CRAN Package Check Results for Package PhylogeneticEM

Last updated on 2021-07-23 22:53:16 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.4.0 59.65 207.02 266.67 OK
r-devel-linux-x86_64-debian-gcc 1.4.0 39.68 127.75 167.43 WARN
r-devel-linux-x86_64-fedora-clang 1.4.0 338.10 OK
r-devel-linux-x86_64-fedora-gcc 1.4.0 326.31 OK
r-devel-windows-x86_64 1.4.0 53.00 331.00 384.00 OK
r-devel-windows-x86_64-gcc10-UCRT 1.4.0 OK
r-patched-linux-x86_64 1.4.0 50.48 193.43 243.91 OK
r-patched-solaris-x86 1.4.0 769.50 OK
r-release-linux-x86_64 1.4.0 46.36 194.66 241.02 OK
r-release-macos-arm64 1.4.0 NOTE
r-release-macos-x86_64 1.4.0 OK
r-release-windows-ix86+x86_64 1.4.0 128.00 525.00 653.00 OK
r-oldrel-macos-x86_64 1.4.0 NOTE
r-oldrel-windows-ix86+x86_64 1.4.0 126.00 531.00 657.00 OK

Check Details

Version: 1.4.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: 'phytools', 'TreeSim'
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.4.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘monkeys.Rmd’ using rmarkdown
    Loading required package: ape
    Loading required package: Matrix
    starting worker pid=5239 on localhost:11910 at 03:42:52.083
    starting worker pid=5238 on localhost:11910 at 03:42:52.086
    Loading required package: PhylogeneticEM
    Loading required package: ape
    Loading required package: PhylogeneticEM
    Loading required package: ape
    Loading required package: Matrix
    Loading required package: Matrix
    loaded PhylogeneticEM and set parent environment
    loaded PhylogeneticEM and set parent environment
    Alpha 0.0131646571083129
    Alpha 0.0517168558708096
    
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     |======================================================================| 100%There are some equivalent solutions to the set of shifts selected by the BGHlsq method.
    There are some equivalent solutions to the set of shifts selected by the BGHlsqraw method.
    There are some equivalent solutions to the set of shifts selected by the BGHmlraw method.
    starting worker pid=22271 on localhost:11910 at 03:43:27.876
    starting worker pid=22272 on localhost:11910 at 03:43:28.010
    Loading required package: PhylogeneticEM
    Loading required package: PhylogeneticEM
    Loading required package: ape
    Loading required package: ape
    Loading required package: Matrix
    Loading required package: Matrix
    loaded PhylogeneticEM and set parent environment
    loaded PhylogeneticEM and set parent environment
    Alpha 0.0517168558708096
    Alpha 0.0131646571083129
    
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     |======================================================================| 100%There are some equivalent solutions to the set of shifts selected by the BGHlsq method.
    There are some equivalent solutions to the set of shifts selected by the BGHml method.
    There are some equivalent solutions to the set of shifts selected by the BGHlsqraw method.
    There are some equivalent solutions to the set of shifts selected by the BGHmlraw method.
    starting worker pid=5713 on localhost:11910 at 03:43:58.541
    starting worker pid=5712 on localhost:11910 at 03:43:58.549
    Loading required package: PhylogeneticEM
    Loading required package: ape
    Loading required package: PhylogeneticEM
    Loading required package: ape
    Loading required package: Matrix
    Loading required package: Matrix
    loaded PhylogeneticEM and set parent environment
    loaded PhylogeneticEM and set parent environment
    Alpha 0.798136621971044
    Alpha 0.0131646571083129
    
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     |======================================================================| 100%There are some equivalent solutions to the set of shifts selected by the BGHlsq method.
    There are some equivalent solutions to the set of shifts selected by the BGHml method.
    There are some equivalent solutions to the set of shifts selected by the BGHlsqraw method.
    There are some equivalent solutions to the set of shifts selected by the BGHmlraw method.
    starting worker pid=13359 on localhost:11910 at 03:44:13.765
    starting worker pid=13358 on localhost:11910 at 03:44:13.859
    Loading required package: PhylogeneticEM
    Loading required package: PhylogeneticEM
    Loading required package: ape
    Loading required package: ape
    Loading required package: Matrix
    Loading required package: Matrix
    loaded PhylogeneticEM and set parent environment
    loaded PhylogeneticEM and set parent environment
    Alpha -0.640578156028118
    Alpha -0.0131646571083129
    
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     |======================================================================| 100%There are some equivalent solutions to the set of shifts selected by the BGHlsq method.
    There are some equivalent solutions to the set of shifts selected by the BGHml method.
    There are some equivalent solutions to the set of shifts selected by the BGHlsqraw method.
    There are some equivalent solutions to the set of shifts selected by the BGHmlraw method.
    --- finished re-building ‘monkeys.Rmd’
    
    Warning messages:
    1: In params_process.PhyloEM(res, K = 5) :
     There are several equivalent solutions for this shift position.
    2: In params_process.PhyloEM(res, K = 5) :
     There are several equivalent solutions for this shift position.
    3: In params_process.PhyloEM(x, method.selection = method.selection) :
     There are several equivalent solutions for this shift position.
    4: In compute_ancestral_traits(x, params, method.selection, what, ...) :
     For K = 3, the log_likelihood of the transformed parameters on the er-scaled tree is different from the log_likelihood of the parameters on the original tree, with a tolerance of 0.000740095979741405.
    --- re-building ‘tutorial.Rmd’ using rmarkdown
    Loading required package: ape
    Loading required package: Matrix
    Quitting from lines 28-32 (tutorial.Rmd)
    Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
    there is no package called 'TreeSim'
    --- failed re-building ‘tutorial.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘tutorial.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.4.0
Check: installed package size
Result: NOTE
     installed size is 5.6Mb
     sub-directories of 1Mb or more:
     libs 4.1Mb
Flavors: r-release-macos-arm64, r-oldrel-macos-x86_64