* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/nscancor.Rcheck’
* using R Under development (unstable) (2023-03-18 r84003)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2)
    GNU Fortran (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2)
* running under: Fedora 34 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘nscancor/DESCRIPTION’ ... OK
* this is package ‘nscancor’ version ‘0.6.1-25’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘nscancor’ can be installed ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking examples with --run-donttest ... ERROR
Running examples in ‘nscancor-Ex.R’ failed
The error most likely occurred in:

> ### Name: mcancor
> ### Title: Non-Negative and Sparse Multi-Domain CCA
> ### Aliases: mcancor
> 
> ### ** Examples
> 
> ## No test: 
> if (requireNamespace("glmnet", quietly = TRUE) &&
+     requireNamespace("PMA", quietly = TRUE)) {
+ 
+   data(breastdata, package="PMA")
+ 
+   set.seed(1)
+ 
+   # Three data domains: a subset of genes, and CGH spots for the first and
+   # second chromosome
+   x <- with(breastdata,
+             list(t(rna)[ , 1:100], t(dna)[ , chrom == 1], t(dna)[ , chrom == 2])
+   )
+ 
+   # Sparse regression functions with different cardinalities for different domains
+   generate_predict <- function(dfmax) {
+     force(dfmax)
+     return(
+       function(x, sc, cc) {
+         en <- glmnet::glmnet(x, sc, alpha = 0.05, intercept = FALSE, dfmax = dfmax)
+         W <- coef(en)
+         return(W[2:nrow(W), ncol(W)])
+       }
+     )
+   }
+   predict <- lapply(c(20, 10, 10), generate_predict)
+ 
+   # Compute two canonical variables per domain
+   mcc <- mcancor(x, predict = predict, nvar = 2)
+ 
+   # Compute another canonical variable for each domain
+   mcc <- mcancor(x, predict = predict, nvar = 3, partial_model = mcc)
+ }
Warning in data(breastdata, package = "PMA") :
  data set ‘breastdata’ not found
Error: object 'breastdata' not found
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run-all.R’
 [10s/10s] OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/nscancor.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 0:38.36, 31.03 + 6.84