CRAN Package Check Results for Package nlmixr2est

Last updated on 2022-08-08 04:50:45 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0.8 361.40 232.53 593.93 OK
r-devel-linux-x86_64-debian-gcc 2.0.8 306.21 167.59 473.80 OK
r-devel-linux-x86_64-fedora-clang 2.0.8 838.14 ERROR
r-devel-linux-x86_64-fedora-gcc 2.0.8 OK
r-devel-windows-x86_64 2.0.8 436.00 307.00 743.00 OK
r-patched-linux-x86_64 2.0.8 291.58 206.98 498.56 OK
r-release-linux-x86_64 2.0.8 OK
r-release-macos-arm64 2.0.8 195.00 NOTE
r-release-macos-x86_64 2.0.8 253.00 NOTE
r-release-windows-x86_64 2.0.8 404.00 297.00 701.00 OK
r-oldrel-macos-arm64 2.0.8 163.00 NOTE
r-oldrel-macos-x86_64 2.0.8 247.00 NOTE
r-oldrel-windows-ix86+x86_64 2.0.8 865.00 425.00 1290.00 NOTE

Additional issues

M1mac

Check Details

Version: 2.0.8
Check: tests
Result: ERROR
     Running ‘testthat.R’ [76s/184s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(rxode2)
     rxode2 2.0.7 using 2 threads (see ?getRxThreads)
     no cache: create with `rxCreateCache()`
     > library(nlmixr2est)
     Loading required package: nlmixr2data
     > verbose_minimization <- FALSE
     > test_check("nlmixr2est")
    
     R Under development (unstable) (2022-08-07 r82694) -- "Unsuffered Consequences"
     Copyright (C) 2022 The R Foundation for Statistical Computing
     Platform: x86_64-pc-linux-gnu (64-bit)
    
     R is free software and comes with ABSOLUTELY NO WARRANTY.
     You are welcome to redistribute it under certain conditions.
     Type 'license()' or 'licence()' for distribution details.
    
     Natural language support but running in an English locale
    
     R is a collaborative project with many contributors.
     Type 'contributors()' for more information and
     'citation()' on how to cite R or R packages in publications.
    
     Type 'demo()' for some demos, 'help()' for on-line help, or
     'help.start()' for an HTML browser interface to help.
     Type 'q()' to quit R.
    
     > library(nlmixr2est)
     Loading required package: nlmixr2data
     > rxode2::rxClean()
     > one.cmt <- function() {
     + ini({
     + tka <- 0.45
     + tcl <- log(c(0, 2.7, 100))
     + tv <- 3.45
     + label("log V")
     + eta.ka ~ 0.6
     + eta.cl ~ 0.3
     + eta.v ~ 0.1
     + add.sd <- 0.7
     + })
     + model({
     + ka <- exp(tka + eta.ka)
     + cl <- exp(tcl + eta.cl)
     + v <- exp(tv + eta.v)
     + linCmt() ~ add(add.sd)
     + })
     + }
     > fit <- nlmixr(one.cmt, theo_sd, est = "saem", control = saemControl(print = 0))
     ℹ parameter labels from comments are typically ignored in non-interactive mode
     ℹ Need to run with the source intact to parse comments
     → loading into symengine environment...
     → pruning branches (`if`/`else`) of saem model...
     ✔ done
     → finding duplicate expressions in saem model...
     [====|====|====|====|====|====|====|====|====|====] 0:00:00
    
     ✔ done
     make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
     make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
    
     rxode2 2.0.7 using 2 threads (see ?getRxThreads)
     no cache: create with `rxCreateCache()`
     Calculating covariance matrix
     [====|====|====|====|====|====|====|====|====|====] 0:00:00
    
     → loading into symengine environment...
     → pruning branches (`if`/`else`) of saem model...
     ✔ done
     → finding duplicate expressions in saem predOnly model 0...
     [====|====|====|====|====|====|====|====|====|====] 0:00:00
    
     → finding duplicate expressions in saem predOnly model 1...
     [====|====|====|====|====|====|====|====|====|====] 0:00:00
    
     → finding duplicate expressions in saem predOnly model 2...
     [====|====|====|====|====|====|====|====|====|====] 0:00:00
    
     ✔ done
     make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
     make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
    
     → Calculating residuals/tables
     ✔ done
     → compress origData in nlmixr2 object, save 5952
     → compress phiM in nlmixr2 object, save 63664
     → compress parHist in nlmixr2 object, save 9544
     Error in qs::qserialize(.obj) : bad version value
     Error: bad version value
     Execution halted
     Error in qs::qsave(.ret, .cacheFile) : bad version value
     Error in qs::qsave(.ret, .cacheFile) : bad version value
     i parameter labels from comments will be replaced by 'label()'
     make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
     make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
    
     i parameter labels from comments will be replaced by 'label()'
     i parameter labels from comments will be replaced by 'label()'
     Error in qs::qserialize(.obj) : bad version value
     Error in qs::qsave(.ret, .cacheFile) : bad version value
     i parameter labels from comments will be replaced by 'label()'
     i parameter labels from comments will be replaced by 'label()'
     [ FAIL 5 | WARN 1 | SKIP 0 | PASS 142 ]
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error (test-00-reload-ll.R:33:3): between session saem ll works ─────────────
     Error in `gzfile(file, "rb")`: cannot open the connection
     Backtrace:
     ▆
     1. ├─withr::with_tempdir(...) at test-00-reload-ll.R:33:2
     2. │ └─withr::with_dir(tmp, code)
     3. │ └─base::force(code)
     4. └─base::readRDS("fit.rds") at test-00-reload-ll.R:39:4
     5. └─base::gzfile(file, "rb")
     ── Error (test-nmobj.R:25:3): nmObject get tests ───────────────────────────────
     Error: bad version value
     Backtrace:
     ▆
     1. ├─base::suppressMessages(...) at test-nmobj.R:25:2
     2. │ └─base::withCallingHandlers(...)
     3. ├─base::suppressWarnings(...)
     4. │ └─base::withCallingHandlers(...)
     5. ├─nlmixr2est::nlmixr(one.cmt, nlmixr2data::theo_sd, est = "focei")
     6. └─nlmixr2est:::nlmixr2.function(...)
     7. └─nlmixr2est:::nlmixr2Est0(.env)
     ── Error (test-np.R:106:3): parameters are updated in fit object ───────────────
     Error: bad version value
     Backtrace:
     ▆
     1. ├─base::suppressMessages(...) at test-np.R:106:2
     2. │ └─base::withCallingHandlers(...)
     3. ├─base::suppressWarnings(...)
     4. │ └─base::withCallingHandlers(...)
     5. ├─nlmixr2est::nlmixr(one.cmt, nlmixr2data::theo_sd, "focei")
     6. └─nlmixr2est:::nlmixr2.function(...)
     7. └─nlmixr2est:::nlmixr2Est0(.env)
     ── Error (test-saem-aic.R:21:3): testing saem without table can add focei objf ──
     Error: bad version value
     Backtrace:
     ▆
     1. ├─base::suppressMessages(...) at test-saem-aic.R:21:2
     2. │ └─base::withCallingHandlers(...)
     3. ├─nlmixr2est::nlmixr(...)
     4. └─nlmixr2est:::nlmixr2.function(...)
     5. └─nlmixr2est:::nlmixr2Est0(.env)
     ── Error (test-table-cmt.R:82:3): proper table outputs ─────────────────────────
     Error: bad version value
     Backtrace:
     ▆
     1. └─nlmixr2est (local) .nlmixr(...) at test-table-cmt.R:82:2
     2. ├─base::suppressMessages(suppressWarnings(nlmixr(...))) at test-table-cmt.R:80:13
     3. │ └─base::withCallingHandlers(...)
     4. ├─base::suppressWarnings(nlmixr(...))
     5. │ └─base::withCallingHandlers(...)
     6. ├─nlmixr2est::nlmixr(...)
     7. └─nlmixr2est:::nlmixr2.function(...)
     8. └─nlmixr2est:::nlmixr2Est0(.env)
    
     [ FAIL 5 | WARN 1 | SKIP 0 | PASS 142 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2.0.8
Check: installed package size
Result: NOTE
     installed size is 27.8Mb
     sub-directories of 1Mb or more:
     libs 26.7Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64