CRAN Package Check Results for Package drugCombo

Last updated on 2021-01-10 14:48:19 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	1.1.1	8.81	229.95	238.76	ERROR
r-devel-linux-x86_64-debian-gcc	1.1.1	6.69	170.17	176.86	ERROR
r-devel-linux-x86_64-fedora-clang	1.1.1			294.33	ERROR
r-devel-linux-x86_64-fedora-gcc	1.1.1			287.15	ERROR
r-devel-windows-ix86+x86_64	1.1.1	20.00	338.00	358.00	ERROR
r-patched-linux-x86_64	1.1.1	8.13	222.77	230.90	OK
r-patched-solaris-x86	1.1.1			432.90	WARN
r-release-linux-x86_64	1.1.1	8.55	220.67	229.22	OK
r-release-macos-x86_64	1.1.1				WARN
r-release-windows-ix86+x86_64	1.1.1	16.00	258.00	274.00	OK
r-oldrel-macos-x86_64	1.1.1				WARN
r-oldrel-windows-ix86+x86_64	1.1.1	12.00	271.00	283.00	OK

Check Details

Version: 1.1.1
Check: tests
Result: ERROR
     Running 'testthat.R' [96s/103s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(drugCombo)
     >
     > test_check("drugCombo")
     == Skipped tests ===============================================================
     * On CRAN (3)

     == Warnings ====================================================================
     -- Warning (test-fitModel.R:143:7): fitted objects are the same for different tau specs --
     `fun.y` is deprecated. Use `fun` instead.
     Backtrace:
     1. base::plot(fitLiteral1, "2d") test-fitModel.R:143:6
     2. drugCombo:::plot.HarbronFit(fitLiteral1, "2d")
     3. drugCombo::fitPlot2d(x, fit2 = y, ...)
     4. ggplot2::stat_summary(fun.y = "mean", color = "black", geom = "point")
     -- Warning (test-fitModel.R:145:7): fitted objects are the same for different tau specs --
     `fun.y` is deprecated. Use `fun` instead.
     Backtrace:
     1. base::plot(...) test-fitModel.R:145:6
     2. drugCombo:::plot.HarbronFit(...)
     3. drugCombo::fitPlot2d(x, fit2 = y, ...)
     4. ggplot2::stat_summary(fun.y = "mean", color = "black", geom = "point")

     == Failed tests ================================================================
     -- Failure (test-tauSurface.R:69:7): tau surface calculation gives the same result with/without tauLog for continuous model --
     `tauCont` not equal to `tauContLog`.
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "QR": Component "qr": Mean relative difference: 0.6170389
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "env": Names: 2 string mismatches
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "env": Component 9: Mean relative difference: 1.831484
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "env": Component 10: Mean relative difference: 1300.55
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "form": formulas differ in contents
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "ind": Names: 2 string mismatches
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "internalPars": Names: 2 string mismatches
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "internalPars": Mean relative difference: 0.5858656
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "rhs": Attributes: < Component "gradient": Mean relative difference: 0.8981842 >
     ...

     [ FAIL 1 | WARN 2 | SKIP 3 | PASS 56 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.1.1
Check: tests
Result: ERROR
     Running ‘testthat.R’ [70s/99s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(drugCombo)
     >
     > test_check("drugCombo")
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     ● On CRAN (3)

     ══ Warnings ════════════════════════════════════════════════════════════════════
     ── Warning (test-fitModel.R:143:7): fitted objects are the same for different tau specs ──
     `fun.y` is deprecated. Use `fun` instead.
     Backtrace:
     1. base::plot(fitLiteral1, "2d") test-fitModel.R:143:6
     2. drugCombo:::plot.HarbronFit(fitLiteral1, "2d")
     3. drugCombo::fitPlot2d(x, fit2 = y, ...)
     4. ggplot2::stat_summary(fun.y = "mean", color = "black", geom = "point")
     ── Warning (test-fitModel.R:145:7): fitted objects are the same for different tau specs ──
     `fun.y` is deprecated. Use `fun` instead.
     Backtrace:
     1. base::plot(...) test-fitModel.R:145:6
     2. drugCombo:::plot.HarbronFit(...)
     3. drugCombo::fitPlot2d(x, fit2 = y, ...)
     4. ggplot2::stat_summary(fun.y = "mean", color = "black", geom = "point")

     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Failure (test-tauSurface.R:69:7): tau surface calculation gives the same result with/without tauLog for continuous model ──
     `tauCont` not equal to `tauContLog`.
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "QR": Component "qr": Mean relative difference: 0.6170389
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "env": Names: 2 string mismatches
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "env": Component 9: Mean relative difference: 1.831484
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "env": Component 10: Mean relative difference: 1300.55
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "form": formulas differ in contents
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "ind": Names: 2 string mismatches
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "internalPars": Names: 2 string mismatches
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "internalPars": Mean relative difference: 0.5858656
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "rhs": Attributes: < Component "gradient": Mean relative difference: 0.8981842 >
     ...

     [ FAIL 1 | WARN 2 | SKIP 3 | PASS 56 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.1.1
Check: tests
Result: ERROR
     Running ‘testthat.R’ [119s/149s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(drugCombo)
     >
     > test_check("drugCombo")
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     ● On CRAN (3)

     ══ Warnings ════════════════════════════════════════════════════════════════════
     ── Warning (test-fitModel.R:143:7): fitted objects are the same for different tau specs ──
     `fun.y` is deprecated. Use `fun` instead.
     Backtrace:
     1. base::plot(fitLiteral1, "2d") test-fitModel.R:143:6
     2. drugCombo:::plot.HarbronFit(fitLiteral1, "2d")
     3. drugCombo::fitPlot2d(x, fit2 = y, ...)
     4. ggplot2::stat_summary(fun.y = "mean", color = "black", geom = "point")
     ── Warning (test-fitModel.R:145:7): fitted objects are the same for different tau specs ──
     `fun.y` is deprecated. Use `fun` instead.
     Backtrace:
     1. base::plot(...) test-fitModel.R:145:6
     2. drugCombo:::plot.HarbronFit(...)
     3. drugCombo::fitPlot2d(x, fit2 = y, ...)
     4. ggplot2::stat_summary(fun.y = "mean", color = "black", geom = "point")

     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Failure (test-tauSurface.R:69:7): tau surface calculation gives the same result with/without tauLog for continuous model ──
     `tauCont` not equal to `tauContLog`.
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "QR": Component "qr": Mean relative difference: 0.6170389
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "env": Names: 2 string mismatches
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "env": Component 9: Mean relative difference: 1.831484
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "env": Component 10: Mean relative difference: 1300.55
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "form": formulas differ in contents
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "ind": Names: 2 string mismatches
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "internalPars": Names: 2 string mismatches
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "internalPars": Mean relative difference: 0.5858656
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "rhs": Attributes: < Component "gradient": Mean relative difference: 0.8981842 >
     ...

     [ FAIL 1 | WARN 2 | SKIP 3 | PASS 56 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.1.1
Check: tests
Result: ERROR
     Running ‘testthat.R’ [119s/144s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(drugCombo)
     >
     > test_check("drugCombo")
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     ● On CRAN (3)

     ══ Warnings ════════════════════════════════════════════════════════════════════
     ── Warning (test-fitModel.R:143:7): fitted objects are the same for different tau specs ──
     `fun.y` is deprecated. Use `fun` instead.
     Backtrace:
     1. base::plot(fitLiteral1, "2d") test-fitModel.R:143:6
     2. drugCombo:::plot.HarbronFit(fitLiteral1, "2d")
     3. drugCombo::fitPlot2d(x, fit2 = y, ...)
     4. ggplot2::stat_summary(fun.y = "mean", color = "black", geom = "point")
     ── Warning (test-fitModel.R:145:7): fitted objects are the same for different tau specs ──
     `fun.y` is deprecated. Use `fun` instead.
     Backtrace:
     1. base::plot(...) test-fitModel.R:145:6
     2. drugCombo:::plot.HarbronFit(...)
     3. drugCombo::fitPlot2d(x, fit2 = y, ...)
     4. ggplot2::stat_summary(fun.y = "mean", color = "black", geom = "point")

     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Failure (test-tauSurface.R:69:7): tau surface calculation gives the same result with/without tauLog for continuous model ──
     `tauCont` not equal to `tauContLog`.
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "QR": Component "qr": Mean relative difference: 0.6170389
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "env": Names: 2 string mismatches
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "env": Component 9: Mean relative difference: 1.831484
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "env": Component 10: Mean relative difference: 1300.55
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "form": formulas differ in contents
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "ind": Names: 2 string mismatches
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "internalPars": Names: 2 string mismatches
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "internalPars": Mean relative difference: 0.5858656
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "rhs": Attributes: < Component "gradient": Mean relative difference: 0.8981842 >
     ...

     [ FAIL 1 | WARN 2 | SKIP 3 | PASS 56 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.1.1
Check: tests
Result: ERROR
     Running 'testthat.R' [147s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(drugCombo)
     >
     > test_check("drugCombo")
     == Skipped tests ===============================================================
     * On CRAN (3)

     == Warnings ====================================================================
     -- Warning (test-fitModel.R:143:7): fitted objects are the same for different tau specs --
     `fun.y` is deprecated. Use `fun` instead.
     Backtrace:
     1. base::plot(fitLiteral1, "2d") test-fitModel.R:143:6
     2. drugCombo:::plot.HarbronFit(fitLiteral1, "2d")
     3. drugCombo::fitPlot2d(x, fit2 = y, ...)
     4. ggplot2::stat_summary(fun.y = "mean", color = "black", geom = "point")
     -- Warning (test-fitModel.R:145:7): fitted objects are the same for different tau specs --
     `fun.y` is deprecated. Use `fun` instead.
     Backtrace:
     1. base::plot(...) test-fitModel.R:145:6
     2. drugCombo:::plot.HarbronFit(...)
     3. drugCombo::fitPlot2d(x, fit2 = y, ...)
     4. ggplot2::stat_summary(fun.y = "mean", color = "black", geom = "point")

     == Failed tests ================================================================
     -- Failure (test-tauSurface.R:69:7): tau surface calculation gives the same result with/without tauLog for continuous model --
     `tauCont` not equal to `tauContLog`.
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "QR": Component "qr": Mean relative difference: 0.6170391
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "env": Names: 2 string mismatches
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "env": Component 9: Mean relative difference: 1.831484
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "env": Component 10: Mean relative difference: 1300.549
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "form": formulas differ in contents
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "ind": Names: 2 string mismatches
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "internalPars": Names: 2 string mismatches
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "internalPars": Mean relative difference: 0.5858653
     Component "surfaceFormula": Component "fit": Component "m": Component "resid": Component "rhs": Attributes: < Component "gradient": Mean relative difference: 0.8981842 >
     ...

     [ FAIL 1 | WARN 2 | SKIP 3 | PASS 56 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 1.1.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘userGuide.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Using constraints: b = 1
    Using constraints: b = 1
    Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
    Using constraints: b = 1
    Using constraints: b = 1
    PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
    Warning in normalizePath(f2) :
     path[1]="webshot6cf13582496.png": No such file or directory
    Warning in file(con, "rb") :
     cannot open file 'webshot6cf13582496.png': No such file or directory
    Quitting from lines 357-358 (userGuide.Rmd)
    Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
    cannot open the connection
    --- failed re-building ‘userGuide.Rmd’

    SUMMARY: processing the following file failed:
     ‘userGuide.Rmd’

    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 1.1.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘userGuide.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Using constraints: b = 1
    Using constraints: b = 1
    Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
    Using constraints: b = 1
    Using constraints: b = 1
    PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
    Warning in normalizePath(f2) :
     path[1]="webshot108755888790.png": No such file or directory
    Warning in file(con, "rb") :
     cannot open file 'webshot108755888790.png': No such file or directory
    Quitting from lines 357-358 (userGuide.Rmd)
    Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
    cannot open the connection
    --- failed re-building ‘userGuide.Rmd’

    SUMMARY: processing the following file failed:
     ‘userGuide.Rmd’

    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-macos-x86_64

Version: 1.1.1
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Flavor: r-oldrel-macos-x86_64

Version: 1.1.1
Check: dependencies in R code
Result: NOTE
No protocol specified
Flavor: r-oldrel-macos-x86_64

Version: 1.1.1
Check: S3 generic/method consistency
Result: WARN
    No protocol specified
    See section ‘Generic functions and methods’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-macos-x86_64

Version: 1.1.1
Check: replacement functions
Result: WARN
    No protocol specified
    The argument of a replacement function which corresponds to the right
    hand side must be named ‘value’.
Flavor: r-oldrel-macos-x86_64

Version: 1.1.1
Check: foreign function calls
Result: NOTE
    No protocol specified
    See chapter ‘System and foreign language interfaces’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-macos-x86_64

Version: 1.1.1
Check: R code for possible problems
Result: NOTE
No protocol specified
Flavor: r-oldrel-macos-x86_64

Version: 1.1.1
Check: for missing documentation entries
Result: WARN
    No protocol specified
    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-macos-x86_64

Version: 1.1.1
Check: for code/documentation mismatches
Result: WARN
    No protocol specified
    No protocol specified
    No protocol specified
Flavor: r-oldrel-macos-x86_64

Version: 1.1.1
Check: Rd \usage sections
Result: NOTE
    No protocol specified
    The \usage entries for S3 methods should use the \method markup and not
    their full name.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-macos-x86_64

Version: 1.1.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘userGuide.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    No protocol specified
    Warning in rgl.init(initValue, onlyNULL) :
     RGL: unable to open X11 display
    Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
    Using constraints: b = 1
    Using constraints: b = 1
    Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
    Using constraints: b = 1
    Using constraints: b = 1
    PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
    Warning in normalizePath(f2) :
     path[1]="webshot219036569873.png": No such file or directory
    Warning in file(con, "rb") :
     cannot open file 'webshot219036569873.png': No such file or directory
    Quitting from lines 357-358 (userGuide.Rmd)
    Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
    cannot open the connection
    --- failed re-building ‘userGuide.Rmd’

    SUMMARY: processing the following file failed:
     ‘userGuide.Rmd’

    Error: Vignette re-building failed.
    Execution halted
Flavor: r-oldrel-macos-x86_64