Last updated on 2026-10-24 15:51:37 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.5 | 10.42 | 88.00 | 98.42 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.5 | 8.33 | 59.22 | 67.55 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.5 | 10.00 | 81.14 | 91.14 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.5 | 64.67 | OK | |||
| r-devel-windows-x86_64 | 1.0.5 | 12.00 | 100.00 | 112.00 | OK | |
| r-patched-linux-x86_64 | 1.0.5 | 10.23 | 76.09 | 86.32 | OK | |
| r-release-linux-x86_64 | 1.0.5 | 10.50 | 76.32 | 86.82 | OK | |
| r-release-macos-arm64 | 1.0.5 | 3.00 | 23.00 | 26.00 | OK | |
| r-release-macos-x86_64 | 1.0.5 | 9.00 | 82.00 | 91.00 | OK | |
| r-release-windows-x86_64 | 1.0.5 | 12.00 | 90.00 | 102.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.5 | 3.00 | 23.00 | 26.00 | OK | |
| r-oldrel-macos-x86_64 | 1.0.5 | 8.00 | 142.00 | 150.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.5 | 16.00 | 111.00 | 127.00 | OK |
Version: 1.0.5
Check: examples
Result: ERROR
Running examples in ‘phers-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getWeights
> ### Title: Calculate phecode-specific weights for phenotype risk scores
> ### Aliases: getWeights
>
> ### ** Examples
>
> library('data.table')
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
> library('survival')
> setDTthreads(1) # default for examples
>
> # map ICD codes to phecodes
> phecodeOccurrences = getPhecodeOccurrences(icdSample)
>
> # calculate weights using the prevalence method
> weightsPrev = getWeights(demoSample, phecodeOccurrences)
>
> # calculate weights using the prevalence method
> # (assign negative weights to those with zero phecode occurrence)
> weightsPrevNeg = getWeights(
+ demoSample, phecodeOccurrences, negativeWeights = TRUE)
>
> # calculate weights using the logistic method
> weightsLogistic = getWeights(
+ demoSample, phecodeOccurrences, method = 'logistic', methodFormula = ~ sex)
>
> # calculate weights using the loglinear method
> phecodeOccurrences2 = phecodeOccurrences[, .(
+ num_occurrences = uniqueN(entry_date)), by = .(person_id, phecode)]
> weightsLoglinear = getWeights(
+ demoSample, phecodeOccurrences2, method = 'loglinear', methodFormula = ~ sex)
>
> # calculate weights using the cox method
> phecodeOccurrences3 = phecodeOccurrences[, .(
+ first_occurrence_date = min(entry_date)) , by = .(person_id, phecode)]
> phecodeOccurrences3 = merge(
+ phecodeOccurrences3, demoSample[, .(person_id, dob)], by = 'person_id')
> phecodeOccurrences3[,
+ occurrence_age := as.numeric((first_occurrence_date - dob)/365.25)]
> phecodeOccurrences3[, `:=`(first_occurrence_date = NULL, dob = NULL)]
> demoSample3 = demoSample[, .(
+ person_id, sex,
+ first_age = as.numeric((first_visit_date - dob)/365.25),
+ last_age = as.numeric((last_visit_date - dob)/365.25))]
> weightsCox = getWeights(
+ demoSample3, phecodeOccurrences3, method = 'cox', methodFormula = ~ sex)
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 1 ; beta may be infinite.
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 1 ; beta may be infinite.
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 1 ; beta may be infinite.
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 1 ; beta may be infinite.
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 1 ; beta may be infinite.
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 1 ; beta may be infinite.
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 1 ; beta may be infinite.
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Error in { : task 1 failed - "subscript out of bounds"
Calls: getWeights -> getWeightsFunc -> doOp -> <Anonymous>
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(phers)
>
> test_check('phers')
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
Extracting number of samples and rownames from geno_test.fam...
Extracting number of variants and colnames from geno_test.bim...
Saving _problems/test_weights-50.R
Saving _problems/test_weights-59.R
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 23 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_weights.R:48:3'): getWeights output (cox model) ────────────────
Error in `{ pheSub = unique(phecodeOccurrences[phecode == phe, .(person_id, phecode, occurrence_age)]) coxInput = merge(demos, pheSub, by = "person_id", all.x = TRUE) coxInput[!is.na(phecode), `:=`(dx_status = 1, age2 = occurrence_age)] coxInput[is.na(phecode), `:=`(dx_status = 0, age2 = last_age)] coxInput[, `:=`(phecode, phe)] coxInput[, `:=`(last_age = NULL, occurrence_age = NULL)] coxInput[age2 == first_age, `:=`(age2, age2 + (1/365.25))] coxInput = coxInput[age2 > first_age] methodFormula = update.formula(methodFormula, Surv(first_age, age2, dx_status) ~ .) fit = coxph(methodFormula, data = coxInput, model = TRUE) coxInput[, `:=`(pred, 1 - exp(-predict(fit, newdata = .SD, type = "expected", se.fit = FALSE)))] coxInput = coxInput[, .(person_id, phecode, pred, dx_status)] }`: task 1 failed - "subscript out of bounds"
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test_weights.R:48:3
2. │ └─base::withCallingHandlers(...)
3. └─phers::getWeights(...)
4. └─phers (local) getWeightsFunc(...)
5. └─foreach (local) doOp(...)
6. └─e$fun(obj, substitute(ex), parent.frame(), e$data)
── Error ('test_weights.R:57:3'): getWeights output (cox model, negative weights) ──
Error in `{ pheSub = unique(phecodeOccurrences[phecode == phe, .(person_id, phecode, occurrence_age)]) coxInput = merge(demos, pheSub, by = "person_id", all.x = TRUE) coxInput[!is.na(phecode), `:=`(dx_status = 1, age2 = occurrence_age)] coxInput[is.na(phecode), `:=`(dx_status = 0, age2 = last_age)] coxInput[, `:=`(phecode, phe)] coxInput[, `:=`(last_age = NULL, occurrence_age = NULL)] coxInput[age2 == first_age, `:=`(age2, age2 + (1/365.25))] coxInput = coxInput[age2 > first_age] methodFormula = update.formula(methodFormula, Surv(first_age, age2, dx_status) ~ .) fit = coxph(methodFormula, data = coxInput, model = TRUE) coxInput[, `:=`(pred, 1 - exp(-predict(fit, newdata = .SD, type = "expected", se.fit = FALSE)))] coxInput = coxInput[, .(person_id, phecode, pred, dx_status)] }`: task 1 failed - "subscript out of bounds"
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test_weights.R:57:3
2. │ └─base::withCallingHandlers(...)
3. └─phers::getWeights(...)
4. └─phers (local) getWeightsFunc(...)
5. └─foreach (local) doOp(...)
6. └─e$fun(obj, substitute(ex), parent.frame(), e$data)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 23 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc