* using log directory ‘/data/gannet/ripley/R/packages/tests-noLD/MXM.Rcheck’
* using R Under development (unstable) (2024-11-05 r87288)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘MXM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MXM’ version ‘1.5.5’
* 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 ‘MXM’ can be installed ... [130s/158s] OK
* checking package directory ... OK
* checking ‘build’ 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [8s/10s] 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 use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [348s/446s] OK
* checking Rd files ... NOTE
checkRd: (-1) bbc.Rd:39: Lost braces
    39 | The "nbdev.mxm" (negative binomial deviance) is missing. For more information on these see \code{\link{cv.ses}}. bold{Note} that they come with "".
       |                                                                                                                      ^
checkRd: (-1) cv.fbed.lmm.reg.Rd:32: Lost braces; missing escapes or markup?
    32 | The folds of the data to use (a list generated by the function generateCVRuns {TunePareto}). If NULL the folds are created internally with the same function.
       |                                                                               ^
checkRd: (-1) cv.gomp.Rd:29: Lost braces; missing escapes or markup?
    29 | The folds of the data to use (a list generated by the function generateCVRuns {TunePareto}). If NULL the folds are created internally with the same function.
       |                                                                               ^
checkRd: (-1) cv.ses.Rd:94: Lost braces; missing escapes or markup?
    94 | The folds of the data to use (a list generated by the function generateCVRuns {TunePareto}). If NULL the folds are created internally with the same function.
       |                                                                               ^
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [49s/79s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [58s/97s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘MMPC_tutorial.Rmd’ using knitr
Warning in xfun::prose_index(text) : Code fences are not balanced
Warning in prose_index(x) : Code fences are not balanced
Warning in xfun::prose_index(text) : Code fences are not balanced
--- finished re-building ‘MMPC_tutorial.Rmd’

--- re-building ‘SES_KMVerrou_11_12.Rmd’ using knitr

Quitting from lines 54-67 [unnamed-chunk-2] (SES_KMVerrou_11_12.Rmd)
Error: processing vignette 'SES_KMVerrou_11_12.Rmd' failed with diagnostics:
cannot open the connection to 'https://archive.ics.uci.edu/ml/machine-learning-databases/wine/wine.data'
--- failed re-building ‘SES_KMVerrou_11_12.Rmd’

--- re-building ‘FS_guide.ltx’ using tex
--- finished re-building ‘FS_guide.ltx’

--- re-building ‘article.ltx’ using tex
--- finished re-building ‘article.ltx’

--- re-building ‘guide.ltx’ using tex
--- finished re-building ‘guide.ltx’

SUMMARY: processing the following file failed:
  ‘SES_KMVerrou_11_12.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [21s/31s] OK
* checking HTML version of manual ... [13s/19s] 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
See
  ‘/data/gannet/ripley/R/packages/tests-noLD/MXM.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 17:52.83, 761.94 + 41.53