Last updated on 2020-08-07 01:50:27 CEST.
| Package | ERROR | OK |
|---|---|---|
| metaSEM | 1 | 11 |
| symSEM | 12 |
Current CRAN status: ERROR: 1, OK: 11
Version: 1.2.4
Check: examples
Result: ERROR
Running examples in ‘metaSEM-Ex.R’ failed
The error most likely occurred in:
> ### Name: BCG
> ### Title: Dataset on the Effectiveness of the BCG Vaccine for Preventing
> ### Tuberculosis
> ### Aliases: BCG
> ### Keywords: datasets
>
> ### ** Examples
>
> data(BCG)
>
> ## Univariate meta-analysis on the log of the odds ratio
> summary( meta(y=ln_OR, v=v_ln_OR, data=BCG,
+ x=cbind(scale(Latitude,scale=FALSE),
+ scale(Year,scale=FALSE))) )
Call:
meta(y = ln_OR, v = v_ln_OR, x = cbind(scale(Latitude, scale = FALSE),
scale(Year, scale = FALSE)), data = BCG)
95% confidence intervals: z statistic approximation (robust=FALSE)
Coefficients:
Estimate Std.Error lbound ubound z value Pr(>|z|)
Intercept1 -0.7166884 NA NA NA NA NA
Slope1_1 -0.0335019 NA NA NA NA NA
Slope1_2 -0.0013515 0.0043422 -0.0098620 0.0071590 -0.3112 0.7556
Tau2_1_1 0.0020944 0.0043420 -0.0064157 0.0106045 0.4824 0.6296
Q statistic on the homogeneity of effect sizes: 163.1649
Degrees of freedom of the Q statistic: 12
P value of the Q statistic: 0
Explained variances (R2):
y1
Tau2 (no predictor) 0.3025
Tau2 (with predictors) 0.0021
R2 0.9931
Number of studies (or clusters): 13
Number of observed statistics: 13
Number of estimated parameters: 4
Degrees of freedom: 9
-2 log likelihood: 13.89208
OpenMx status1: 6 ("0" or "1": The optimization is considered fine.
Other values may indicate problems.)
Warning in print.summary.meta(x) :
OpenMx status1 is neither 0 or 1. You are advised to 'rerun' it again.
>
> ## Multivariate meta-analysis on the log of the odds
> ## The conditional sampling covariance is 0
> bcg <- meta(y=cbind(ln_Odd_V, ln_Odd_NV), data=BCG,
+ v=cbind(v_ln_Odd_V, cov_V_NV, v_ln_Odd_NV))
> summary(bcg)
Call:
meta(y = cbind(ln_Odd_V, ln_Odd_NV), v = cbind(v_ln_Odd_V, cov_V_NV,
v_ln_Odd_NV), data = BCG)
95% confidence intervals: z statistic approximation (robust=FALSE)
Coefficients:
Estimate Std.Error lbound ubound z value Pr(>|z|)
Intercept1 -4.833744 NA NA NA NA NA
Intercept2 -4.095975 NA NA NA NA NA
Tau2_1_1 1.431371 0.155074 1.127431 1.735310 9.2302 < 2.2e-16 ***
Tau2_2_1 1.757327 0.034542 1.689626 1.825027 50.8755 < 2.2e-16 ***
Tau2_2_2 2.407333 0.265609 1.886749 2.927916 9.0635 < 2.2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Q statistic on the homogeneity of effect sizes: 5270.386
Degrees of freedom of the Q statistic: 24
P value of the Q statistic: 0
Heterogeneity indices (based on the estimated Tau2):
Estimate
Intercept1: I2 (Q statistic) 0.9887
Intercept2: I2 (Q statistic) 0.9955
Number of studies (or clusters): 13
Number of observed statistics: 26
Number of estimated parameters: 5
Degrees of freedom: 21
-2 log likelihood: 66.17587
OpenMx status1: 6 ("0" or "1": The optimization is considered fine.
Other values may indicate problems.)
Warning in print.summary.meta(x) :
OpenMx status1 is neither 0 or 1. You are advised to 'rerun' it again.
>
> plot(bcg)
Warning in .solve(x = object$mx.fit@output$calculatedHessian, parameters = my.name) :
Error in solving the Hessian matrix. Generalized inverse is used. The standard errors may not be trustworthy.
Warning in sqrt(c(x[xind, xind], x[yind, yind])) : NaNs produced
Error in if (scale[1] > 0) r <- r/scale[1] :
missing value where TRUE/FALSE needed
Calls: plot -> plot.meta -> points -> ellipse -> ellipse.default
Execution halted
Flavor: r-patched-solaris-x86
Version: 1.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [17s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(metaSEM)
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)
"SLSQP" is set as the default optimizer in OpenMx.
mxOption(NULL, "Gradient algorithm") is set at "central".
mxOption(NULL, "Optimality tolerance") is set at "6.3e-14".
mxOption(NULL, "Gradient iterations") is set at "2".
>
> test_check("metaSEM")
── 1. Failure: metaFIML() works correctly (@test_utilities.R#545) ─────────────
`coef1a` not equal to `coef1b`.
5/5 mismatches (average diff: 0.374)
[1] 0.01560 - 0.1 == -0.0844
[2] 0.00391 - 0.1 == -0.0961
[3] 0.59805 - 0.1 == 0.4981
[4] -0.32955 - 0.1 == -0.4295
[5] 0.86395 - 0.1 == 0.7639
── 2. Failure: metaFIML() works correctly (@test_utilities.R#547) ─────────────
fit1a$mx.fit$output$Minus2LogLikelihood not equal to fit1b$output$Minus2LogLikelihood.
1/1 mismatches
[1] -155 - 185 == -341
Error in running mxModel:
<simpleError: The job for model 'Meta analysis with FIML' exited abnormally with the error message: Non-conformable matrices in horizontal concatenation (cbind). First argument has 4 rows, and argument #2 has 0 rows.>
── 3. Error: metaFIML() works correctly (@test_utilities.R#551) ───────────────
The job for model 'Meta analysis with FIML' exited abnormally with the error message: Non-conformable matrices in horizontal concatenation (cbind). First argument has 4 rows, and argument #2 has 0 rows.
Backtrace:
1. metaSEM::metaFIML(y = r, v = r_v, x = JP_alpha, av = IDV, data = Jaramillo05)
Error: C stack usage 279221396 is too close to the limit
<simpleError: The job for model 'TSSEM1 Correlation' exited abnormally with the error message: User interrupt>
── 4. Error: Handling NA in diagonals in tssem1FEM() correctly (@test_utilities.
The job for model 'TSSEM1 Correlation' exited abnormally with the error message: User interrupt
Backtrace:
1. metaSEM::tssem1(Cov = list(C1, C2, C3), n = c(50, 50, 50), method = "FEM")
2. metaSEM::tssem1FEM(...)
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 90 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 4 ]
1. Failure: metaFIML() works correctly (@test_utilities.R#545)
2. Failure: metaFIML() works correctly (@test_utilities.R#547)
3. Error: metaFIML() works correctly (@test_utilities.R#551)
4. Error: Handling NA in diagonals in tssem1FEM() correctly (@test_utilities.R#644)
Error: testthat unit tests failed
Execution halted
Flavor: r-patched-solaris-x86
Current CRAN status: OK: 12