* using log directory ‘/srv/hornik/tmp/CRAN/PMA.Rcheck’
* using R Under development (unstable) (2023-07-18 r84705)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 16.0.6 (3)
    GNU Fortran (Debian 12.3.0-5) 12.3.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘PMA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PMA’ version ‘1.2-2’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/4s] NOTE
Maintainer: ‘Rob Tibshirani <tibs@stanford.edu>’

Size of tarball: 6704107 bytes
* 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 serialization versions ... OK
* checking whether package ‘PMA’ can be installed ... [8s/8s] OK
* used C compiler: ‘Debian clang version 16.0.6 (3)’
* used C++ compiler: ‘Debian clang version 16.0.6 (3)’
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking use of S3 registration ... 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 ... [5s/5s] NOTE
CheckPMDV: no visible global function definition for ‘mean.na’
PMDL1L1: no visible global function definition for ‘mean.na’
SPC: no visible global function definition for ‘mean.na’
Undefined global functions or variables:
  mean.na
* checking Rd files ... [0s/0s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [3s/3s] ERROR
Running examples in ‘PMA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PMD
> ### Title: Get a penalized matrix decomposition for a data matrix.
> ### Aliases: PMD
> 
> ### ** Examples
> 
> 
> 
> # Try PMD with L1 penalty on rows and columns: type="standard"
> # A simple simulated example
> set.seed(1)
> # Our data is a rank-one matrix, plus noise. The underlying components
> # contain 50 and 75 non-zero elements, respectively.
> u <- matrix(c(rnorm(50), rep(0,150)),
+ ncol=1)
> v <- matrix(c(rnorm(75),rep(0,225)), ncol=1)
> x <- u%*%t(v)+
+ matrix(rnorm(200*300),ncol=300)
> # We can use cross-validation to try to find optimal value of sumabs
> cv.out <- PMD.cv(x, type="standard", sumabss=seq(0.1, 0.6, len=20))
Error in mean.na(x) : could not find function "mean.na"
Calls: PMD.cv -> PMDL1L1.cv -> CheckPMDV
Execution halted
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 2 NOTEs