Failures on R-devel (4.2)

[topepo]

Perhaps CRAN has not sent any emails about this but mixOmics is failing on the next R-devel. Today is the deadline for reverse dependencies to resubmit before being removed from CRAN.

Testing below uses mixOmics 6.19.1.

library(mixOmics) 
#> Loading required package: MASS
#> Loading required package: lattice
#> Loading required package: ggplot2
#> 
#> Loaded mixOmics 6.19.1
#> Thank you for using mixOmics!
#> Tutorials: http://mixomics.org
#> Bookdown vignette: https://mixomicsteam.github.io/Bookdown
#> Questions, issues: Follow the prompts at http://mixomics.org/contact-us
#> Cite us:  citation('mixOmics')
data(linnerud)
X <- linnerud$exercise
Y <- linnerud$physiological
linn.pls <- pls(X, Y, mode = "classic")
predict(linn.pls , X)
#> Error in is(object, c("rgcca", "sparse.rgcca")): length(class2) == 1L is not TRUE

^{Created on 2022-02-07 by the reprex package (v2.0.1)}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R Under development (unstable) (2022-02-06 r81658)
#>  os       macOS Catalina 10.15.7
#>  system   x86_64, darwin17.0
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       America/New_York
#>  date     2022-02-07
#>  pandoc   2.14.0.3 @ /Applications/RStudio.app/Contents/MacOS/pandoc/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package      * version date (UTC) lib source
#>  BiocParallel   1.29.12 2022-01-16 [1] Bioconductor
#>  cli            3.1.1   2022-01-20 [1] CRAN (R 4.2.0)
#>  colorspace     2.0-2   2021-06-24 [1] CRAN (R 4.2.0)
#>  corpcor        1.6.10  2021-09-16 [1] CRAN (R 4.2.0)
#>  crayon         1.4.2   2021-10-29 [1] CRAN (R 4.2.0)
#>  digest         0.6.29  2021-12-01 [1] CRAN (R 4.2.0)
#>  dplyr          1.0.7   2021-06-18 [1] CRAN (R 4.2.0)
#>  ellipse        0.4.2   2020-05-27 [1] CRAN (R 4.2.0)
#>  ellipsis       0.3.2   2021-04-29 [1] CRAN (R 4.2.0)
#>  evaluate       0.14    2019-05-28 [1] CRAN (R 4.2.0)
#>  fansi          1.0.2   2022-01-14 [1] CRAN (R 4.2.0)
#>  fastmap        1.1.0   2021-01-25 [1] CRAN (R 4.2.0)
#>  fs             1.5.2   2021-12-08 [1] CRAN (R 4.2.0)
#>  generics       0.1.2   2022-01-31 [1] CRAN (R 4.2.0)
#>  ggplot2      * 3.3.5   2021-06-25 [1] CRAN (R 4.2.0)
#>  ggrepel        0.9.1   2021-01-15 [1] CRAN (R 4.2.0)
#>  glue           1.6.1   2022-01-22 [1] CRAN (R 4.2.0)
#>  gridExtra      2.3     2017-09-09 [1] CRAN (R 4.2.0)
#>  gtable         0.3.0   2019-03-25 [1] CRAN (R 4.2.0)
#>  highr          0.9     2021-04-16 [1] CRAN (R 4.2.0)
#>  htmltools      0.5.2   2021-08-25 [1] CRAN (R 4.2.0)
#>  igraph         1.2.11  2022-01-04 [1] CRAN (R 4.2.0)
#>  knitr          1.37    2021-12-16 [1] CRAN (R 4.2.0)
#>  lattice      * 0.20-45 2021-09-22 [1] CRAN (R 4.2.0)
#>  lifecycle      1.0.1   2021-09-24 [1] CRAN (R 4.2.0)
#>  magrittr       2.0.2   2022-01-26 [1] CRAN (R 4.2.0)
#>  MASS         * 7.3-55  2022-01-16 [1] CRAN (R 4.2.0)
#>  Matrix         1.4-0   2021-12-08 [1] CRAN (R 4.2.0)
#>  matrixStats    0.61.0  2021-09-17 [1] CRAN (R 4.2.0)
#>  mixOmics     * 6.19.1  2021-11-19 [1] Bioconduc~
#>  munsell        0.5.0   2018-06-12 [1] CRAN (R 4.2.0)
#>  pillar         1.7.0   2022-02-01 [1] CRAN (R 4.2.0)
#>  pkgconfig      2.0.3   2019-09-22 [1] CRAN (R 4.2.0)
#>  plyr           1.8.6   2020-03-03 [1] CRAN (R 4.2.0)
#>  purrr          0.3.4   2020-04-17 [1] CRAN (R 4.2.0)
#>  R6             2.5.1   2021-08-19 [1] CRAN (R 4.2.0)
#>  rARPACK        0.11-0  2016-03-10 [1] CRAN (R 4.2.0)
#>  RColorBrewer   1.1-2   2014-12-07 [1] CRAN (R 4.2.0)
#>  Rcpp           1.0.8   2022-01-13 [1] CRAN (R 4.2.0)
#>  reprex         2.0.1   2021-08-05 [1] CRAN (R 4.2.0)
#>  reshape2       1.4.4   2020-04-09 [1] CRAN (R 4.2.0)
#>  rlang          1.0.1   2022-02-03 [1] CRAN (R 4.2.0)
#>  rmarkdown      2.11    2021-09-14 [1] CRAN (R 4.2.0)
#>  RSpectra       0.16-0  2019-12-01 [1] CRAN (R 4.2.0)
#>  rstudioapi     0.13    2020-11-12 [1] CRAN (R 4.2.0)
#>  scales         1.1.1   2020-05-11 [1] CRAN (R 4.2.0)
#>  sessioninfo    1.2.2   2021-12-06 [1] CRAN (R 4.2.0)
#>  stringi        1.7.6   2021-11-29 [1] CRAN (R 4.2.0)
#>  stringr        1.4.0   2019-02-10 [1] CRAN (R 4.2.0)
#>  tibble         3.1.6   2021-11-07 [1] CRAN (R 4.2.0)
#>  tidyr          1.2.0   2022-02-01 [1] CRAN (R 4.2.0)
#>  tidyselect     1.1.1   2021-04-30 [1] CRAN (R 4.2.0)
#>  utf8           1.2.2   2021-07-24 [1] CRAN (R 4.2.0)
#>  vctrs          0.3.8   2021-04-29 [1] CRAN (R 4.2.0)
#>  withr          2.4.3   2021-11-30 [1] CRAN (R 4.2.0)
#>  xfun           0.29    2021-12-14 [1] CRAN (R 4.2.0)
#>  yaml           2.2.2   2022-01-25 [1] CRAN (R 4.2.0)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

From: Prof Brian Ripley [email protected]
Date: Monday, January 24, 2022 at 5:49 AM
To: Marco Scutari [email protected], Keaven Anderson [email protected], Cristiane Taniguti [email protected], Max Kuhn [email protected], Darren Colby [email protected]
Subject: CRAN packages fairml gsDesign onemap plsmod spacejamr
These are misusing methods::is.

The help page is ambiguous, but the code has been written assuming
'class2' is a character string (a vector of length one). Perhaps you
intended inherits()?

Your packages have

Error in is(object, fair.regressions) : length(class2) == 1L is not TRUE
Calls: summary ... is.data.frame -> fitted -> fitted.fair.model -> is

Error in methods::is(x, c("gsProbability", "gsDesign")): l

Error in is(input.obj, c("onemap", "outcross", "f2", "backcross",
"riself", :

Error in is(object, c("rgcca", "sparse.rgcca")) :

Error in methods::is(window, c("spacejamr", "owin"))

These are showing for at least one platform on their CRAN results pages,
and other R-devel platforms will follow.

Please correct before 2022-02-07 to safely retain your package on CRAN.