CRAN Package Check Results for Package stockR

Last updated on 2021-01-25 22:49:20 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.74 4.95 59.78 64.73 OK
r-devel-linux-x86_64-debian-gcc 1.0.74 3.33 45.49 48.82 OK
r-devel-linux-x86_64-fedora-clang 1.0.74 85.52 OK
r-devel-linux-x86_64-fedora-gcc 1.0.74 77.56 OK
r-devel-windows-ix86+x86_64 1.0.74 11.00 315.00 326.00 OK
r-patched-linux-x86_64 1.0.74 4.44 57.74 62.18 OK
r-patched-solaris-x86 1.0.74 832.20 OK
r-release-linux-x86_64 1.0.74 4.27 57.04 61.31 WARN
r-release-macos-x86_64 1.0.74 OK
r-release-windows-ix86+x86_64 1.0.74 11.00 254.00 265.00 OK
r-oldrel-macos-x86_64 1.0.74 OK
r-oldrel-windows-ix86+x86_64 1.0.74 8.00 287.00 295.00 OK

Check Details

Version: 1.0.74
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘stockR.Rnw’ using knitr
    Removing any SNP with no variation amongst *any* fish (there are 87 of them)
    Finding starting values using K-means on rotated data (using specified number of PCAs)
    Maximising the log-likelihood to obtain parameter estimates
    Iter: 0 | Marg. Logl: -304832.654 | pis: 0.3 0.258 0.442 | Max change: Inf
    Iter: 1 | Marg. Logl: -304813.806 | pis: 0.25 0.144 0.606 | Max change: 0.16375
    Iter: 2 | Marg. Logl: -297901.731 | pis: 0.22 0.076 0.704 | Max change: 0.21
    Iter: 3 | Marg. Logl: -294081.482 | pis: 0.206 0.044 0.75 | Max change: 0.1845091
    Iter: 4 | Marg. Logl: -292034.948 | pis: 0.201 0.033 0.766 | Max change: 0.283562
    Iter: 5 | Marg. Logl: -291230.411 | pis: 0.2 0.03 0.77 | Max change: 0.2242654
    Iter: 6 | Marg. Logl: -291066.455 | pis: 0.2 0.03 0.77 | Max change: 0.0727568
    Iter: 7 | Marg. Logl: -291057.875 | pis: 0.2 0.03 0.77 | Max change: 0.0088197
    Converged | Marg. Logl: -291057.875 | pis: 0.2 0.03 0.77 | Max change: 0
    Done!
    Removing any SNP with no variation amongst *any* fish (there are 64 of them)
    Finding starting values using K-means on rotated data (using specified number of PCAs)
    Maximising the log-likelihood to obtain parameter estimates
    Iter: 0 | Marg. Logl: -306336.884 | pis: 0.3 0.333 0.367 | Max change: Inf
    Iter: 1 | Marg. Logl: -306336.536 | pis: 0.25 0.333 0.417 | Max change: 0.05
    Iter: 2 | Marg. Logl: -293977.255 | pis: 0.22 0.333 0.447 | Max change: 0.195
    Iter: 3 | Marg. Logl: -289505.139 | pis: 0.206 0.333 0.461 | Max change: 0.1595455
    Iter: 4 | Marg. Logl: -288359.221 | pis: 0.201 0.333 0.465 | Max change: 0.0903575
    Iter: 5 | Marg. Logl: -288186.585 | pis: 0.2 0.333 0.467 | Max change: 0.0338744
    Iter: 6 | Marg. Logl: -288177.04 | pis: 0.2 0.333 0.467 | Max change: 0.0078457
    Iter: 7 | Marg. Logl: -288176.99 | pis: 0.2 0.333 0.467 | Max change: 0.000877
    Converged | Marg. Logl: -288176.99 | pis: 0.2 0.333 0.467 | Max change: 0
    Done!
    Removing any SNP with no variation amongst *any* fish (there are 0 of them)
    Finding starting values using K-means on rotated data (using specified number of PCAs)
    Maximising the log-likelihood to obtain parameter estimates
    Iter: 0 | Marg. Logl: -214046.816 | pis: 0.315 0.318 0.368 | Max change: Inf
    Iter: 1 | Marg. Logl: -214045.154 | pis: 0.288 0.294 0.419 | Max change: 0.05125
    Iter: 2 | Marg. Logl: -204480.391 | pis: 0.271 0.279 0.45 | Max change: 0.1884454
    Iter: 3 | Marg. Logl: -200961.073 | pis: 0.263 0.273 0.464 | Max change: 0.1507497
    Iter: 4 | Marg. Logl: -200044.62 | pis: 0.261 0.271 0.469 | Max change: 0.0864159
    Iter: 5 | Marg. Logl: -199899.674 | pis: 0.26 0.27 0.47 | Max change: 0.0325932
    Iter: 6 | Marg. Logl: -199892.211 | pis: 0.26 0.27 0.47 | Max change: 0.0075643
    Iter: 7 | Marg. Logl: -199892.177 | pis: 0.26 0.27 0.47 | Max change: 0.0008459
    Converged | Marg. Logl: -199892.177 | pis: 0.26 0.27 0.47 | Max change: 0
    Done!
    Error: processing vignette 'stockR.Rnw' failed with diagnostics:
    Running ‘texi2dvi’ on ‘stockR.tex’ failed.
    LaTeX errors:
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.93 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.93 \begin{document}
    
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.93 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.93 \begin{document}
    
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.93 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.93 \begin{document}
    
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.93 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.93 \begin{document}
    
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.93 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.93 \begin{document}
    
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.93 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.93 \begin{document}
    
    --- failed re-building ‘stockR.Rnw’
    
    SUMMARY: processing the following file failed:
     ‘stockR.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-linux-x86_64