Last updated on 2024-09-20 18:49:41 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.5 | 34.45 | 173.27 | 207.72 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.5 | 23.96 | 127.78 | 151.74 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.1.5 | 352.63 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.5 | 407.26 | OK | |||
| r-devel-windows-x86_64 | 0.1.5 | 33.00 | 263.00 | 296.00 | NOTE | |
| r-patched-linux-x86_64 | 0.1.4 | 36.87 | 189.39 | 226.26 | OK | |
| r-release-linux-x86_64 | 0.1.4 | 33.39 | 189.55 | 222.94 | ERROR | |
| r-release-macos-arm64 | 0.1.5 | 117.00 | NOTE | |||
| r-release-macos-x86_64 | 0.1.4 | 284.00 | NOTE | |||
| r-release-windows-x86_64 | 0.1.5 | 38.00 | 264.00 | 302.00 | NOTE | |
| r-oldrel-macos-arm64 | 0.1.5 | 11.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 0.1.4 | 298.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 0.1.5 | 39.00 | 266.00 | 305.00 | NOTE |
Version: 0.1.5
Check: installed package size
Result: NOTE
installed size is 7.4Mb
sub-directories of 1Mb or more:
libs 3.3Mb
mods 3.4Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, r-release-macos-arm64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 0.1.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [97s/131s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(nonmem2rx)
> library(rxode2)
rxode2 2.1.3 using 3 threads (see ?getRxThreads)
no cache: create with `rxCreateCache()`
> setRxThreads(1L)
> library(data.table)
> setDTthreads(1L)
>
>
> test_check("nonmem2rx")
$ABBREV record syntax error error:
================================================================================
:ERR: will not change var type from 'EPS' to 'THETA':
:001: REPLACE EPS(ECL)=THETA(4)
================================================================================
:ERR: will not change var type from 'THETA' to 'ETA':
:001: REPLACE THETA(CL,V1,Q,V2)=ETA(1,2,3,4)
================================================================================
:ERR: 'MOD' function not supported in translation:
:001: CL = MOD(C)
================================================================================
:ERR: 'INT' function not supported in translation:
:001: CL = INT(C)
================================================================================
:ERR: 'A#' NONMEM reserved variable is not translated:
:001: CL = A12345
================================================================================
:ERR: 'C#' NONMEM reserved variable is not translated:
:001: CL = C12345
================================================================================
:ERR: 'COMACT' NONMEM reserved variable is not translated:
:001: A = COMACT
================================================================================
:ERR: 'COMSAV' NONMEM reserved variable is not translated:
:001: A = COMSAV
================================================================================
:ERR: 'CALL PASS(MODE)' statements not supported in translation:
:001: CALL PASS(MODE)
================================================================================
:ERR: 'CALL SUPP(# , #)' statements not supported in translation:
:001: CALL SUPP(0 , 1)
================================================================================
:ERR: DT(#) not supported in translation:
:001: C=DT(3)
================================================================================
:ERR: MNEXT(#) not supported in translation:
:001: C=MNEXT(3)
================================================================================
:ERR: COM(#) not supported in translation:
:001: C=COM(3)
================================================================================
:ERR: PCMT(#) not supported in translation:
:001: C=PCMT(3)
================================================================================
:ERR: DA(#, #) not supported in translation:
:001: DA(1, 2) = -KEL*A(1)
================================================================================
:ERR: DP(#, #) not supported in translation:
:001: DP(1, 2) = -KEL*A(1)
================================================================================
:ERR: 'TSCALE' NONMEM reserved variable is not translated:
:001: TSCALE = 4
================================================================================
:ERR: 'XSCALE' NONMEM reserved variable is not translated:
:001: XSCALE = 4
================================================================================
:ERR: 'CALL GETETA(ETA)' not supported in translation:
:001: CALL GETETA(ETA)
================================================================================
$PRED syntax error:
:001: ,
^
================================================================================
:ERR: can only request depot and central compartments for solved systems in rxode2 translations:
:001: f3=1
================================================================================
:ERR: can only request depot and central compartments for solved systems in rxode2 translations:
:001: f3=1
================================================================================
:ERR: F0/FO is not supported in translation:
:001: F0=3
================================================================================
i getting information from '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/nonmem2rx/TheopdExt.ctl'
i reading in lst file
i seeing if file argument is actually lst file
i not list file, control stream
i done
i splitting control stream by records
i done
i Processing record $INPUT
i Processing record $gTHETA
i Processing record $OMEGA
i Processing record $SIGMA
i Processing record $PROBLEM
i Processing record $DATA
i Processing record $ESTIMATION
i Ignore record $ESTIMATION
i Processing record $COVARIANCE
i Ignore record $COVARIANCE
i Processing record $PRED
i Processing record $TABLE
i final parameters not updated, will skip validation
i changing most variables to lower case
i done
i replace theta names
i done
i replace eta names
i done
i getting information from '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/nonmem2rx/Theopd.ctl'
i reading in lst file
i seeing if file argument is actually lst file
i not list file, control stream
i done
i splitting control stream by records
i done
i Processing record $INPUT
i Processing record $gTHETA
i Processing record $OMEGA
i Processing record $SIGMA
i Processing record $PROBLEM
i Processing record $DATA
i Processing record $ESTIMATION
i Ignore record $ESTIMATION
i Processing record $COVARIANCE
i Ignore record $COVARIANCE
i Processing record $PRED
i Processing record $TABLE
i final parameters not updated, will skip validation
i changing most variables to lower case
i done
i replace theta names
i done
i replace eta names
i done
$DATA syntax error:
:001: matt.csv matt=.csv
^
================================================================================
$INPUT syntax error:
:001: matt~1
^
================================================================================
$MODEL syntax error:
:001: malformed
^
================================================================================
:ERR: $OMEGA or $SIGMA BLOCK(N) does not have enough elements:
:001: BLOCK(3) 6. .005 .3 .0002 .006
================================================================================
:ERR: $OMEGA or $SIGMA BLOCK(N) has too many elements:
:001: BLOCK(3) 6. .005 .3 .0002 .006 .4 .4
================================================================================
:ERR: (FIXED/UNINT .4) is not supported in an $OMEGA or $SIGMA BLOCK:
:001: BLOCK(3) 6. .005 .3 .0002 .006 (fix .4)
================================================================================
$OMEGA syntax error:
:001: garbage
^
================================================================================
:ERR: REPLACE requesting data item replacement for 'NOINP' which is not defined in the $INPUT record:
:001: REPLACE ETA(NOINP)=ETA(0,2,3)
================================================================================
-----------------------
String Comparison Tests
-----------------------
INTENTIONAL UNIT TEST FAILURE to show what a unit test failure looks like!
FAILED at line 210 in function _nonmem2rx_parse_strncmpci! strncmpci("hey", "HEY", 3) != 'h' - 'H'
a: strncmpci("hey", "HEY", 3) is 0
b: 'h' - 'H' is 32
------ beginning ------
<1b>[32mAll unit tests passed!<1b>[m
$SUB syntax error:
:001: tranvan1
^
================================================================================
:ERR: $SUBROUTINES 'INFN' unsupported for translation:
:001: INFN=matt.f
================================================================================
:ERR: $SUBROUTINES 'TOL' subroutine from external fortran unsupported for translation:
:001: TOL=matt.f
================================================================================
:ERR: $SUBROUTINES 'ATOL' subroutine from external fortran unsupported for translation:
:001: ATOL=matt.f
================================================================================
:ERR: $SUBROUTINES 'SSATOL' subroutine from external fortran unsupported for translation:
:001: SSATOL=matt.f
================================================================================
$TAB syntax error:
:001: fun=funny.csv
^
================================================================================
:ERR: the NAMES() statement named more parameters than present in this $THETA block, error in translation:
:001: NAMES(V1,CL,Q,V2) (0.0,7.0) (0.0,7.0) (0.0,7.0)
================================================================================
$THETA syntax error:
:001: garbage
^
================================================================================
<1b>[1mlotri syntax error:
=================================================================================<1b>[0m
lotri error:
lower triangular matrix not correct size
did you mean something like:
theta1 + theta2 + theta3 + theta4 + theta5 + theta6 + theta7 + theta8 + theta9 + theta10 + theta11 + theta12 + theta13 + eta1 + omega.1.2 + omega.1.3 + omega.1.4 + omega.1.5 + omega.1.6 + omega.1.7 + omega.1.8 + omega.1.9 + omega.1.10 + omega.1.11 + omega.1.12 + eta2 + omega.2.3 + omega.2.4 + omega.2.5 + omega.2.6 + omega.2.7 + omega.2.8 + omega.2.9 + omega.2.10 + omega.2.11 + omega.2.12 + eta3 + omega.3.4 + omega.3.5 + omega.3.6 + omega.3.7 + omega.3.8 + omega.3.9 + omega.3.10 + omega.3.11 + omega.3.12 + eta4 + omega.4.5 + omega.4.6 + omega.4.7 + omega.4.8 + omega.4.9 + omega.4.10 + omega.4.11 + omega.4.12 + eta5 + omega.5.6 + omega.5.7 + omega.5.8 + omega.5.9 + omega.5.10 + omega.5.11 + omega.5.12 + eta6 + omega.6.7 + omega.6.8 + omega.6.9 + omega.6.10 + omega.6.11 + omega.6.12 + eta7 + omega.7.8 + omega.7.9 + omega.7.10 + omega.7.11 + omega.7.12 + eta8 + omega.8.9 + omega.8.10 + omega.8.11 + omega.8.12 + eta9 + omega.9.10 + omega.9.11 + omega.9.12 + eta10 + omega.10.11 + omega.10.12 + eta11 + omega.11.12 + eta12 + eps1+v1+v2+v3+v4+v5+v6+v7+v8+v9+v10+v11+v12+v13+v14+v15+v16+v17+v18+v19+v20+v21+v22+v23+v24+v25+v26+v27~c(1.30441367197642,
0, 0,
0, 0, 0,
0, 0, 0, 0,
0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0,
<1b>[1m:001<1b>[0m: theta1 + theta2 + theta3 + theta4 + theta5 + theta6 + theta7 + theta8 + theta9 + theta10 + theta11 + theta12 + theta13 + eta1 + omega.1.2 + omega.1.3 + omega.1.4 + omega.1.5 + omega.1.6 + omega.1.7 + omega.1.8 + omega.1.9 + omega.1.10 + omega.1.11 + omega.1.12 + eta2 + omega.2.3 + omega.2.4 + omega.2.5 + omega.2.6 + omega.2.7 + omega.2.8 + omega.2.9 + omega.2.10 + omega.2.11 + omega.2.12 + eta3 + omega.3.4 + omega.3.5 + omega.3.6 + omega.3.7 + omega.3.8 + omega.3.9 + omega.3.10 + omega.3.11 + omega.3.12 + eta4 + omega.4.5 + omega.4.6 + omega.4.7 + omega.4.8 + omega.4.9 + omega.4.10 + omega.4.11 + omega.4.12 + eta5 + omega.5.6 + omega.5.7 + omega.5.8 + omega.5.9 + omega.5.10 + omega.5.11 + omega.5.12 + eta6 + omega.6.7 + omega.6.8 + omega.6.9 + omega.6.10 + omega.6.11 + omega.6.12 + eta7 + omega.7.8 + omega.7.9 + omega.7.10 + omega.7.11 + omega.7.12 + eta8 + omega.8.9 + omega.8.10 + omega.8.11 + omega.8.12 + eta9 + omega.9.10 + omega.9.11 + omega.9.12 + eta10 + omega.10.11 + omega.10.12 + eta11 + omega.11.12 + eta12 + eps1 ~ c(1.30441367197642, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1.58844936874363, 4.85473065684898, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.00539049655208395, -0.0748282195029211, 0.0238050759878246, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -0.0346163870505972, -0.0412181533880286, 0.00156764723796178, 0.00761353116573484, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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<1b>[1m=================================================================================<1b>[0m
i try to get covariance a different method (slower)
[ FAIL 9 | WARN 2 | SKIP 15 | PASS 750 ]
══ Skipped tests (15) ══════════════════════════════════════════════════════════
• On CRAN (15): 'test-as-nonmem2rx.R:2:3', 'test-external-models.R:6:5',
'test-full-parsing.R:8:30', 'test-linCmt.R:2:3', 'test-model-load.R:7:5',
'test-nm75.R:7:5', 'test-piping.R:7:5', 'test-print.R:2:3',
'test-read-nonmemData.R:3:5', 'test-read-nonmemData.R:19:5',
'test-rename.R:7:5', 'test-rxsolve.R:11:5', 'test-sim-iwres.R:2:3',
'test-sim-iwres.R:62:3', 'test-vdiff.R:2:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-eta-order.R:7:3'): eta order ─────────────────────────────────
dimnames(f$omega)[[1]] (`actual`) not equal to c("BSV.KTR", "BSV.Vp", "BSV.BIO", "BSV.Q", "BSV.CLint", "BSV.Vc") (`expected`).
`actual`: "BSV.CLint" "BSV.Vc" "BSV.KTR" "BSV.Vp" "BSV.BIO" "BSV.Q"
`expected`: "BSV.KTR" "BSV.Vp" "BSV.BIO" "BSV.Q" "BSV.CLint" "BSV.Vc"
── Failure ('test-omega.R:12:5'): test omega ───────────────────────────────────
.nonmem2rx$ini (`actual`) not equal to `eq` (`expected`).
actual vs expected
- "eta1 ~ fix(0.09)"
- "eta2 ~ fix(1e-04, 0.09)"
- "eta3 ~ fix(1e-04, 1e-04, 0.09)"
+ "eta1 + eta2 + eta3 ~ fix(0.09, 1e-04, 0.09, 1e-04, 1e-04, 0.09)"
Backtrace:
▆
1. └─nonmem2rx (local) .o(...) at test-omega.R:94:3
2. └─testthat::expect_equal(.nonmem2rx$ini, eq) at test-omega.R:12:5
── Failure ('test-omega.R:12:5'): test omega ───────────────────────────────────
.nonmem2rx$ini (`actual`) not equal to `eq` (`expected`).
actual vs expected
- "eta1 ~ fix(0.09)"
- "eta2 ~ fix(1e-04, 0.09)"
- "eta3 ~ fix(1e-04, 1e-04, 0.09)"
+ "eta1 + eta2 + eta3 ~ fix(0.09, 1e-04, 0.09, 1e-04, 1e-04, 0.09)"
Backtrace:
▆
1. └─nonmem2rx (local) .o(...) at test-omega.R:103:3
2. └─testthat::expect_equal(.nonmem2rx$ini, eq) at test-omega.R:12:5
── Failure ('test-omega.R:12:5'): test omega ───────────────────────────────────
.nonmem2rx$ini (`actual`) not equal to `eq` (`expected`).
actual vs expected
- "eta1 ~ c(eta1 = 0.1)"
- "eta2 ~ c(eta1 = 0.01, eta2 = 0.1)"
- "eta3 ~ c(eta1 = 0.01, eta2 = 0.01, eta3 = 0.1)"
- "eta4 ~ c(eta1 = 0.01, eta2 = 0.01, eta3 = 0.01, eta4 = 0.1)"
- "eta5 ~ c(eta1 = 0.01, eta2 = 0.01, eta3 = 0.01, eta4 = 0.01, eta5 = 0.1)"
- "eta6 ~ c(eta1 = 0.01, eta2 = 0.01, eta3 = 0.01, eta4 = 0.01, eta5 = 0.01, eta6 = 0.1)"
+ "eta1 + eta2 + eta3 + eta4 + eta5 + eta6 ~ c(0.1, 0.01, 0.1, 0.01, 0.01, 0.1, 0.01, 0.01, 0.01, 0.1, 0.01, 0.01, 0.01, 0.01, 0.1, 0.01, 0.01, 0.01, 0.01, 0.01, 0.1)"
Backtrace:
▆
1. └─nonmem2rx (local) .o(...) at test-omega.R:107:3
2. └─testthat::expect_equal(.nonmem2rx$ini, eq) at test-omega.R:12:5
── Failure ('test-omega.R:12:5'): test omega ───────────────────────────────────
.nonmem2rx$ini (`actual`) not equal to `eq` (`expected`).
actual vs expected
- "eta1 ~ c(eta1 = 0.1)"
- "eta2 ~ c(eta1 = 0.01, eta2 = 0.1)"
- "eta3 ~ c(eta1 = 0.01, eta2 = 0.01, eta3 = 0.1)"
- "eta4 ~ c(eta1 = 0.01, eta2 = 0.01, eta3 = 0.01, eta4 = 0.1)"
- "eta5 ~ c(eta1 = 0.01, eta2 = 0.01, eta3 = 0.01, eta4 = 0.01, eta5 = 0.1)"
- "eta6 ~ c(eta1 = 0.01, eta2 = 0.01, eta3 = 0.01, eta4 = 0.01, eta5 = 0.01, eta6 = 0.1)"
+ "eta1 + eta2 + eta3 + eta4 + eta5 + eta6 ~ c(0.1, 0.01, 0.1, 0.01, 0.01, 0.1, 0.01, 0.01, 0.01, 0.1, 0.01, 0.01, 0.01, 0.01, 0.1, 0.01, 0.01, 0.01, 0.01, 0.01, 0.1)"
"eta7 ~ 0.02"
Backtrace:
▆
1. └─nonmem2rx (local) .o(...) at test-omega.R:110:3
2. └─testthat::expect_equal(.nonmem2rx$ini, eq) at test-omega.R:12:5
── Failure ('test-omega.R:12:5'): test omega ───────────────────────────────────
.nonmem2rx$ini (`actual`) not equal to `eq` (`expected`).
actual vs expected
- "eta1 ~ 0.03"
- "eta2 ~ c(0.01, 0.03)"
- "eta3 ~ c(0.01, 0.01, 0.03)"
- "eta4 ~ c(0.01, 0.01, 0.01, 0.03)"
+ "eta1 + eta2 + eta3 + eta4 ~ c(0.03, 0.01, 0.03, 0.01, 0.01, 0.03, 0.01, 0.01, 0.01, 0.03)"
Backtrace:
▆
1. └─nonmem2rx (local) .o(...) at test-omega.R:170:3
2. └─testthat::expect_equal(.nonmem2rx$ini, eq) at test-omega.R:12:5
── Failure ('test-omega.R:12:5'): test omega ───────────────────────────────────
.nonmem2rx$ini (`actual`) not equal to `eq` (`expected`).
actual vs expected
- "eta1 ~ fix(0.03)"
- "eta2 ~ fix(0.01, 0.03)"
- "eta3 ~ fix(0.01, 0.01, 0.03)"
- "eta4 ~ fix(0.01, 0.01, 0.01, 0.03)"
+ "eta1 + eta2 + eta3 + eta4 ~ fix(0.03, 0.01, 0.03, 0.01, 0.01, 0.03, 0.01, 0.01, 0.01, 0.03)"
Backtrace:
▆
1. └─nonmem2rx (local) .o(...) at test-omega.R:173:3
2. └─testthat::expect_equal(.nonmem2rx$ini, eq) at test-omega.R:12:5
── Failure ('test-omega.R:12:5'): test omega ───────────────────────────────────
.nonmem2rx$ini (`actual`) not equal to `eq` (`expected`).
actual vs expected
- "eta1 ~ fix(0.03)"
- "eta2 ~ fix(0.01, 0.03)"
- "eta3 ~ fix(0.01, 0.01, 0.03)"
- "eta4 ~ fix(0.01, 0.01, 0.01, 0.03)"
+ "eta1 + eta2 + eta3 + eta4 ~ fix(0.03, 0.01, 0.03, 0.01, 0.01, 0.03, 0.01, 0.01, 0.01, 0.03)"
Backtrace:
▆
1. └─nonmem2rx (local) .o(...) at test-omega.R:176:3
2. └─testthat::expect_equal(.nonmem2rx$ini, eq) at test-omega.R:12:5
── Failure ('test-omega.R:12:5'): test omega ───────────────────────────────────
.nonmem2rx$ini (`actual`) not equal to `eq` (`expected`).
actual vs expected
- "eta1 ~ fix(0.03)"
- "eta2 ~ fix(0.01, 0.03)"
- "eta3 ~ fix(0.01, 0.01, 0.03)"
- "eta4 ~ fix(0.01, 0.01, 0.01, 0.03)"
+ "eta1 + eta2 + eta3 + eta4 ~ fix(0.03, 0.01, 0.03, 0.01, 0.01, 0.03, 0.01, 0.01, 0.01, 0.03)"
Backtrace:
▆
1. └─nonmem2rx (local) .o(...) at test-omega.R:179:3
2. └─testthat::expect_equal(.nonmem2rx$ini, eq) at test-omega.R:12:5
[ FAIL 9 | WARN 2 | SKIP 15 | PASS 750 ]
Deleting unused snapshots:
• vdiff/first-plot.svg
• vdiff/first-pred-plot.svg
• vdiff/second-plot-gg-logxy.svg
• vdiff/second-plot-gg.svg
• vdiff/second-plot-logxy.svg
• vdiff/second-plot.svg
• vdiff/second-pred-plot-gg-logxy.svg
• vdiff/second-pred-plot-gg.svg
• vdiff/second-pred-plot-logxy.svg
• vdiff/second-pred-plot.svg
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.1.4
Check: installed package size
Result: NOTE
installed size is 9.2Mb
sub-directories of 1Mb or more:
libs 5.1Mb
mods 3.3Mb
Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64
Version: 0.1.5
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavor: r-oldrel-macos-arm64