes, the report helps. Thanks! Can you please also enter brew info morpheus in the Terminal and send us the output? Your (unfortunately currently not working) Morpheus must still be installed for this. That output would help us with troubleshooting.

Best,

Diego

Diego Jahn

unread,

Jan 17, 2023, 9:35:12 AM1/17/23

to Morpheus users

One other addition: Besides the one from 'brew info morpheus', can you please send the output from 'brew config' as well as 'brew doctor'? Maybe we can find a clue there.

Maya Kaul

unread,

Jan 17, 2023, 9:41:46 AM1/17/23

to Diego Jahn, Morpheus users

brew info (previously failed to reply-all):

Warning: Treating morpheus as a formula. For the cask, use homebrew/cask/morpheus

==> morpheus-lab/morpheus/morpheus: stable 2.3.3 (bottled)

Modelling environment for multi-cellular systems biology

https://morpheus.gitlab.io/

/usr/local/Cellar/morpheus/2.3.3 (14 files, 16.3MB) *

Poured from bottle on 2023-01-16 at 12:18:51

From: https://github.com/morpheus-lab/homebrew-morpheus/blob/HEAD/Formula/morpheus.rb

License: BSD-3-Clause

==> Dependencies

Build: boost ✔, cmake ✔, doxygen ✔

Required: ffmpeg ✔, gnuplot ✔, graphviz ✔, libomp ✔, libtiff ✔, qt@5 ✔

==> Caveats

To start the Morpheus GUI, type the following command:

morpheus-gui

Or add Morpheus to your Applications folder with:

ln -sf /usr/local/opt/morpheus/Morpheus.app /Applications

brew config:

HOMEBREW_VERSION: 3.6.19

ORIGIN: https://github.com/Homebrew/brew

HEAD: 3e257890da96b4cc44f5933e3a54aee2b47549de

Last commit: 4 days ago

Branch: stable

Core tap ORIGIN: https://github.com/Homebrew/homebrew-core

Core tap HEAD: 314306d169ed1c3a183bfd15ab9143568a71ea6f

Core tap last commit: 16 hours ago

Core tap branch: master

HOMEBREW_PREFIX: /usr/local

HOMEBREW_CASK_OPTS: []

HOMEBREW_DISPLAY: /private/tmp/com.apple.launchd.97x1H8mzQs/org.xquartz:0

HOMEBREW_MAKE_JOBS: 8

Homebrew Ruby: 2.6.8 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.6.8_1/bin/ruby

CPU: octa-core 64-bit westmere

Clang: 14.0.0 build 1400

Git: 2.37.1 => /Applications/Xcode.app/Contents/Developer/usr/bin/git

Curl: 7.84.0 => /usr/bin/curl

macOS: 13.0-x86_64

CLT: 14.2.0.0.1.1668646533

Xcode: 14.2

Rosetta 2: true

brew doctor:

Please note that these warnings are just used to help the Homebrew maintainers

with debugging if you file an issue. If everything you use Homebrew for is

working fine: please don't worry or file an issue; just ignore this. Thanks!

Warning: Homebrew is not on the default git origin branch and may not receive

updates. If this is a surprise to you, check out the default branch with:

git -C $(brew --repo) checkout master"

Warning: Unbrewed dylibs were found in /usr/local/lib.

If you didn't put them there on purpose they could cause problems when

building Homebrew formulae, and may need to be deleted.

Unexpected dylibs:

/usr/local/lib/libpandaseq-url.0.dylib

/usr/local/lib/libpandaseq.7.dylib

/usr/local/lib/libtcl8.6.dylib

/usr/local/lib/libtk8.6.dylib

Warning: Unbrewed header files were found in /usr/local/include.

If you didn't put them there on purpose they could cause problems when

building Homebrew formulae, and may need to be deleted.

Unexpected header files:

/usr/local/include/fakemysql.h

/usr/local/include/fakepq.h

/usr/local/include/fakesql.h

/usr/local/include/itcl.h

/usr/local/include/itcl2TclOO.h

/usr/local/include/itclDecls.h

/usr/local/include/itclInt.h

/usr/local/include/itclIntDecls.h

/usr/local/include/itclMigrate2TclCore.h

/usr/local/include/itclTclIntStubsFcn.h

/usr/local/include/mysqlStubs.h

/usr/local/include/node/cppgc/allocation.h

/usr/local/include/node/cppgc/common.h

/usr/local/include/node/cppgc/custom-space.h

/usr/local/include/node/cppgc/garbage-collected.h

/usr/local/include/node/cppgc/heap.h

/usr/local/include/node/cppgc/internal/accessors.h

/usr/local/include/node/cppgc/internal/api-constants.h

/usr/local/include/node/cppgc/internal/compiler-specific.h

/usr/local/include/node/cppgc/internal/finalizer-trait.h

/usr/local/include/node/cppgc/internal/gc-info.h

/usr/local/include/node/cppgc/internal/logging.h

/usr/local/include/node/cppgc/internal/persistent-node.h

/usr/local/include/node/cppgc/internal/pointer-policies.h

/usr/local/include/node/cppgc/internal/prefinalizer-handler.h

/usr/local/include/node/cppgc/liveness-broker.h

/usr/local/include/node/cppgc/macros.h

/usr/local/include/node/cppgc/member.h

/usr/local/include/node/cppgc/persistent.h

/usr/local/include/node/cppgc/platform.h

/usr/local/include/node/cppgc/prefinalizer.h

/usr/local/include/node/cppgc/source-location.h

/usr/local/include/node/cppgc/trace-trait.h

/usr/local/include/node/cppgc/type-traits.h

/usr/local/include/node/cppgc/visitor.h

/usr/local/include/node/js_native_api.h

/usr/local/include/node/js_native_api_types.h

/usr/local/include/node/libplatform/libplatform-export.h

/usr/local/include/node/libplatform/libplatform.h

/usr/local/include/node/libplatform/v8-tracing.h

/usr/local/include/node/node.h

/usr/local/include/node/node_api.h

/usr/local/include/node/node_api_types.h

/usr/local/include/node/node_buffer.h

/usr/local/include/node/node_object_wrap.h

/usr/local/include/node/node_version.h

/usr/local/include/node/openssl/aes.h

/usr/local/include/node/openssl/archs/BSD-x86/asm/crypto/buildinf.h

/usr/local/include/node/openssl/archs/BSD-x86/asm/crypto/include/internal/bn_conf.h

/usr/local/include/node/openssl/archs/BSD-x86/asm/crypto/include/internal/dso_conf.h

/usr/local/include/node/openssl/archs/BSD-x86/asm/include/openssl/opensslconf.h

/usr/local/include/node/openssl/archs/BSD-x86/asm/include/progs.h

/usr/local/include/node/openssl/archs/BSD-x86/asm_avx2/crypto/buildinf.h

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Warning: Unbrewed '.la' files were found in /usr/local/lib.

If you didn't put them there on purpose they could cause problems when

building Homebrew formulae, and may need to be deleted.

Unexpected '.la' files:

/usr/local/lib/libpandaseq-url.la

/usr/local/lib/libpandaseq.la

Warning: Unbrewed '.pc' files were found in /usr/local/lib/pkgconfig.

If you didn't put them there on purpose they could cause problems when

building Homebrew formulae, and may need to be deleted.

Unexpected '.pc' files:

/usr/local/lib/pkgconfig/pandaseq-2-url.pc

/usr/local/lib/pkgconfig/pandaseq-2.pc

/usr/local/lib/pkgconfig/tcl.pc

/usr/local/lib/pkgconfig/tk.pc

Warning: Unbrewed static libraries were found in /usr/local/lib.

If you didn't put them there on purpose they could cause problems when

building Homebrew formulae, and may need to be deleted.

Unexpected static libraries:

/usr/local/lib/libpandaseq-url.a

/usr/local/lib/libpandaseq.a

/usr/local/lib/libtclstub8.6.a

/usr/local/lib/libtkstub8.6.a

Warning: Homebrew's "sbin" was not found in your PATH but you have installed

formulae that put executables in /usr/local/sbin.

Consider setting your PATH for example like so:

echo 'export PATH="/usr/local/sbin:$PATH"' >> ~/.zshrc

Warning: Broken symlinks were found. Remove them with `brew cleanup`:

/usr/local/share/man/man1/npx.1

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Maya Kaul

unread,

Jan 19, 2023, 2:09:54 AM1/19/23

to Morpheus users

resolved! (I think?)

Fix:

ran "brew doctor" again while trying to diff morpheus-functional and morpheus-nonfunctional computers.
message had changed since yesterday, and this time I got this vaguely fed-up warning.

Warning: Your Homebrew's prefix is not /opt/homebrew.
Many of Homebrew's bottles (binary packages) can only be used with the default prefix.
Consider uninstalling Homebrew and reinstalling into the default prefix.
It is expected behaviour that some formulae will fail to build in this unsupported configuration.
It is expected behaviour that Homebrew will be buggy and slow.
Do not create any issues about this on Homebrew's GitHub repositories.
Do not create any issues even if you think this message is unrelated.
Any opened issues will be immediately closed without response.
Do not ask for help from Mac Homebrew on Twitter.
You may ask for help in Homebrew's discussions but are unlikely to receive a response.
Try to figure out the problem yourself and submit a fix as a pull request.We will review it but may or may not accept it.

Yep. uninstalling and reinstalling homebrew (https://ralphjsmit.com/uninstall-homebrew), and then following morpheus installation directions worked.

Thank you so much for your help! I would not have found this without it.

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