- using R version 4.6.1 Patched (2026-06-28 r90209)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-15 (Debian 15.3.0-1) 15.3.0
GNU Fortran (Debian 15.3.0-1) 15.3.0
- running under: Debian GNU/Linux forky/sid
- using session charset: UTF-8
* current time: 2026-07-08 18:04:40 UTC
- checking for file ‘pprof/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘pprof’ version ‘1.0.3’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘pprof’ can be installed ... OK
See the install log for details.
- used C++ compiler: ‘g++-15 (Debian 15.3.0-1) 15.3.0’
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [5s/7s] OK
- checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
- checking whether the package can be unloaded cleanly ... [4s/5s] OK
- checking whether the namespace can be loaded with stated dependencies ... [4s/6s] OK
- checking whether the namespace can be unloaded cleanly ... [5s/6s] OK
- checking loading without being on the library search path ... [5s/6s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [36s/47s] OK
- checking Rd files ... [1s/1s] OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... [0s/0s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compilation flags used ... OK
- checking compiled code ... OK
- checking examples ... [24s/38s] ERROR
Running examples in ‘pprof-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SM_output.logis_re
> ### Title: Calculate direct/indirect standardized ratios/rates from a
> ### fitted 'logis_re' object
> ### Aliases: SM_output.logis_re
>
> ### ** Examples
>
> data(ExampleDataBinary)
> outcome = ExampleDataBinary$Y
> covar = ExampleDataBinary$Z
> ProvID = ExampleDataBinary$ProvID
> fit_re <- logis_re(Y = outcome, Z = covar, ProvID = ProvID)
Input format: Y, Z, and ProvID.
Error: Downdated VtV is not positive definite
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SM_output.logis_cre 13.698 0.085 22.666
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [54s/64s] ERROR
Running ‘testthat.R’ [54s/63s]
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(pprof)
>
> test_check("pprof")
Input format: Y, Z, and ProvID.
Input format: Y, Z, and ProvID.
Input format: Y, Z, and ProvID.
3 out of 100 remaining providers with no events.
0 out of 100 remaining providers with all events.
After screening, 38.77% of all records exhibit occurrences of events (Y = 1)
Implementing SerBIN algorithm (Rcpp) for fixed provider effects model ...
Iter 1: Minimum criterion across all checks is 5.022e-01;
Iter 2: Minimum criterion across all checks is 1.422e-01;
Iter 3: Minimum criterion across all checks is 3.528e-02;
Iter 4: Minimum criterion across all checks is 5.671e-03;
Iter 5: Minimum criterion across all checks is 1.214e-03;
Iter 6: Minimum criterion across all checks is 2.151e-04;
Iter 7: Minimum criterion across all checks is 6.647e-05;
Iter 8: Minimum criterion across all checks is 7.565e-06;
serBIN (Rcpp) algorithm converged after 8 iterations!
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Input format: Y, Z, and ProvID.
Saving _problems/test-SM_output-99.R
Saving _problems/test-SM_output-125.R
Input format: Y, Z, and ProvID.
Input format: Y, Z, and ProvID.
Input format: Y, Z, and ProvID.
3 out of 100 remaining providers with no events.
0 out of 100 remaining providers with all events.
After screening, 38.77% of all records exhibit occurrences of events (Y = 1)
Implementing SerBIN algorithm (Rcpp) for fixed provider effects model ...
Iter 1: Minimum criterion across all checks is 5.022e-01;
Iter 2: Minimum criterion across all checks is 1.422e-01;
Iter 3: Minimum criterion across all checks is 3.528e-02;
Iter 4: Minimum criterion across all checks is 5.671e-03;
Iter 5: Minimum criterion across all checks is 1.214e-03;
Iter 6: Minimum criterion across all checks is 2.151e-04;
Iter 7: Minimum criterion across all checks is 6.647e-05;
Iter 8: Minimum criterion across all checks is 7.565e-06;
serBIN (Rcpp) algorithm converged after 8 iterations!
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Input format: Y, Z, and ProvID.
Saving _problems/test-confint-132.R
Saving _problems/test-confint-165.R
Input format: Y, Z, and ProvID.
Input format: data, Y.char, Z.char, and ProvID.char.
Input format: formula and data.
Input format: Y, Z, and ProvID.
Input format: data, Y.char, Z.char, and ProvID.char.
Input format: formula and data.
Input format: Y, Z, and ProvID.
3 out of 100 remaining providers with no events.
0 out of 100 remaining providers with all events.
After screening, 38.77% of all records exhibit occurrences of events (Y = 1)
Implementing SerBIN algorithm (Rcpp) for fixed provider effects model ...
Iter 1: Minimum criterion across all checks is 5.022e-01;
Iter 2: Minimum criterion across all checks is 1.422e-01;
Iter 3: Minimum criterion across all checks is 3.528e-02;
Iter 4: Minimum criterion across all checks is 5.671e-03;
Iter 5: Minimum criterion across all checks is 1.214e-03;
Iter 6: Minimum criterion across all checks is 2.151e-04;
Iter 7: Minimum criterion across all checks is 6.647e-05;
Iter 8: Minimum criterion across all checks is 7.565e-06;
serBIN (Rcpp) algorithm converged after 8 iterations!
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Input format: data, Y.char, Z.char, and ProvID.char.
3 out of 100 remaining providers with no events.
0 out of 100 remaining providers with all events.
After screening, 38.77% of all records exhibit occurrences of events (Y = 1)
Implementing SerBIN algorithm (Rcpp) for fixed provider effects model ...
Iter 1: Minimum criterion across all checks is 5.022e-01;
Iter 2: Minimum criterion across all checks is 1.422e-01;
Iter 3: Minimum criterion across all checks is 3.528e-02;
Iter 4: Minimum criterion across all checks is 5.671e-03;
Iter 5: Minimum criterion across all checks is 1.214e-03;
Iter 6: Minimum criterion across all checks is 2.151e-04;
Iter 7: Minimum criterion across all checks is 6.647e-05;
Iter 8: Minimum criterion across all checks is 7.565e-06;
serBIN (Rcpp) algorithm converged after 8 iterations!
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Input format: formula and data.
3 out of 100 remaining providers with no events.
0 out of 100 remaining providers with all events.
After screening, 38.77% of all records exhibit occurrences of events (Y = 1)
Implementing SerBIN algorithm (Rcpp) for fixed provider effects model ...
Iter 1: Minimum criterion across all checks is 5.022e-01;
Iter 2: Minimum criterion across all checks is 1.422e-01;
Iter 3: Minimum criterion across all checks is 3.528e-02;
Iter 4: Minimum criterion across all checks is 5.671e-03;
Iter 5: Minimum criterion across all checks is 1.214e-03;
Iter 6: Minimum criterion across all checks is 2.151e-04;
Iter 7: Minimum criterion across all checks is 6.647e-05;
Iter 8: Minimum criterion across all checks is 7.565e-06;
serBIN (Rcpp) algorithm converged after 8 iterations!
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Input format: Y, Z, and ProvID.
Saving _problems/test-logis_re-13.R
Input format: Y, Z, and ProvID.
Input format: Y, Z, and ProvID.
Input format: Y, Z, and ProvID.
3 out of 100 remaining providers with no events.
0 out of 100 remaining providers with all events.
After screening, 38.77% of all records exhibit occurrences of events (Y = 1)
Implementing SerBIN algorithm (Rcpp) for fixed provider effects model ...
Iter 1: Minimum criterion across all checks is 5.022e-01;
Iter 2: Minimum criterion across all checks is 1.422e-01;
Iter 3: Minimum criterion across all checks is 3.528e-02;
Iter 4: Minimum criterion across all checks is 5.671e-03;
Iter 5: Minimum criterion across all checks is 1.214e-03;
Iter 6: Minimum criterion across all checks is 2.151e-04;
Iter 7: Minimum criterion across all checks is 6.647e-05;
Iter 8: Minimum criterion across all checks is 7.565e-06;
serBIN (Rcpp) algorithm converged after 8 iterations!
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Input format: Y, Z, and ProvID.
Saving _problems/test-summary-90.R
Input format: Y, Z, and ProvID.
Input format: Y, Z, and ProvID.
Input format: Y, Z, and ProvID.
3 out of 100 remaining providers with no events.
0 out of 100 remaining providers with all events.
After screening, 38.77% of all records exhibit occurrences of events (Y = 1)
Implementing SerBIN algorithm (Rcpp) for fixed provider effects model ...
Iter 1: Minimum criterion across all checks is 5.022e-01;
Iter 2: Minimum criterion across all checks is 1.422e-01;
Iter 3: Minimum criterion across all checks is 3.528e-02;
Iter 4: Minimum criterion across all checks is 5.671e-03;
Iter 5: Minimum criterion across all checks is 1.214e-03;
Iter 6: Minimum criterion across all checks is 2.151e-04;
Iter 7: Minimum criterion across all checks is 6.647e-05;
Iter 8: Minimum criterion across all checks is 7.565e-06;
serBIN (Rcpp) algorithm converged after 8 iterations!
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Input format: Y, Z, and ProvID.
Saving _problems/test-test-106.R
Saving _problems/test-test-129.R
[ FAIL 8 | WARN 0 | SKIP 0 | PASS 130 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-SM_output.R:99:3'): SM_output.logis_re function behaves correctly ──
<Rcpp::exception/C++Error/error/condition>
Error: Downdated VtV is not positive definite
Backtrace:
▆
1. └─pprof::logis_re(Y = Y, Z = Z, ProvID = ProvID) at test-SM_output.R:99:3
2. └─lme4::glmer(...)
3. └─lme4::optimizeGlmer(...)
4. └─lme4:::optwrap(...)
5. ├─base::withCallingHandlers(...)
6. ├─base::do.call(optfun, arglist)
7. └─lme4 (local) `<fn>`(...)
8. ├─nM$newf(fn(nM$xeval()))
9. │ └─base::stopifnot(length(value <- as.numeric(value)) == 1L)
10. └─lme4 (local) fn(nM$xeval())
11. └─lme4 (local) pwrssUpdate(...)
── Error ('test-SM_output.R:125:3'): SM_output.logis_cre function behaves correctly ──
<Rcpp::exception/C++Error/error/condition>
Error: Downdated VtV is not positive definite
Backtrace:
▆
1. └─pprof::logis_cre(...) at test-SM_output.R:125:3
2. └─lme4::glmer(...)
3. └─lme4::optimizeGlmer(...)
4. └─lme4:::optwrap(...)
5. ├─base::withCallingHandlers(...)
6. ├─base::do.call(optfun, arglist)
7. └─lme4 (local) `<fn>`(...)
8. ├─nM$newf(fn(nM$xeval()))
9. │ └─base::stopifnot(length(value <- as.numeric(value)) == 1L)
10. └─lme4 (local) fn(nM$xeval())
11. └─lme4 (local) pwrssUpdate(...)
── Error ('test-confint.R:132:3'): test.logis_re function behaves correctly ────
<Rcpp::exception/C++Error/error/condition>
Error: Downdated VtV is not positive definite
Backtrace:
▆
1. └─pprof::logis_re(Y = Y, Z = Z, ProvID = ProvID) at test-confint.R:132:3
2. └─lme4::glmer(...)
3. └─lme4::optimizeGlmer(...)
4. └─lme4:::optwrap(...)
5. ├─base::withCallingHandlers(...)
6. ├─base::do.call(optfun, arglist)
7. └─lme4 (local) `<fn>`(...)
8. ├─nM$newf(fn(nM$xeval()))
9. │ └─base::stopifnot(length(value <- as.numeric(value)) == 1L)
10. └─lme4 (local) fn(nM$xeval())
11. └─lme4 (local) pwrssUpdate(...)
── Error ('test-confint.R:165:3'): test.logis_cre function behaves correctly ───
<Rcpp::exception/C++Error/error/condition>
Error: Downdated VtV is not positive definite
Backtrace:
▆
1. └─pprof::logis_cre(...) at test-confint.R:165:3
2. └─lme4::glmer(...)
3. └─lme4::optimizeGlmer(...)
4. └─lme4:::optwrap(...)
5. ├─base::withCallingHandlers(...)
6. ├─base::do.call(optfun, arglist)
7. └─lme4 (local) `<fn>`(...)
8. ├─nM$newf(fn(nM$xeval()))
9. │ └─base::stopifnot(length(value <- as.numeric(value)) == 1L)
10. └─lme4 (local) fn(nM$xeval())
11. └─lme4 (local) pwrssUpdate(...)
── Error ('test-logis_re.R:13:3'): logis_re function behaves correctly ─────────
<Rcpp::exception/C++Error/error/condition>
Error: Downdated VtV is not positive definite
Backtrace:
▆
1. └─pprof::logis_re(Y = Y, Z = Z, ProvID = ProvID) at test-logis_re.R:13:3
2. └─lme4::glmer(...)
3. └─lme4::optimizeGlmer(...)
4. └─lme4:::optwrap(...)
5. └─lme4:::deriv12(fn, opt$par, fx = opt$value)
6. └─lme4 (local) fun(xas, ...)
7. └─lme4 (local) pwrssUpdate(...)
── Error ('test-summary.R:90:3'): summary.logis_re function behaves correctly ──
<Rcpp::exception/C++Error/error/condition>
Error: Downdated VtV is not positive definite
Backtrace:
▆
1. └─pprof::logis_re(Y = Y, Z = Z, ProvID = ProvID) at test-summary.R:90:3
2. └─lme4::glmer(...)
3. └─lme4::optimizeGlmer(...)
4. └─lme4:::optwrap(...)
5. ├─base::withCallingHandlers(...)
6. ├─base::do.call(optfun, arglist)
7. └─lme4 (local) `<fn>`(...)
8. ├─nM$newf(fn(nM$xeval()))
9. │ └─base::stopifnot(length(value <- as.numeric(value)) == 1L)
10. └─lme4 (local) fn(nM$xeval())
11. └─lme4 (local) pwrssUpdate(...)
── Error ('test-test.R:106:3'): test.logis_re function behaves correctly ───────
<Rcpp::exception/C++Error/error/condition>
Error: Downdated VtV is not positive definite
Backtrace:
▆
1. └─pprof::logis_re(Y = Y, Z = Z, ProvID = ProvID) at test-test.R:106:3
2. └─lme4::glmer(...)
3. └─lme4::optimizeGlmer(...)
4. └─lme4:::optwrap(...)
5. ├─base::withCallingHandlers(...)
6. ├─base::do.call(optfun, arglist)
7. └─lme4 (local) `<fn>`(...)
8. ├─nM$newf(fn(nM$xeval()))
9. │ └─base::stopifnot(length(value <- as.numeric(value)) == 1L)
10. └─lme4 (local) fn(nM$xeval())
11. └─lme4 (local) pwrssUpdate(...)
── Error ('test-test.R:129:3'): test.logis_cre function behaves correctly ──────
<Rcpp::exception/C++Error/error/condition>
Error: Downdated VtV is not positive definite
Backtrace:
▆
1. └─pprof::logis_cre(...) at test-test.R:129:3
2. └─lme4::glmer(...)
3. └─lme4::optimizeGlmer(...)
4. └─lme4:::optwrap(...)
5. ├─base::withCallingHandlers(...)
6. ├─base::do.call(optfun, arglist)
7. └─lme4 (local) `<fn>`(...)
8. ├─nM$newf(fn(nM$xeval()))
9. │ └─base::stopifnot(length(value <- as.numeric(value)) == 1L)
10. └─lme4 (local) fn(nM$xeval())
11. └─lme4 (local) pwrssUpdate(...)
[ FAIL 8 | WARN 0 | SKIP 0 | PASS 130 ]
Error:
! Test failures.
Execution halted
- checking PDF version of manual ... [6s/9s] OK
- checking HTML version of manual ... [5s/8s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 2 ERRORs