Last updated on 2025-12-24 09:50:10 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| ctsem | 4 | 2 | 5 |
| ctsemOMX | 7 | 6 |
Current CRAN status: ERROR: 4, NOTE: 2, OK: 5
Version: 3.10.4
Check: examples
Result: ERROR
Running examples in ‘ctsem-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ctACF
> ### Title: Continuous Time Autocorrelation Function (ctACF)
> ### Aliases: ctACF
>
> ### ** Examples
>
> data.table::setDTthreads(1) #ignore this line
> # Example usage:
> head(ctstantestdat)
id time Y1 Y2 TD1 TI1 TI2 TI3
4 1 0.000000 8.628419 13.55213 0 -0.05380504 -1.366299 -0.2074973
5 1 0.123705 NA 11.34075 NA -0.05380504 -1.366299 -0.2074973
6 1 0.594186 7.500058 12.33738 0 -0.05380504 -1.366299 -0.2074973
7 1 0.888842 6.834832 12.63265 1 -0.05380504 -1.366299 -0.2074973
8 1 1.186905 7.010044 11.90834 0 -0.05380504 -1.366299 -0.2074973
9 1 1.624510 6.791367 10.21116 0 -0.05380504 -1.366299 -0.2074973
> ctACF(ctstantestdat,varnames=c('Y1'),idcol='id',timecol='time',nboot=5)
Loading required namespace: collapse
Error in `[.data.table`(dat, , `:=`(.timediff, c(NA, diff(get(timecol)))), :
attempt access index 8/8 in VECTOR_ELT
Calls: ctACF -> quantile -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 3.10.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [100s/127s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ctsem)
Loading required package: Rcpp
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
> pdf(NULL)
> test_check("ctsem")
Saving _problems/test-intervalise-12.R
Saving _problems/test-reshaping-30.R
[,1] [,2]
[1,] "0" "0"
[2,] "0" "diff"
[,1]
[1,] "0"
[,1]
[1,] "0"
[2,] "cint"
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
starting worker pid=1704197 on localhost:34338 at 23:39:30.866
starting worker pid=1704198 on localhost:34338 at 23:39:31.611
Loading required package: data.table
Loading required package: data.table
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
starting worker pid=1713545 on localhost:39191 at 23:40:03.554
starting worker pid=1713544 on localhost:39191 at 23:40:03.956
Loading required package: data.table
Loading required package: data.table
Attaching package: ‘data.table’
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
The following object is masked from ‘package:base’:
%notin%
SAMPLING FOR MODEL 'ctsm' NOW (CHAIN 1).
SAMPLING FOR MODEL 'ctsm' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.010495 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 104.95 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 1:
Chain 1: Gradient evaluation took 0.019997 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 199.97 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
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Chain 2:
Chain 2: Elapsed Time: 25.372 seconds (Warm-up)
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Chain 2: 39.261 seconds (Total)
Chain 2:
Chain 1:
Chain 1: Elapsed Time: 23.852 seconds (Warm-up)
Chain 1: 15.426 seconds (Sampling)
Chain 1: 39.278 seconds (Total)
Chain 1:
[ FAIL 2 | WARN 0 | SKIP 16 | PASS 6 ]
══ Skipped tests (16) ══════════════════════════════════════════════════════════
• empty test (16): , , , , , , , , , , , , , , ,
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-intervalise.R:10:3'): intervals ────────────────────────────────
Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─ctsem::ctLongToWide(...) at test-intervalise.R:10:3
2. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id]
3. └─data.table:::`[.data.table`(...)
── Error ('test-reshaping.R:29:3'): reshaping1 ─────────────────────────────────
Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─ctsem::ctLongToWide(...) at test-reshaping.R:29:3
2. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id]
3. └─data.table:::`[.data.table`(...)
[ FAIL 2 | WARN 0 | SKIP 16 | PASS 6 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 3.10.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [83s/99s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ctsem)
Loading required package: Rcpp
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
> pdf(NULL)
> test_check("ctsem")
Saving _problems/test-intervalise-12.R
Saving _problems/test-reshaping-30.R
[,1] [,2]
[1,] "0" "0"
[2,] "0" "diff"
[,1]
[1,] "0"
[,1]
[1,] "0"
[2,] "cint"
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
starting worker pid=2133466 on localhost:31896 at 15:35:16.115
starting worker pid=2133467 on localhost:31896 at 15:35:16.398
Loading required package: data.table
Loading required package: data.table
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
starting worker pid=2193928 on localhost:33512 at 15:35:38.459
starting worker pid=2193929 on localhost:33512 at 15:35:38.789
Loading required package: data.table
Loading required package: data.table
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
SAMPLING FOR MODEL 'ctsm' NOW (CHAIN 1).
SAMPLING FOR MODEL 'ctsm' NOW (CHAIN 2).
Chain 1:
Chain 1: Gradient evaluation took 0.017387 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 173.87 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 2:
Chain 2: Gradient evaluation took 0.011818 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 118.18 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
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Chain 1:
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Chain 2: Elapsed Time: 25.776 seconds (Warm-up)
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Chain 2: 38.346 seconds (Total)
Chain 2:
[ FAIL 2 | WARN 0 | SKIP 16 | PASS 6 ]
══ Skipped tests (16) ══════════════════════════════════════════════════════════
• empty test (16): , , , , , , , , , , , , , , ,
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-intervalise.R:10:3'): intervals ────────────────────────────────
Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─ctsem::ctLongToWide(...) at test-intervalise.R:10:3
2. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id]
3. └─data.table:::`[.data.table`(...)
── Error ('test-reshaping.R:29:3'): reshaping1 ─────────────────────────────────
Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─ctsem::ctLongToWide(...) at test-reshaping.R:29:3
2. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id]
3. └─data.table:::`[.data.table`(...)
[ FAIL 2 | WARN 0 | SKIP 16 | PASS 6 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 3.10.4
Check: examples
Result: ERROR
Running examples in ‘ctsem-Ex.R’ failed
The error most likely occurred in:
> ### Name: ctACF
> ### Title: Continuous Time Autocorrelation Function (ctACF)
> ### Aliases: ctACF
>
> ### ** Examples
>
> data.table::setDTthreads(1) #ignore this line
> # Example usage:
> head(ctstantestdat)
id time Y1 Y2 TD1 TI1 TI2 TI3
4 1 0.000000 8.628419 13.55213 0 -0.05380504 -1.366299 -0.2074973
5 1 0.123705 NA 11.34075 NA -0.05380504 -1.366299 -0.2074973
6 1 0.594186 7.500058 12.33738 0 -0.05380504 -1.366299 -0.2074973
7 1 0.888842 6.834832 12.63265 1 -0.05380504 -1.366299 -0.2074973
8 1 1.186905 7.010044 11.90834 0 -0.05380504 -1.366299 -0.2074973
9 1 1.624510 6.791367 10.21116 0 -0.05380504 -1.366299 -0.2074973
> ctACF(ctstantestdat,varnames=c('Y1'),idcol='id',timecol='time',nboot=5)
Loading required namespace: collapse
Error in `[.data.table`(dat, , `:=`(.timediff, c(NA, diff(get(timecol)))), :
attempt access index 8/8 in VECTOR_ELT
Calls: ctACF -> quantile -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 3.10.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [181s/327s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ctsem)
Loading required package: Rcpp
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
> pdf(NULL)
> test_check("ctsem")
Saving _problems/test-intervalise-12.R
Saving _problems/test-reshaping-30.R
[,1] [,2]
[1,] "0" "0"
[2,] "0" "diff"
[,1]
[1,] "0"
[,1]
[1,] "0"
[2,] "cint"
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
starting worker pid=1558680 on localhost:28220 at 17:45:03.882
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
starting worker pid=1558681 on localhost:28220 at 17:45:07.151
Loading required package: data.table
Loading required package: data.table
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
starting worker pid=1564202 on localhost:38575 at 17:46:17.958
starting worker pid=1564201 on localhost:38575 at 17:46:18.762
Loading required package: data.table
Loading required package: data.table
Attaching package: ‘data.table’
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
The following object is masked from ‘package:base’:
%notin%
SAMPLING FOR MODEL 'ctsm' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.039327 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 393.27 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
SAMPLING FOR MODEL 'ctsm' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.061976 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 619.76 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
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Chain 2:
Chain 2: Elapsed Time: 84.339 seconds (Warm-up)
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Chain 2: 121.148 seconds (Total)
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Chain 1:
Chain 1: Elapsed Time: 85.138 seconds (Warm-up)
Chain 1: 38.077 seconds (Sampling)
Chain 1: 123.215 seconds (Total)
Chain 1:
[ FAIL 2 | WARN 0 | SKIP 16 | PASS 6 ]
══ Skipped tests (16) ══════════════════════════════════════════════════════════
• empty test (16): , , , , , , , , , , , , , , ,
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-intervalise.R:10:3'): intervals ────────────────────────────────
Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─ctsem::ctLongToWide(...) at test-intervalise.R:10:3
2. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id]
3. └─data.table:::`[.data.table`(...)
── Error ('test-reshaping.R:29:3'): reshaping1 ─────────────────────────────────
Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─ctsem::ctLongToWide(...) at test-reshaping.R:29:3
2. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id]
3. └─data.table:::`[.data.table`(...)
[ FAIL 2 | WARN 0 | SKIP 16 | PASS 6 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 3.10.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [137s/164s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ctsem)
Loading required package: Rcpp
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
> pdf(NULL)
> test_check("ctsem")
Saving _problems/test-intervalise-12.R
Saving _problems/test-reshaping-30.R
[,1] [,2]
[1,] "0" "0"
[2,] "0" "diff"
[,1]
[1,] "0"
[,1]
[1,] "0"
[2,] "cint"
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
starting worker pid=3476290 on localhost:37464 at 06:54:02.652
starting worker pid=3476291 on localhost:37464 at 06:54:05.122
Loading required package: data.table
Loading required package: data.table
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
starting worker pid=3482066 on localhost:28695 at 06:54:42.127
starting worker pid=3482067 on localhost:28695 at 06:54:44.506
Loading required package: data.table
Loading required package: data.table
Attaching package: ‘data.table’
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
The following object is masked from ‘package:base’:
%notin%
SAMPLING FOR MODEL 'ctsm' NOW (CHAIN 2).
SAMPLING FOR MODEL 'ctsm' NOW (CHAIN 1).
Chain 2:
Chain 2: Gradient evaluation took 0.011708 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 117.08 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
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Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 259.86 seconds.
Chain 1: Adjust your expectations accordingly!
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[ FAIL 2 | WARN 0 | SKIP 16 | PASS 6 ]
══ Skipped tests (16) ══════════════════════════════════════════════════════════
• empty test (16): , , , , , , , , , , , , , , ,
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-intervalise.R:10:3'): intervals ────────────────────────────────
Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─ctsem::ctLongToWide(...) at test-intervalise.R:10:3
2. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id]
3. └─data.table:::`[.data.table`(...)
── Error ('test-reshaping.R:29:3'): reshaping1 ─────────────────────────────────
Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─ctsem::ctLongToWide(...) at test-reshaping.R:29:3
2. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id]
3. └─data.table:::`[.data.table`(...)
[ FAIL 2 | WARN 0 | SKIP 16 | PASS 6 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 3.10.4
Check: installed package size
Result: NOTE
installed size is 201.7Mb
sub-directories of 1Mb or more:
R 2.0Mb
data 1.7Mb
libs 196.6Mb
Flavor: r-oldrel-macos-arm64
Version: 3.10.4
Check: for GNU extensions in Makefiles
Result: NOTE
GNU make is a SystemRequirements.
Flavor: r-oldrel-macos-arm64
Version: 3.10.4
Flags: --no-vignettes
Check: installed package size
Result: NOTE
installed size is 11.6Mb
sub-directories of 1Mb or more:
R 1.2Mb
data 1.7Mb
libs 7.3Mb
Flavor: r-oldrel-windows-x86_64
Current CRAN status: ERROR: 7, OK: 6
Version: 1.0.7
Check: examples
Result: ERROR
Running examples in ‘ctsemOMX-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ctGenerateFromFit
> ### Title: Generates data according to the model estimated in a ctsemFit
> ### object.
> ### Aliases: ctGenerateFromFit
>
> ### ** Examples
>
>
> data(AnomAuth)
> AnomAuthmodel <- ctModel(LAMBDA = matrix(c(1, 0, 0, 1), nrow = 2, ncol = 2),
+ Tpoints = 5, n.latent = 2, n.manifest = 2, MANIFESTVAR=diag(0, 2))
Type "omx" is still supported but requires ctsemOMX package installation. "ct" or "dt" are recommended types.
CINT specified via single value -- filling 2 * 1 matrix:
[,1]
[1,] "0"
[2,] "0"
> AnomAuthfit <- ctFit(AnomAuth, AnomAuthmodel)
wide format data detected
Running ctsemCarefulFit with 14 parameters
Running ctsem with 14 parameters
Beginning initial fit attempt
Running ctsem with 14 parameters
Lowest minimum so far: 23415.9290488409
Solution found
Solution found! Final fit=23415.929 (started at 85069.46) (1 attempt(s): 1 valid, 0 errors)
>
> dwide <- ctGenerateFromFit(AnomAuthfit,timestep=1,n.subjects=5,wide=TRUE)
Error in `[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), :
attempt access index 4/4 in VECTOR_ELT
Calls: ctGenerateFromFit ... withCallingHandlers -> ctGenerate -> ctLongToWide -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.0.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [14s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ctsemOMX)
Loading required package: ctsem
Loading required package: Rcpp
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
Loading required package: OpenMx
Attaching package: 'ctsemOMX'
The following objects are masked from 'package:ctsem':
ctFit, ctIndplot
> pdf(NULL)
> test_check("ctsemOMX")
Saving _problems/test-intervalise-12.R
Saving _problems/test-kalmanVram-35.R
Saving _problems/test-reshaping-30.R
[ FAIL 3 | WARN 0 | SKIP 3 | PASS 0 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): , ,
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-intervalise.R:10:3'): intervals ────────────────────────────────
Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─ctsem::ctLongToWide(...) at test-intervalise.R:10:3
2. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id]
3. └─data.table:::`[.data.table`(...)
── Error ('test-kalmanVram.R:35:1'): time calc ─────────────────────────────────
Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 7/7 in VECTOR_ELT
Backtrace:
▆
1. └─ctsemOMX::ctRefineTo(...) at test-kalmanVram.R:35:1
2. └─ctsemOMX::ctFit(datawide, m, nofit = TRUE, ...)
3. └─ctsem::ctLongToWide(...)
4. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id]
5. └─data.table:::`[.data.table`(...)
── Error ('test-reshaping.R:29:3'): reshaping1 ─────────────────────────────────
Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─ctsem::ctLongToWide(...) at test-reshaping.R:29:3
2. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id]
3. └─data.table:::`[.data.table`(...)
[ FAIL 3 | WARN 0 | SKIP 3 | PASS 0 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.7
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘ctsemOMX.rnw’ using knitr
Quitting from ctsemOMX.rnw:315-323 [longformatconversion]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
---
Backtrace:
x
1. \-ctsem::ctLongToWide(...)
2. +-data_long[, `:=`(discrete.time.point = 1:.N), by = id]
3. \-data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'ctsemOMX.rnw' failed with diagnostics:
attempt access index 8/8 in VECTOR_ELT
--- failed re-building ‘ctsemOMX.rnw’
SUMMARY: processing the following file failed:
‘ctsemOMX.rnw’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.0.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [10s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ctsemOMX)
Loading required package: ctsem
Loading required package: Rcpp
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
Loading required package: OpenMx
Attaching package: 'ctsemOMX'
The following objects are masked from 'package:ctsem':
ctFit, ctIndplot
> pdf(NULL)
> test_check("ctsemOMX")
Saving _problems/test-intervalise-12.R
Saving _problems/test-kalmanVram-35.R
Saving _problems/test-reshaping-30.R
[ FAIL 3 | WARN 0 | SKIP 3 | PASS 0 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): , ,
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-intervalise.R:10:3'): intervals ────────────────────────────────
Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─ctsem::ctLongToWide(...) at test-intervalise.R:10:3
2. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id]
3. └─data.table:::`[.data.table`(...)
── Error ('test-kalmanVram.R:35:1'): time calc ─────────────────────────────────
Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 7/7 in VECTOR_ELT
Backtrace:
▆
1. └─ctsemOMX::ctRefineTo(...) at test-kalmanVram.R:35:1
2. └─ctsemOMX::ctFit(datawide, m, nofit = TRUE, ...)
3. └─ctsem::ctLongToWide(...)
4. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id]
5. └─data.table:::`[.data.table`(...)
── Error ('test-reshaping.R:29:3'): reshaping1 ─────────────────────────────────
Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─ctsem::ctLongToWide(...) at test-reshaping.R:29:3
2. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id]
3. └─data.table:::`[.data.table`(...)
[ FAIL 3 | WARN 0 | SKIP 3 | PASS 0 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.7
Check: examples
Result: ERROR
Running examples in ‘ctsemOMX-Ex.R’ failed
The error most likely occurred in:
> ### Name: ctGenerateFromFit
> ### Title: Generates data according to the model estimated in a ctsemFit
> ### object.
> ### Aliases: ctGenerateFromFit
>
> ### ** Examples
>
>
> data(AnomAuth)
> AnomAuthmodel <- ctModel(LAMBDA = matrix(c(1, 0, 0, 1), nrow = 2, ncol = 2),
+ Tpoints = 5, n.latent = 2, n.manifest = 2, MANIFESTVAR=diag(0, 2))
Type "omx" is still supported but requires ctsemOMX package installation. "ct" or "dt" are recommended types.
CINT specified via single value -- filling 2 * 1 matrix:
[,1]
[1,] "0"
[2,] "0"
> AnomAuthfit <- ctFit(AnomAuth, AnomAuthmodel)
wide format data detected
Running ctsemCarefulFit with 14 parameters
Running ctsem with 14 parameters
Beginning initial fit attempt
Running ctsem with 14 parameters
Lowest minimum so far: 23415.9290488409
Solution found
Solution found! Final fit=23415.929 (started at 85069.46) (1 attempt(s): 1 valid, 0 errors)
>
> dwide <- ctGenerateFromFit(AnomAuthfit,timestep=1,n.subjects=5,wide=TRUE)
Error in `[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), :
attempt access index 4/4 in VECTOR_ELT
Calls: ctGenerateFromFit ... withCallingHandlers -> ctGenerate -> ctLongToWide -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [23s/63s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ctsemOMX)
Loading required package: ctsem
Loading required package: Rcpp
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
Loading required package: OpenMx
To take full advantage of multiple cores, use:
mxOption(key='Number of Threads', value=parallel::detectCores()) #now
Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx)
Attaching package: 'ctsemOMX'
The following objects are masked from 'package:ctsem':
ctFit, ctIndplot
> pdf(NULL)
> test_check("ctsemOMX")
Saving _problems/test-intervalise-12.R
Saving _problems/test-kalmanVram-35.R
Saving _problems/test-reshaping-30.R
[ FAIL 3 | WARN 0 | SKIP 3 | PASS 0 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): , ,
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-intervalise.R:10:3'): intervals ────────────────────────────────
Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─ctsem::ctLongToWide(...) at test-intervalise.R:10:3
2. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id]
3. └─data.table:::`[.data.table`(...)
── Error ('test-kalmanVram.R:35:1'): time calc ─────────────────────────────────
Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 7/7 in VECTOR_ELT
Backtrace:
▆
1. └─ctsemOMX::ctRefineTo(...) at test-kalmanVram.R:35:1
2. └─ctsemOMX::ctFit(datawide, m, nofit = TRUE, ...)
3. └─ctsem::ctLongToWide(...)
4. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id]
5. └─data.table:::`[.data.table`(...)
── Error ('test-reshaping.R:29:3'): reshaping1 ─────────────────────────────────
Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─ctsem::ctLongToWide(...) at test-reshaping.R:29:3
2. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id]
3. └─data.table:::`[.data.table`(...)
[ FAIL 3 | WARN 0 | SKIP 3 | PASS 0 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.7
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘ctsemOMX.rnw’ using knitr
Quitting from ctsemOMX.rnw:315-323 [longformatconversion]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 8/8 in VECTOR_ELT
---
Backtrace:
x
1. \-ctsem::ctLongToWide(...)
2. +-data_long[, `:=`(discrete.time.point = 1:.N), by = id]
3. \-data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'ctsemOMX.rnw' failed with diagnostics:
attempt access index 8/8 in VECTOR_ELT
--- failed re-building ‘ctsemOMX.rnw’
SUMMARY: processing the following file failed:
‘ctsemOMX.rnw’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [15s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ctsemOMX)
Loading required package: ctsem
Loading required package: Rcpp
ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions
Loading required package: OpenMx
To take full advantage of multiple cores, use:
mxOption(key='Number of Threads', value=parallel::detectCores()) #now
Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx)
Attaching package: 'ctsemOMX'
The following objects are masked from 'package:ctsem':
ctFit, ctIndplot
> pdf(NULL)
> test_check("ctsemOMX")
Saving _problems/test-intervalise-12.R
Saving _problems/test-kalmanVram-35.R
Saving _problems/test-reshaping-30.R
[ FAIL 3 | WARN 0 | SKIP 3 | PASS 0 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): , ,
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-intervalise.R:10:3'): intervals ────────────────────────────────
Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─ctsem::ctLongToWide(...) at test-intervalise.R:10:3
2. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id]
3. └─data.table:::`[.data.table`(...)
── Error ('test-kalmanVram.R:35:1'): time calc ─────────────────────────────────
Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 7/7 in VECTOR_ELT
Backtrace:
▆
1. └─ctsemOMX::ctRefineTo(...) at test-kalmanVram.R:35:1
2. └─ctsemOMX::ctFit(datawide, m, nofit = TRUE, ...)
3. └─ctsem::ctLongToWide(...)
4. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id]
5. └─data.table:::`[.data.table`(...)
── Error ('test-reshaping.R:29:3'): reshaping1 ─────────────────────────────────
Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─ctsem::ctLongToWide(...) at test-reshaping.R:29:3
2. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id]
3. └─data.table:::`[.data.table`(...)
[ FAIL 3 | WARN 0 | SKIP 3 | PASS 0 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.0.7
Check: package dependencies
Result: ERROR
Package required but not available: ‘ctsem’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64
Version: 1.0.7
Flags: --no-vignettes
Check: package dependencies
Result: ERROR
Package required but not available: 'OpenMx'
See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Flavor: r-oldrel-windows-x86_64