CRAN Package Check Results for Package seqHMM

Last updated on 2021-12-02 22:56:07 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2.0 440.98 677.07 1118.05 OK
r-devel-linux-x86_64-debian-gcc 1.2.0 306.64 171.80 478.44 ERROR
r-devel-linux-x86_64-fedora-clang 1.2.0 1058.13 ERROR
r-devel-linux-x86_64-fedora-gcc 1.2.0 952.67 ERROR
r-devel-windows-x86_64-new-UL 1.2.0 538.00 630.00 1168.00 NOTE
r-devel-windows-x86_64-new-TK 1.2.0 OK
r-devel-windows-x86_64-old 1.2.0 561.00 362.00 923.00 NOTE
r-patched-linux-x86_64 1.2.0 388.30 451.11 839.41 OK
r-patched-solaris-x86 1.2.0 1138.80 NOTE
r-release-linux-x86_64 1.2.0 363.45 455.19 818.64 OK
r-release-macos-arm64 1.2.0 NOTE
r-release-macos-x86_64 1.2.0 NOTE
r-release-windows-ix86+x86_64 1.2.0 1093.00 551.00 1644.00 NOTE
r-oldrel-macos-x86_64 1.2.0 NOTE
r-oldrel-windows-ix86+x86_64 1.2.0 1002.00 9.00 1011.00 ERROR

Check Details

Version: 1.2.0
Check: examples
Result: ERROR
    Running examples in ‘seqHMM-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: simulate_hmm
    > ### Title: Simulate hidden Markov models
    > ### Aliases: simulate_hmm
    >
    > ### ** Examples
    >
    > # Parameters for the HMM
    > emission_probs <- matrix(c(0.5, 0.2, 0.5, 0.8), 2, 2)
    > transition_probs <- matrix(c(5/6, 1/6, 1/6, 5/6), 2, 2)
    > initial_probs <- c(1, 0)
    >
    > # Setting the seed for simulation
    > set.seed(1)
    >
    > # Simulating sequences
    > sim <- simulate_hmm(
    + n_sequences = 10, initial_probs = initial_probs,
    + transition_probs = transition_probs,
    + emission_probs = emission_probs,
    + sequence_length = 20)
    >
    > ssplot(sim, sortv = "mds.obs", type = "I")
    Error in dimnames(x) <- dn :
     length of 'dimnames' [1] not equal to array extent
    Calls: ssplot -> do.call -> <Anonymous>
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.2.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘seqHMM.Rnw’ using knitr
    Please cite seqHMM in publications by using:
    
     Helske S, Helske J (2019). Mixture Hidden Markov Models for Sequence Data: The seqHMM Package in R. Journal of
    Statistical Software, 88(3), 1-32. doi: 10.18637/jss.v088.i03.
     [>] 8 distinct states appear in the data:
     1 = 0
     2 = 1
     3 = 2
     4 = 3
     5 = 4
     6 = 5
     7 = 6
     8 = 7
     [>] state coding:
     [alphabet] [label] [long label]
     1 0 0 parent
     2 1 1 left
     3 2 2 married
     4 3 3 left+marr
     5 4 4 child
     6 5 5 left+child
     7 6 6 left+marr+ch
     8 7 7 divorced
     [>] 2000 sequences in the data set
     [>] min/max sequence length: 16/16
     [>] 3 distinct states appear in the data:
     1 = divorced
     2 = married
     3 = single
     [>] state coding:
     [alphabet] [label] [long label]
     1 single single single
     2 married married married
     3 divorced divorced divorced
     [>] 2000 sequences in the data set
     [>] min/max sequence length: 16/16
     [>] 2 distinct states appear in the data:
     1 = childless
     2 = children
     [>] state coding:
     [alphabet] [label] [long label]
     1 childless childless childless
     2 children children children
     [>] 2000 sequences in the data set
     [>] min/max sequence length: 16/16
     [>] 2 distinct states appear in the data:
     1 = left home
     2 = with parents
     [>] state coding:
     [alphabet] [label] [long label]
     1 with parents with parents with parents
     2 left home left home left home
     [>] 2000 sequences in the data set
     [>] min/max sequence length: 16/16
    Quitting from lines 435-449 (seqHMM.Rnw)
    Error: processing vignette ‘seqHMM.Rnw’ failed with diagnostics:
    length of ‘dimnames’ [1] not equal to array extent
    --- failed re-building ‘seqHMM.Rnw’
    
    --- re-building ‘seqHMM_algorithms.Rnw’ using knitr
    --- finished re-building ‘seqHMM_algorithms.Rnw’
    
    --- re-building ‘seqHMM_estimation.Rnw’ using knitr
    --- finished re-building ‘seqHMM_estimation.Rnw’
    
    --- re-building ‘seqHMM_visualization.Rnw’ using knitr
     [>] 8 distinct states appear in the data:
     1 = 0
     2 = 1
     3 = 2
     4 = 3
     5 = 4
     6 = 5
     7 = 6
     8 = 7
     [>] state coding:
     [alphabet] [label] [long label]
     1 0 0 parent
     2 1 1 left
     3 2 2 married
     4 3 3 left+marr
     5 4 4 child
     6 5 5 left+child
     7 6 6 left+marr+ch
     8 7 7 divorced
     [>] 2000 sequences in the data set
     [>] min/max sequence length: 16/16
     [>] 3 distinct states appear in the data:
     1 = divorced
     2 = married
     3 = single
     [>] state coding:
     [alphabet] [label] [long label]
     1 single single single
     2 married married married
     3 divorced divorced divorced
     [>] 2000 sequences in the data set
     [>] min/max sequence length: 16/16
     [>] 2 distinct states appear in the data:
     1 = childless
     2 = children
     [>] state coding:
     [alphabet] [label] [long label]
     1 childless childless childless
     2 children children children
     [>] 2000 sequences in the data set
     [>] min/max sequence length: 16/16
     [>] 2 distinct states appear in the data:
     1 = left home
     2 = with parents
     [>] state coding:
     [alphabet] [label] [long label]
     1 with parents with parents with parents
     2 left home left home left home
     [>] 2000 sequences in the data set
     [>] min/max sequence length: 16/16
    Quitting from lines 56-71 (seqHMM_visualization.Rnw)
    Error: processing vignette ‘seqHMM_visualization.Rnw’ failed with diagnostics:
    length of ‘dimnames’ [1] not equal to array extent
    --- failed re-building ‘seqHMM_visualization.Rnw’
    
    SUMMARY: processing the following files failed:
     ‘seqHMM.Rnw’ ‘seqHMM_visualization.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.2.0
Check: installed package size
Result: NOTE
     installed size is 19.6Mb
     sub-directories of 1Mb or more:
     doc 6.3Mb
     libs 12.4Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64-new-UL, r-devel-windows-x86_64-old, r-patched-solaris-x86, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64

Version: 1.2.0
Check: examples
Result: ERROR
    Running examples in ‘seqHMM-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: simulate_hmm
    > ### Title: Simulate hidden Markov models
    > ### Aliases: simulate_hmm
    >
    > ### ** Examples
    >
    > # Parameters for the HMM
    > emission_probs <- matrix(c(0.5, 0.2, 0.5, 0.8), 2, 2)
    > transition_probs <- matrix(c(5/6, 1/6, 1/6, 5/6), 2, 2)
    > initial_probs <- c(1, 0)
    >
    > # Setting the seed for simulation
    > set.seed(1)
    >
    > # Simulating sequences
    > sim <- simulate_hmm(
    + n_sequences = 10, initial_probs = initial_probs,
    + transition_probs = transition_probs,
    + emission_probs = emission_probs,
    + sequence_length = 20)
    >
    > ssplot(sim, sortv = "mds.obs", type = "I")
    Error in dimnames(x) <- dn :
     length of 'dimnames' [1] not equal to array extent
    Calls: ssplot -> do.call -> <Anonymous>
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.2.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘seqHMM.Rnw’ using knitr
    Please cite seqHMM in publications by using:
    
     Helske S, Helske J (2019). Mixture Hidden Markov Models for Sequence Data: The seqHMM Package in R. Journal of
    Statistical Software, 88(3), 1-32. doi: 10.18637/jss.v088.i03.
     [>] 8 distinct states appear in the data:
     1 = 0
     2 = 1
     3 = 2
     4 = 3
     5 = 4
     6 = 5
     7 = 6
     8 = 7
     [>] state coding:
     [alphabet] [label] [long label]
     1 0 0 parent
     2 1 1 left
     3 2 2 married
     4 3 3 left+marr
     5 4 4 child
     6 5 5 left+child
     7 6 6 left+marr+ch
     8 7 7 divorced
     [>] 2000 sequences in the data set
     [>] min/max sequence length: 16/16
     [>] 3 distinct states appear in the data:
     1 = divorced
     2 = married
     3 = single
     [>] state coding:
     [alphabet] [label] [long label]
     1 single single single
     2 married married married
     3 divorced divorced divorced
     [>] 2000 sequences in the data set
     [>] min/max sequence length: 16/16
     [>] 2 distinct states appear in the data:
     1 = childless
     2 = children
     [>] state coding:
     [alphabet] [label] [long label]
     1 childless childless childless
     2 children children children
     [>] 2000 sequences in the data set
     [>] min/max sequence length: 16/16
     [>] 2 distinct states appear in the data:
     1 = left home
     2 = with parents
     [>] state coding:
     [alphabet] [label] [long label]
     1 with parents with parents with parents
     2 left home left home left home
     [>] 2000 sequences in the data set
     [>] min/max sequence length: 16/16
    Quitting from lines 435-449 (seqHMM.Rnw)
    Error: processing vignette 'seqHMM.Rnw' failed with diagnostics:
    length of 'dimnames' [1] not equal to array extent
    --- failed re-building ‘seqHMM.Rnw’
    
    --- re-building ‘seqHMM_algorithms.Rnw’ using knitr
    --- finished re-building ‘seqHMM_algorithms.Rnw’
    
    --- re-building ‘seqHMM_estimation.Rnw’ using knitr
    --- finished re-building ‘seqHMM_estimation.Rnw’
    
    --- re-building ‘seqHMM_visualization.Rnw’ using knitr
     [>] 8 distinct states appear in the data:
     1 = 0
     2 = 1
     3 = 2
     4 = 3
     5 = 4
     6 = 5
     7 = 6
     8 = 7
     [>] state coding:
     [alphabet] [label] [long label]
     1 0 0 parent
     2 1 1 left
     3 2 2 married
     4 3 3 left+marr
     5 4 4 child
     6 5 5 left+child
     7 6 6 left+marr+ch
     8 7 7 divorced
     [>] 2000 sequences in the data set
     [>] min/max sequence length: 16/16
     [>] 3 distinct states appear in the data:
     1 = divorced
     2 = married
     3 = single
     [>] state coding:
     [alphabet] [label] [long label]
     1 single single single
     2 married married married
     3 divorced divorced divorced
     [>] 2000 sequences in the data set
     [>] min/max sequence length: 16/16
     [>] 2 distinct states appear in the data:
     1 = childless
     2 = children
     [>] state coding:
     [alphabet] [label] [long label]
     1 childless childless childless
     2 children children children
     [>] 2000 sequences in the data set
     [>] min/max sequence length: 16/16
     [>] 2 distinct states appear in the data:
     1 = left home
     2 = with parents
     [>] state coding:
     [alphabet] [label] [long label]
     1 with parents with parents with parents
     2 left home left home left home
     [>] 2000 sequences in the data set
     [>] min/max sequence length: 16/16
    Quitting from lines 56-71 (seqHMM_visualization.Rnw)
    Error: processing vignette 'seqHMM_visualization.Rnw' failed with diagnostics:
    length of 'dimnames' [1] not equal to array extent
    --- failed re-building ‘seqHMM_visualization.Rnw’
    
    SUMMARY: processing the following files failed:
     ‘seqHMM.Rnw’ ‘seqHMM_visualization.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.2.0
Check: whether package can be installed
Result: ERROR
    Installation failed.
Flavor: r-oldrel-windows-ix86+x86_64