CRAN Package Check Results for Package RxODE

Last updated on 2020-04-25 01:53:16 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.9.2-0 237.68 200.68 438.36 ERROR
r-devel-linux-x86_64-debian-gcc 0.9.2-0 242.01 209.55 451.56 NOTE
r-devel-linux-x86_64-fedora-clang 0.9.2-0 486.67 NOTE
r-devel-linux-x86_64-fedora-gcc 0.9.2-0 767.09 NOTE
r-devel-windows-ix86+x86_64 0.9.2-0 575.00 454.00 1029.00 ERROR
r-patched-linux-x86_64 0.9.2-0 258.86 264.44 523.30 NOTE
r-patched-osx-x86_64 0.9.2-0 WARN
r-patched-solaris-x86 0.9.2-0 662.90 NOTE
r-release-linux-x86_64 0.9.2-0 243.96 263.71 507.67 NOTE
r-release-windows-ix86+x86_64 0.9.2-0 534.00 1095.00 1629.00 NOTE
r-release-osx-x86_64 0.9.2-0 NOTE
r-oldrel-windows-ix86+x86_64 0.9.1-9 368.00 326.00 694.00 ERROR
r-oldrel-osx-x86_64 0.9.2-0 ERROR

Check Details

Version: 0.9.2-0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'SnakeCharmR', 'installr', 'vdiffr'
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.9.2-0
Check: tests
Result: ERROR
     Running 'testthat.R' [68s/77s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(RxODE)
     > test_check("RxODE")
     OMP: Warning #96: Cannot form a team with 32 threads, using 3 instead.
     OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
     -- 1. Error: plot tests (@test-plot.R#91) -------------------------------------
     there is no package called 'vdiffr'
     Backtrace:
     1. vdiffr::expect_doppelganger
     2. base::getExportedValue(pkg, name)
     3. base::asNamespace(ns)
     4. base::getNamespace(ns)
     5. base::loadNamespace(name)
     6. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     7. base:::withOneRestart(expr, restarts[[1L]])
     8. base:::doWithOneRestart(return(expr), restart)
    
    
     == testthat results ===========================================================
     [ OK: 891 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 1 ]
     1. Error: plot tests (@test-plot.R#91)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.9.2-0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'SnakeCharmR', 'installr'
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-patched-osx-x86_64, r-patched-solaris-x86, r-release-linux-x86_64

Version: 0.9.2-0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'SnakeCharmR'
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64

Version: 0.9.2-0
Check: installed package size
Result: NOTE
     installed size is 7.3Mb
     sub-directories of 1Mb or more:
     libs 5.9Mb
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64

Version: 0.9.2-0
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'testthat.R' [61s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(RxODE)
     > test_check("RxODE")
Flavor: r-devel-windows-ix86+x86_64

Version: 0.9.2-0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘RxODE-intro.Rmd’ using rmarkdown
    dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
     Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
     Expected in: /usr/lib/libSystem.B.dylib
    
    dyld: Symbol not found: ____chkstk_darwin
     Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
     Expected in: /usr/lib/libSystem.B.dylib
    
    Error: processing vignette 'RxODE-intro.Rmd' failed with diagnostics:
    pandoc document conversion failed with error 6
    --- failed re-building ‘RxODE-intro.Rmd’
    
    --- re-building ‘RxODE-syntax.Rmd’ using rmarkdown
    dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
     Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
     Expected in: /usr/lib/libSystem.B.dylib
    
    dyld: Symbol not found: ____chkstk_darwin
     Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
     Expected in: /usr/lib/libSystem.B.dylib
    
    Error: processing vignette 'RxODE-syntax.Rmd' failed with diagnostics:
    pandoc document conversion failed with error 6
    --- failed re-building ‘RxODE-syntax.Rmd’
    
    SUMMARY: processing the following files failed:
     ‘RxODE-intro.Rmd’ ‘RxODE-syntax.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-osx-x86_64

Version: 0.9.2-0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘installr’
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.9.1-9
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'SnakeCharmR'
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.9.1-9
Check: installed package size
Result: NOTE
     installed size is 6.7Mb
     sub-directories of 1Mb or more:
     libs 5.5Mb
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.9.1-9
Check: for missing documentation entries
Result: WARN
    Undocumented code objects:
     'type_sum.rxRateDur'
    All user-level objects in a package should have documentation entries.
    See chapter 'Writing R documentation files' in the 'Writing R
    Extensions' manual.
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.9.1-9
Check: running examples for arch ‘i386’
Result: ERROR
    Running examples in 'RxODE-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: RxODE
    > ### Title: Create an ODE-based model specification
    > ### Aliases: RxODE
    > ### Keywords: models nonlinear
    >
    > ### ** Examples
    >
    > # Step 1 - Create a model specification
    > ode <- "
    + # A 4-compartment model, 3 PK and a PD (effect) compartment
    + # (notice state variable names 'depot', 'centr', 'peri', 'eff')
    +
    + C2 = centr/V2;
    + C3 = peri/V3;
    + d/dt(depot) =-KA*depot;
    + d/dt(centr) = KA*depot - CL*C2 - Q*C2 + Q*C3;
    + d/dt(peri) = Q*C2 - Q*C3;
    + d/dt(eff) = Kin - Kout*(1-C2/(EC50+C2))*eff;
    + "
    >
    > m1 <- RxODE(model = ode)
    > print(m1)
    RxODE 0.9.1-9 model named rx_a5af0dfe0cd9b3b2b376195f83d75e38_i38 model (ready).
    m1$state: depot, centr, peri, eff
    m1$params: V2, V3, KA, CL, Q, Kin, Kout, EC50
    m1$lhs: C2, C3
    >
    > # Step 2 - Create the model input as an EventTable,
    > # including dosing and observation (sampling) events
    >
    > # QD (once daily) dosing for 5 days.
    >
    > qd <- eventTable(amount.units = "ug", time.units = "hours")
    > qd$add.dosing(dose = 10000, nbr.doses = 5, dosing.interval = 24)
    >
    > # Sample the system hourly during the first day, every 8 hours
    > # then after
    >
    > qd$add.sampling(0:24)
    > qd$add.sampling(seq(from = 24+8, to = 5*24, by = 8))
    >
    > # Step 3 - set starting parameter estimates and initial
    > # values of the state
    >
    > theta <-
    + c(KA = .291, CL = 18.6,
    + V2 = 40.2, Q = 10.5, V3 = 297.0,
    + Kin = 1.0, Kout = 1.0, EC50 = 200.0)
    >
    > # init state variable
    > inits <- c(0, 0, 0, 1);
    >
    > # Step 4 - Fit the model to the data
    >
    > qd.cp <- m1$solve(theta, events = qd, inits)
    Warning in rxSolve_(object, .ctl, .nms, .xtra, params, events, inits, setupOnly = .setupOnly) :
     Assumed order of inputs: depot, centr, peri, eff
    >
    > head(qd.cp)
     time C2 C3 depot centr peri eff
    [1,] 0 0.00000 0.0000000 10000.000 0.000 0.0000 1.000000
    [2,] 1 43.99334 0.9113641 7475.157 1768.532 270.6751 1.083968
    [3,] 2 54.50866 2.6510696 5587.797 2191.248 787.3677 1.179529
    [4,] 3 51.65163 4.4243597 4176.966 2076.396 1314.0348 1.227523
    [5,] 4 44.37513 5.9432612 3122.347 1783.880 1765.1486 1.233503
    [6,] 5 36.46382 7.1389804 2334.004 1465.845 2120.2772 1.214084
    >
    > # This returns a matrix. Note that you can also
    > # solve using name initial values. For example:
    >
    > inits <- c(eff = 1);
    >
    > qd.cp <- solve(m1, theta, events = qd, inits);
    >
    > print(qd.cp)
    ______________________________ Solved RxODE object _____________________________
    -- Parameters (qd.cp$params): --------------------------------------------------
    
     V2 V3 KA CL Q Kin Kout EC50
     40.200 297.000 0.291 18.600 10.500 1.000 1.000 200.000
    -- Initial Conditions (qd.cp$inits): -------------------------------------------
    depot centr peri eff
     0 0 0 1
    -- First part of data (object): ------------------------------------------------
    # A tibble: 37 x 7
     time C2 C3 depot centr peri eff
     [h] <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
    1 0 0 0 10000 0 0 1
    2 1 44.0 0.911 7475. 1769. 271. 1.08
    3 2 54.5 2.65 5588. 2191. 787. 1.18
    4 3 51.7 4.42 4177. 2076. 1314. 1.23
    5 4 44.4 5.94 3122. 1784. 1765. 1.23
    6 5 36.5 7.14 2334. 1466. 2120. 1.21
    # ... with 31 more rows
    ________________________________________________________________________________
    >
    > plot(qd.cp)
    Error in get(as.character(FUN), mode = "function", envir = envir) :
     object 'guide_none' of mode 'function' was not found
    Calls: <Anonymous> ... lapply -> FUN -> f -> lapply -> FUN -> match.fun -> get
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.9.1-9
Check: running examples for arch ‘x64’
Result: ERROR
    Running examples in 'RxODE-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: RxODE
    > ### Title: Create an ODE-based model specification
    > ### Aliases: RxODE
    > ### Keywords: models nonlinear
    >
    > ### ** Examples
    >
    > # Step 1 - Create a model specification
    > ode <- "
    + # A 4-compartment model, 3 PK and a PD (effect) compartment
    + # (notice state variable names 'depot', 'centr', 'peri', 'eff')
    +
    + C2 = centr/V2;
    + C3 = peri/V3;
    + d/dt(depot) =-KA*depot;
    + d/dt(centr) = KA*depot - CL*C2 - Q*C2 + Q*C3;
    + d/dt(peri) = Q*C2 - Q*C3;
    + d/dt(eff) = Kin - Kout*(1-C2/(EC50+C2))*eff;
    + "
    >
    > m1 <- RxODE(model = ode)
    > print(m1)
    RxODE 0.9.1-9 model named rx_f320152852f29ce97e721bde4c4e81a0_x6 model (ready).
    m1$state: depot, centr, peri, eff
    m1$params: V2, V3, KA, CL, Q, Kin, Kout, EC50
    m1$lhs: C2, C3
    >
    > # Step 2 - Create the model input as an EventTable,
    > # including dosing and observation (sampling) events
    >
    > # QD (once daily) dosing for 5 days.
    >
    > qd <- eventTable(amount.units = "ug", time.units = "hours")
    > qd$add.dosing(dose = 10000, nbr.doses = 5, dosing.interval = 24)
    >
    > # Sample the system hourly during the first day, every 8 hours
    > # then after
    >
    > qd$add.sampling(0:24)
    > qd$add.sampling(seq(from = 24+8, to = 5*24, by = 8))
    >
    > # Step 3 - set starting parameter estimates and initial
    > # values of the state
    >
    > theta <-
    + c(KA = .291, CL = 18.6,
    + V2 = 40.2, Q = 10.5, V3 = 297.0,
    + Kin = 1.0, Kout = 1.0, EC50 = 200.0)
    >
    > # init state variable
    > inits <- c(0, 0, 0, 1);
    >
    > # Step 4 - Fit the model to the data
    >
    > qd.cp <- m1$solve(theta, events = qd, inits)
    Warning in rxSolve_(object, .ctl, .nms, .xtra, params, events, inits, setupOnly = .setupOnly) :
     Assumed order of inputs: depot, centr, peri, eff
    >
    > head(qd.cp)
     time C2 C3 depot centr peri eff
    [1,] 0 0.00000 0.0000000 10000.000 0.000 0.0000 1.000000
    [2,] 1 43.99334 0.9113641 7475.157 1768.532 270.6751 1.083968
    [3,] 2 54.50866 2.6510696 5587.797 2191.248 787.3677 1.179529
    [4,] 3 51.65163 4.4243597 4176.966 2076.396 1314.0348 1.227523
    [5,] 4 44.37513 5.9432612 3122.347 1783.880 1765.1486 1.233503
    [6,] 5 36.46382 7.1389804 2334.004 1465.845 2120.2772 1.214084
    >
    > # This returns a matrix. Note that you can also
    > # solve using name initial values. For example:
    >
    > inits <- c(eff = 1);
    >
    > qd.cp <- solve(m1, theta, events = qd, inits);
    >
    > print(qd.cp)
    ______________________________ Solved RxODE object _____________________________
    -- Parameters (qd.cp$params): --------------------------------------------------
    
     V2 V3 KA CL Q Kin Kout EC50
     40.200 297.000 0.291 18.600 10.500 1.000 1.000 200.000
    -- Initial Conditions (qd.cp$inits): -------------------------------------------
    depot centr peri eff
     0 0 0 1
    -- First part of data (object): ------------------------------------------------
    # A tibble: 37 x 7
     time C2 C3 depot centr peri eff
     [h] <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
    1 0 0 0 10000 0 0 1
    2 1 44.0 0.911 7475. 1769. 271. 1.08
    3 2 54.5 2.65 5588. 2191. 787. 1.18
    4 3 51.7 4.42 4177. 2076. 1314. 1.23
    5 4 44.4 5.94 3122. 1784. 1765. 1.23
    6 5 36.5 7.14 2334. 1466. 2120. 1.21
    # ... with 31 more rows
    ________________________________________________________________________________
    >
    > plot(qd.cp)
    Error in get(as.character(FUN), mode = "function", envir = envir) :
     object 'guide_none' of mode 'function' was not found
    Calls: <Anonymous> ... lapply -> FUN -> f -> lapply -> FUN -> match.fun -> get
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.9.2-0
Check: whether package can be installed
Result: ERROR
    Installation failed.
Flavor: r-oldrel-osx-x86_64