LocAlignR App Crashing after install

[samantha1-tsne]

I attempted to download and open the LocAlignR app. After successful installation, it failed to open. Below is the log file generated from this issue.

========== Tue Mar 31 10:40:40 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/pmk/env/global/bin:/opt/X11/bin
INSTALL_BIN=/Users/hogese/miniforge3/bin/conda
Selected runtime executable: /Users/hogese/miniforge3/bin/conda
Launching LocAlignR

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
/var/folders/w2/vmnzgdq910gb91yks9z4hw15hbfkqx/T/tmpmxvidx10: line 3: 56152 Segmentation fault: 11 R -q -e 'LocAlignR::run_app()'

ERROR conda.cli.main_run:execute(125): conda run R -q -e LocAlignR::run_app() failed. (See above for error)

LocAlignR::run_app()

========== Tue Mar 31 10:48:27 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/pmk/env/global/bin:/opt/X11/bin
INSTALL_BIN=/Users/hogese/miniforge3/bin/conda
Selected runtime executable: /Users/hogese/miniforge3/bin/conda
Launching LocAlignR

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
/var/folders/w2/vmnzgdq910gb91yks9z4hw15hbfkqx/T/tmpd4lbx2t3: line 3: 58919 Segmentation fault: 11 R -q -e 'LocAlignR::run_app()'

ERROR conda.cli.main_run:execute(125): conda run R -q -e LocAlignR::run_app() failed. (See above for error)

LocAlignR::run_app()

========== Tue Mar 31 10:52:58 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/pmk/env/global/bin:/opt/X11/bin
INSTALL_BIN=/Users/hogese/miniforge3/bin/conda
Selected runtime executable: /Users/hogese/miniforge3/bin/conda
Launching LocAlignR

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
/var/folders/w2/vmnzgdq910gb91yks9z4hw15hbfkqx/T/tmp4k65em22: line 3: 60983 Segmentation fault: 11 R -q -e 'LocAlignR::run_app()'

ERROR conda.cli.main_run:execute(125): conda run R -q -e LocAlignR::run_app() failed. (See above for error)

LocAlignR::run_app()

========== Tue Mar 31 10:56:14 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/usr/bin:/bin:/usr/sbin:/sbin
INSTALL_BIN=/Users/hogese/miniforge3/bin/conda
Selected runtime executable: /Users/hogese/miniforge3/bin/conda
Launching LocAlignR

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
/var/folders/w2/vmnzgdq910gb91yks9z4hw15hbfkqx/T/tmpsdp74lr1: line 3: 62141 Segmentation fault: 11 R -q -e 'LocAlignR::run_app()'

ERROR conda.cli.main_run:execute(125): conda run R -q -e LocAlignR::run_app() failed. (See above for error)

LocAlignR::run_app()

========== Tue Mar 31 11:09:02 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/pmk/env/global/bin:/opt/X11/bin
INSTALL_BIN=/Users/hogese/miniforge3/bin/conda
Selected runtime executable: /Users/hogese/miniforge3/bin/conda
Launching LocAlignR

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
/var/folders/w2/vmnzgdq910gb91yks9z4hw15hbfkqx/T/tmp4f4o9rj8: line 3: 16139 Segmentation fault: 11 R -q -e 'LocAlignR::run_app()'

ERROR conda.cli.main_run:execute(125): conda run R -q -e LocAlignR::run_app() failed. (See above for error)

LocAlignR::run_app()

========== Tue Mar 31 11:11:08 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/usr/bin:/bin:/usr/sbin:/sbin
INSTALL_BIN=/Users/hogese/miniforge3/bin/conda
Selected runtime executable: /Users/hogese/miniforge3/bin/conda
Launching LocAlignR

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
/var/folders/w2/vmnzgdq910gb91yks9z4hw15hbfkqx/T/tmpu3vibmb9: line 3: 17229 Segmentation fault: 11 R -q -e 'LocAlignR::run_app()'

ERROR conda.cli.main_run:execute(125): conda run R -q -e LocAlignR::run_app() failed. (See above for error)

LocAlignR::run_app()

========== Tue Mar 31 11:12:13 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/usr/bin:/bin:/usr/sbin:/sbin
INSTALL_BIN=/Users/hogese/miniforge3/bin/conda
Selected runtime executable: /Users/hogese/miniforge3/bin/conda
Launching LocAlignR

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
/var/folders/w2/vmnzgdq910gb91yks9z4hw15hbfkqx/T/tmp5u_w1utp: line 3: 18281 Segmentation fault: 11 R -q -e 'LocAlignR::run_app()'

ERROR conda.cli.main_run:execute(125): conda run R -q -e LocAlignR::run_app() failed. (See above for error)

LocAlignR::run_app()

========== Tue Mar 31 13:07:57 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/Users/hogese/miniforge3/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/pmk/env/global/bin:/opt/X11/bin
INSTALL_BIN=/Users/hogese/miniforge3/bin/conda
Selected runtime executable: /Users/hogese/miniforge3/bin/conda
Launching LocAlignR

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
/var/folders/w2/vmnzgdq910gb91yks9z4hw15hbfkqx/T/tmpkvh96cp9: line 3: 25017 Segmentation fault: 11 R -q -e 'LocAlignR::run_app()'

ERROR conda.cli.main_run:execute(125): conda run R -q -e LocAlignR::run_app() failed. (See above for error)

LocAlignR::run_app()

========== Tue Mar 31 13:09:46 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/usr/bin:/bin:/usr/sbin:/sbin
INSTALL_BIN=/Users/hogese/miniforge3/bin/conda
Selected runtime executable: /Users/hogese/miniforge3/bin/conda
Launching LocAlignR

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
/var/folders/w2/vmnzgdq910gb91yks9z4hw15hbfkqx/T/tmpfsxf2ynr: line 3: 26507 Segmentation fault: 11 R -q -e 'LocAlignR::run_app()'

ERROR conda.cli.main_run:execute(125): conda run R -q -e LocAlignR::run_app() failed. (See above for error)

LocAlignR::run_app()

========== Tue Mar 31 13:11:09 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/usr/bin:/bin:/usr/sbin:/sbin
INSTALL_BIN=/Users/hogese/miniforge3/bin/conda
Selected runtime executable: /Users/hogese/miniforge3/bin/conda
Launching LocAlignR

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
/var/folders/w2/vmnzgdq910gb91yks9z4hw15hbfkqx/T/tmpr9gy3jj3: line 3: 28326 Segmentation fault: 11 R -q -e 'LocAlignR::run_app()'

ERROR conda.cli.main_run:execute(125): conda run R -q -e LocAlignR::run_app() failed. (See above for error)

LocAlignR::run_app()

============================================================
[2026-04-07 09:40:12] Starting LocAlignR launcher
[2026-04-07 09:40:12] HOME=/Users/hogese
[2026-04-07 09:40:12] PATH=/Users/hogese/miniforge3/bin:/Users/hogese/miniforge3/condabin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/pmk/env/global/bin:/opt/X11/bin
[2026-04-07 09:40:12] INSTALL_BIN=/Users/hogese/miniforge3/bin/mamba
[2026-04-07 09:40:12] Selected runtime executable: /Users/hogese/miniforge3/bin/mamba
[2026-04-07 09:40:12] Environment check exit status: 0

1
[1] 1

[2026-04-07 09:40:12] Package check exit status: 0

packageVersion(LocAlignR)
[1] ‘0.2.0’

[2026-04-07 09:40:26] Launching application

LocAlignR::run_app()

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
[2026-04-07 09:40:31] Launch command exit status: 139
[2026-04-07 09:40:31] ERROR: LocAlignR failed during launch.

Please send this log file:
/Users/hogese/Library/Logs/LocAlignR/launcher.log

============================================================
[2026-04-30 21:51:14] Starting LocAlignR launcher
[2026-04-30 21:51:14] HOME=/Users/hogese
[2026-04-30 21:51:14] PATH=/Users/hogese/miniforge3/bin:/Users/hogese/miniforge3/condabin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/pkg/env/active/bin:/opt/pmk/env/global/bin:/opt/X11/bin
[2026-04-30 21:51:14] INSTALL_BIN=/Users/hogese/miniforge3/bin/mamba
[2026-04-30 21:51:14] Selected runtime executable: /Users/hogese/miniforge3/bin/mamba
[2026-04-30 21:51:14] Environment check exit status: 0

1
[1] 1

[2026-04-30 21:51:14] Package check exit status: 0

packageVersion(LocAlignR)
[1] ‘0.2.0’

[2026-04-30 21:51:25] Launching application

LocAlignR::run_app()

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
[2026-04-30 21:51:39] Launch command exit status: 139
[2026-04-30 21:51:39] ERROR: LocAlignR failed during launch.

Please send this log file:
/Users/hogese/Library/Logs/LocAlignR/launcher.log

============================================================
[2026-05-06 14:16:48] Starting LocAlignR launcher
[2026-05-06 14:16:48] HOME=/Users/hogese
[2026-05-06 14:16:48] PATH=/Users/hogese/miniforge3/bin:/Users/hogese/miniforge3/condabin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/pkg/env/active/bin:/opt/pmk/env/global/bin:/opt/X11/bin
[2026-05-06 14:16:48] INSTALL_BIN=/Users/hogese/miniforge3/bin/mamba
[2026-05-06 14:16:48] Selected runtime executable: /Users/hogese/miniforge3/bin/mamba
[2026-05-06 14:16:48] Environment check exit status: 0

1
[1] 1

[2026-05-06 14:16:48] Package check exit status: 0

packageVersion(LocAlignR)
[1] ‘0.2.0’

[2026-05-06 14:18:49] Launching application

LocAlignR::run_app()

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
[2026-05-06 14:18:52] Launch command exit status: 139
[2026-05-06 14:18:52] ERROR: LocAlignR failed during launch.

Please send this log file:
/Users/hogese/Library/Logs/LocAlignR/launcher.log

[samantha1-tsne]

This is the output I got when running the installer today. The app crashed before successfully loading again.

========== Tue Mar 31 10:40:40 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/pmk/env/global/bin:/opt/X11/bin
INSTALL_BIN=/Users/hogese/miniforge3/bin/conda
Selected runtime executable: /Users/hogese/miniforge3/bin/conda
Launching LocAlignR

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
/var/folders/w2/vmnzgdq910gb91yks9z4hw15hbfkqx/T/tmpmxvidx10: line 3: 56152 Segmentation fault: 11 R -q -e 'LocAlignR::run_app()'

ERROR conda.cli.main_run:execute(125): conda run R -q -e LocAlignR::run_app() failed. (See above for error)

LocAlignR::run_app()

========== Tue Mar 31 10:48:27 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/pmk/env/global/bin:/opt/X11/bin
INSTALL_BIN=/Users/hogese/miniforge3/bin/conda
Selected runtime executable: /Users/hogese/miniforge3/bin/conda
Launching LocAlignR

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
/var/folders/w2/vmnzgdq910gb91yks9z4hw15hbfkqx/T/tmpd4lbx2t3: line 3: 58919 Segmentation fault: 11 R -q -e 'LocAlignR::run_app()'

ERROR conda.cli.main_run:execute(125): conda run R -q -e LocAlignR::run_app() failed. (See above for error)

LocAlignR::run_app()

========== Tue Mar 31 10:52:58 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/pmk/env/global/bin:/opt/X11/bin
INSTALL_BIN=/Users/hogese/miniforge3/bin/conda
Selected runtime executable: /Users/hogese/miniforge3/bin/conda
Launching LocAlignR

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
/var/folders/w2/vmnzgdq910gb91yks9z4hw15hbfkqx/T/tmp4k65em22: line 3: 60983 Segmentation fault: 11 R -q -e 'LocAlignR::run_app()'

ERROR conda.cli.main_run:execute(125): conda run R -q -e LocAlignR::run_app() failed. (See above for error)

LocAlignR::run_app()

========== Tue Mar 31 10:56:14 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/usr/bin:/bin:/usr/sbin:/sbin
INSTALL_BIN=/Users/hogese/miniforge3/bin/conda
Selected runtime executable: /Users/hogese/miniforge3/bin/conda
Launching LocAlignR

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
/var/folders/w2/vmnzgdq910gb91yks9z4hw15hbfkqx/T/tmpsdp74lr1: line 3: 62141 Segmentation fault: 11 R -q -e 'LocAlignR::run_app()'

ERROR conda.cli.main_run:execute(125): conda run R -q -e LocAlignR::run_app() failed. (See above for error)

LocAlignR::run_app()

========== Tue Mar 31 11:09:02 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/pmk/env/global/bin:/opt/X11/bin
INSTALL_BIN=/Users/hogese/miniforge3/bin/conda
Selected runtime executable: /Users/hogese/miniforge3/bin/conda
Launching LocAlignR

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
/var/folders/w2/vmnzgdq910gb91yks9z4hw15hbfkqx/T/tmp4f4o9rj8: line 3: 16139 Segmentation fault: 11 R -q -e 'LocAlignR::run_app()'

ERROR conda.cli.main_run:execute(125): conda run R -q -e LocAlignR::run_app() failed. (See above for error)

LocAlignR::run_app()

========== Tue Mar 31 11:11:08 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/usr/bin:/bin:/usr/sbin:/sbin
INSTALL_BIN=/Users/hogese/miniforge3/bin/conda
Selected runtime executable: /Users/hogese/miniforge3/bin/conda
Launching LocAlignR

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
/var/folders/w2/vmnzgdq910gb91yks9z4hw15hbfkqx/T/tmpu3vibmb9: line 3: 17229 Segmentation fault: 11 R -q -e 'LocAlignR::run_app()'

ERROR conda.cli.main_run:execute(125): conda run R -q -e LocAlignR::run_app() failed. (See above for error)

LocAlignR::run_app()

========== Tue Mar 31 11:12:13 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/usr/bin:/bin:/usr/sbin:/sbin
INSTALL_BIN=/Users/hogese/miniforge3/bin/conda
Selected runtime executable: /Users/hogese/miniforge3/bin/conda
Launching LocAlignR

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
/var/folders/w2/vmnzgdq910gb91yks9z4hw15hbfkqx/T/tmp5u_w1utp: line 3: 18281 Segmentation fault: 11 R -q -e 'LocAlignR::run_app()'

ERROR conda.cli.main_run:execute(125): conda run R -q -e LocAlignR::run_app() failed. (See above for error)

LocAlignR::run_app()

========== Tue Mar 31 13:07:57 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/Users/hogese/miniforge3/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/pmk/env/global/bin:/opt/X11/bin
INSTALL_BIN=/Users/hogese/miniforge3/bin/conda
Selected runtime executable: /Users/hogese/miniforge3/bin/conda
Launching LocAlignR

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
/var/folders/w2/vmnzgdq910gb91yks9z4hw15hbfkqx/T/tmpkvh96cp9: line 3: 25017 Segmentation fault: 11 R -q -e 'LocAlignR::run_app()'

ERROR conda.cli.main_run:execute(125): conda run R -q -e LocAlignR::run_app() failed. (See above for error)

LocAlignR::run_app()

========== Tue Mar 31 13:09:46 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/usr/bin:/bin:/usr/sbin:/sbin
INSTALL_BIN=/Users/hogese/miniforge3/bin/conda
Selected runtime executable: /Users/hogese/miniforge3/bin/conda
Launching LocAlignR

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
/var/folders/w2/vmnzgdq910gb91yks9z4hw15hbfkqx/T/tmpfsxf2ynr: line 3: 26507 Segmentation fault: 11 R -q -e 'LocAlignR::run_app()'

ERROR conda.cli.main_run:execute(125): conda run R -q -e LocAlignR::run_app() failed. (See above for error)

LocAlignR::run_app()

========== Tue Mar 31 13:11:09 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/usr/bin:/bin:/usr/sbin:/sbin
INSTALL_BIN=/Users/hogese/miniforge3/bin/conda
Selected runtime executable: /Users/hogese/miniforge3/bin/conda
Launching LocAlignR

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
/var/folders/w2/vmnzgdq910gb91yks9z4hw15hbfkqx/T/tmpr9gy3jj3: line 3: 28326 Segmentation fault: 11 R -q -e 'LocAlignR::run_app()'

ERROR conda.cli.main_run:execute(125): conda run R -q -e LocAlignR::run_app() failed. (See above for error)

LocAlignR::run_app()

============================================================
[2026-04-07 09:40:12] Starting LocAlignR launcher
[2026-04-07 09:40:12] HOME=/Users/hogese
[2026-04-07 09:40:12] PATH=/Users/hogese/miniforge3/bin:/Users/hogese/miniforge3/condabin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/pmk/env/global/bin:/opt/X11/bin
[2026-04-07 09:40:12] INSTALL_BIN=/Users/hogese/miniforge3/bin/mamba
[2026-04-07 09:40:12] Selected runtime executable: /Users/hogese/miniforge3/bin/mamba
[2026-04-07 09:40:12] Environment check exit status: 0

1
[1] 1

[2026-04-07 09:40:12] Package check exit status: 0

packageVersion(LocAlignR)
[1] ‘0.2.0’

[2026-04-07 09:40:26] Launching application

LocAlignR::run_app()

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
[2026-04-07 09:40:31] Launch command exit status: 139
[2026-04-07 09:40:31] ERROR: LocAlignR failed during launch.

Please send this log file:
/Users/hogese/Library/Logs/LocAlignR/launcher.log

============================================================
[2026-04-30 21:51:14] Starting LocAlignR launcher
[2026-04-30 21:51:14] HOME=/Users/hogese
[2026-04-30 21:51:14] PATH=/Users/hogese/miniforge3/bin:/Users/hogese/miniforge3/condabin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/pkg/env/active/bin:/opt/pmk/env/global/bin:/opt/X11/bin
[2026-04-30 21:51:14] INSTALL_BIN=/Users/hogese/miniforge3/bin/mamba
[2026-04-30 21:51:14] Selected runtime executable: /Users/hogese/miniforge3/bin/mamba
[2026-04-30 21:51:14] Environment check exit status: 0

1
[1] 1

[2026-04-30 21:51:14] Package check exit status: 0

packageVersion(LocAlignR)
[1] ‘0.2.0’

[2026-04-30 21:51:25] Launching application

LocAlignR::run_app()

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
[2026-04-30 21:51:39] Launch command exit status: 139
[2026-04-30 21:51:39] ERROR: LocAlignR failed during launch.

Please send this log file:
/Users/hogese/Library/Logs/LocAlignR/launcher.log

============================================================
[2026-05-06 14:16:48] Starting LocAlignR launcher
[2026-05-06 14:16:48] HOME=/Users/hogese
[2026-05-06 14:16:48] PATH=/Users/hogese/miniforge3/bin:/Users/hogese/miniforge3/condabin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/pkg/env/active/bin:/opt/pmk/env/global/bin:/opt/X11/bin
[2026-05-06 14:16:48] INSTALL_BIN=/Users/hogese/miniforge3/bin/mamba
[2026-05-06 14:16:48] Selected runtime executable: /Users/hogese/miniforge3/bin/mamba
[2026-05-06 14:16:48] Environment check exit status: 0

1
[1] 1

[2026-05-06 14:16:48] Package check exit status: 0

packageVersion(LocAlignR)
[1] ‘0.2.0’

[2026-05-06 14:18:49] Launching application

LocAlignR::run_app()

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
7: loadNamespace(package, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(package, ...), error = function(e) e)
12: requireNamespace("shiny", quietly = TRUE)
13: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
[2026-05-06 14:18:52] Launch command exit status: 139
[2026-05-06 14:18:52] ERROR: LocAlignR failed during launch.

Please send this log file:
/Users/hogese/Library/Logs/LocAlignR/launcher.log
========== Thu May 7 07:22:02 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/Users/hogese/miniforge3/bin:/Users/hogese/miniforge3/condabin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/pkg/env/active/bin:/opt/pmk/env/global/bin:/opt/X11/bin
INSTALL_BIN=/Users/hogese/miniforge3/bin/mamba
Selected runtime executable: /Users/hogese/miniforge3/bin/mamba
Launching LocAlignR

LocAlignR::run_app()

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(package, lib.loc)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)}, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return && !quietly) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA)})
8: library(pkg, character.only = TRUE)
9: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
10: suppressPackageStartupMessages(library(pkg, character.only = TRUE))
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch({ suppressPackageStartupMessages(library(pkg, character.only = TRUE)) TRUE}, error = function(e) { log_line("ERROR while loading ", pkg, ": ", conditionMessage(e)) FALSE})
15: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
========== Thu May 7 07:24:28 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/Users/hogese/miniforge3/bin:/Users/hogese/miniforge3/condabin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/pkg/env/active/bin:/opt/pmk/env/global/bin:/opt/X11/bin
INSTALL_BIN=/Users/hogese/miniforge3/bin/mamba
Selected runtime executable: /Users/hogese/miniforge3/bin/mamba
Launching LocAlignR

LocAlignR::run_app()

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(package, lib.loc)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)}, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return && !quietly) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA)})
8: library(pkg, character.only = TRUE)
9: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
10: suppressPackageStartupMessages(library(pkg, character.only = TRUE))
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch({ suppressPackageStartupMessages(library(pkg, character.only = TRUE)) TRUE}, error = function(e) { log_line("ERROR while loading ", pkg, ": ", conditionMessage(e)) FALSE})
15: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
========== Thu May 14 10:43:24 EDT 2026 ==========
Starting launcher
HOME=/Users/hogese
PATH=/Users/hogese/miniforge3/bin:/Users/hogese/miniforge3/condabin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/pkg/env/active/bin:/opt/pmk/env/global/bin:/opt/X11/bin
INSTALL_BIN=/Users/hogese/miniforge3/bin/mamba
Selected runtime executable: /Users/hogese/miniforge3/bin/mamba
Launching LocAlignR

LocAlignR::run_app()

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(package, lib.loc)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)}, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return && !quietly) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA)})
8: library(pkg, character.only = TRUE)
9: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
10: suppressPackageStartupMessages(library(pkg, character.only = TRUE))
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch({ suppressPackageStartupMessages(library(pkg, character.only = TRUE)) TRUE}, error = function(e) { log_line("ERROR while loading ", pkg, ": ", conditionMessage(e)) FALSE})
15: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...

============================================================
[2026-05-14 10:48:11] Starting LocAlignR launcher
[2026-05-14 10:48:11] HOME=/Users/hogese
[2026-05-14 10:48:11] PATH=/Users/hogese/miniforge3/bin:/Users/hogese/miniforge3/condabin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/pkg/env/active/bin:/opt/pmk/env/global/bin:/opt/X11/bin
[2026-05-14 10:48:11] INSTALL_BIN=/Users/hogese/miniforge3/bin/mamba
[2026-05-14 10:48:11] Selected runtime executable: /Users/hogese/miniforge3/bin/mamba
[2026-05-14 10:48:11] Environment check exit status: 0

1
[1] 1

[2026-05-14 10:48:11] Package check exit status: 0

packageVersion(LocAlignR)
[1] ‘0.2.0’

[2026-05-14 10:50:11] Launching application

LocAlignR::run_app()

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(package, lib.loc)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)}, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return && !quietly) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA)})
8: library(pkg, character.only = TRUE)
9: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
10: suppressPackageStartupMessages(library(pkg, character.only = TRUE))
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch({ suppressPackageStartupMessages(library(pkg, character.only = TRUE)) TRUE}, error = function(e) { log_line("ERROR while loading ", pkg, ": ", conditionMessage(e)) FALSE})
15: LocAlignR::run_app()
An irrecoverable exception occurred. R is aborting now ...
[2026-05-14 10:50:14] Launch command exit status: 139
[2026-05-14 10:50:14] ERROR: LocAlignR failed during launch.

Please send this log file:
/Users/hogese/Library/Logs/LocAlignR/launcher.log