I'm not sure if this is a bug, or a limitation of predict(), but when I try to use predict() on an PLS object created by opls() where X and Y are both matrices with multiple columns, it throws an error.

library(ropls)

data(sacurine)
attach(sacurine)

train.X <- dataMatrix[1:130, ]
train.Y <- sampleMetadata[1:130, 1:2]
sacurine.pls <- opls(train.X, as.matrix(train.Y))
#> PLS
#> 130 samples x 109 variables and 2 responses
#> standard scaling of predictors and response(s)
#>       R2X(cum) R2Y(cum) Q2(cum) RMSEE pre ort
#> Total    0.203    0.343   0.156  6.19   2   0

test.X <- dataMatrix[131:183, ]
predict(sacurine.pls, test.X)
#> Error in dimnames(predMCNFcVcn) <- list(rownames(newdata), "pred"): length of 'dimnames' [2] not equal to array extent


devtools::session_info()
#> Session info -------------------------------------------------------------
#>  setting  value                       
#>  version  R version 3.4.4 (2018-03-15)
#>  system   x86_64, darwin15.6.0        
#>  ui       X11                         
#>  language (EN)                        
#>  collate  en_US.UTF-8                 
#>  tz       America/New_York            
#>  date     2018-06-20
#> Packages -----------------------------------------------------------------
#>  package      * version date       source                          
#>  backports      1.1.2   2017-12-13 CRAN (R 3.4.3)                  
#>  base         * 3.4.4   2018-03-15 local                           
#>  Biobase        2.36.2  2017-05-04 Bioconductor                    
#>  BiocGenerics   0.22.1  2017-10-07 Bioconductor                    
#>  compiler       3.4.4   2018-03-15 local                           
#>  datasets     * 3.4.4   2018-03-15 local                           
#>  devtools       1.13.5  2018-02-18 CRAN (R 3.4.3)                  
#>  digest         0.6.15  2018-01-28 CRAN (R 3.4.3)                  
#>  evaluate       0.10.1  2017-06-24 CRAN (R 3.4.0)                  
#>  graphics     * 3.4.4   2018-03-15 local                           
#>  grDevices    * 3.4.4   2018-03-15 local                           
#>  htmltools      0.3.6   2017-04-28 cran (@0.3.6)                   
#>  knitr          1.20    2018-02-20 CRAN (R 3.4.3)                  
#>  magrittr       1.5     2014-11-22 CRAN (R 3.4.0)                  
#>  memoise        1.1.0   2017-04-21 CRAN (R 3.4.0)                  
#>  methods      * 3.4.4   2018-03-15 local                           
#>  parallel       3.4.4   2018-03-15 local                           
#>  Rcpp           0.12.17 2018-05-18 CRAN (R 3.4.4)                  
#>  rmarkdown      1.9     2018-03-01 CRAN (R 3.4.3)                  
#>  ropls        * 1.8.0   2017-04-25 Bioconductor                    
#>  rprojroot      1.3-2   2018-01-03 CRAN (R 3.4.3)                  
#>  stats        * 3.4.4   2018-03-15 local                           
#>  stringi        1.2.2   2018-05-02 CRAN (R 3.4.4)                  
#>  stringr        1.3.1   2018-05-10 CRAN (R 3.4.4)                  
#>  tools          3.4.4   2018-03-15 local                           
#>  utils        * 3.4.4   2018-03-15 local                           
#>  withr          2.1.2   2018-06-07 Github (jimhester/withr@dbcd7cd)
#>  yaml           2.1.19  2018-05-01 CRAN (R 3.4.4)

Thanks for reporting this bug which has been fixed in the 1.13.2 version of ropls (dev).

Etienne.