* using log directory '/scratch/th798/data.table-revdeps/2022-11-12/tasks/1294/xgboost.Rcheck'
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: ASCII
* checking for file 'xgboost/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'xgboost' version '1.6.0.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking:
  'DiagrammeR', 'Ckmeans.1d.dp', 'vcd', 'lintr', 'igraph', 'float',
  'titanic'
* 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 'xgboost' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 64.1Mb
  sub-directories of 1Mb or more:
    libs  63.2Mb
* 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 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 cross-references ... NOTE
Package unavailable to check Rd xrefs: 'DiagrammeR'
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'xgboost-Ex.R' failed
The error most likely occurred in:

> ### Name: xgb.ggplot.deepness
> ### Title: Plot model trees deepness
> ### Aliases: xgb.ggplot.deepness xgb.plot.deepness
> 
> ### ** Examples
> 
> 
> data(agaricus.train, package='xgboost')
> 
> # Change max_depth to a higher number to get a more significant result
> bst <- xgboost(data = agaricus.train$data, label = agaricus.train$label, max_depth = 6,
+                eta = 0.1, nthread = 2, nrounds = 50, objective = "binary:logistic",
+                subsample = 0.5, min_child_weight = 2)
[1]	train-logloss:0.600003 
[2]	train-logloss:0.524033 
[3]	train-logloss:0.459649 
[4]	train-logloss:0.405417 
[5]	train-logloss:0.359278 
[6]	train-logloss:0.319218 
[7]	train-logloss:0.284446 
[8]	train-logloss:0.254133 
[9]	train-logloss:0.227677 
[10]	train-logloss:0.204192 
[11]	train-logloss:0.183195 
[12]	train-logloss:0.164763 
[13]	train-logloss:0.148895 
[14]	train-logloss:0.134068 
[15]	train-logloss:0.121147 
[16]	train-logloss:0.109301 
[17]	train-logloss:0.099045 
[18]	train-logloss:0.089818 
[19]	train-logloss:0.081742 
[20]	train-logloss:0.074330 
[21]	train-logloss:0.067892 
[22]	train-logloss:0.061658 
[23]	train-logloss:0.056055 
[24]	train-logloss:0.050891 
[25]	train-logloss:0.046377 
[26]	train-logloss:0.042650 
[27]	train-logloss:0.038807 
[28]	train-logloss:0.035790 
[29]	train-logloss:0.032877 
[30]	train-logloss:0.030181 
[31]	train-logloss:0.027812 
[32]	train-logloss:0.025544 
[33]	train-logloss:0.023470 
[34]	train-logloss:0.021666 
[35]	train-logloss:0.019980 
[36]	train-logloss:0.018528 
[37]	train-logloss:0.017192 
[38]	train-logloss:0.015929 
[39]	train-logloss:0.014977 
[40]	train-logloss:0.013998 
[41]	train-logloss:0.013148 
[42]	train-logloss:0.012292 
[43]	train-logloss:0.011556 
[44]	train-logloss:0.010909 
[45]	train-logloss:0.010316 
[46]	train-logloss:0.009684 
[47]	train-logloss:0.009265 
[48]	train-logloss:0.008787 
[49]	train-logloss:0.008370 
[50]	train-logloss:0.007953 
> 
> xgb.plot.deepness(bst)
Error: igraph package is required for plotting the graph deepness.
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... ERROR
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  [11:26:47] WARNING: amalgamation/../src/gbm/gbtree.cc:82: DANGER AHEAD: You have manually specified `updater` parameter. The `tree_method` parameter will be ignored. Incorrect sequence of updaters will produce undefined behavior. For common uses, we recommend using `tree_method` parameter instead.
  
  | |         7 | update trees in an existing model                               [11:26:47] WARNING: amalgamation/../src/gbm/gbtree.cc:82: DANGER AHEAD: You have manually specified `updater` parameter. The `tree_method` parameter will be ignored. Incorrect sequence of updaters will produce undefined behavior. For common uses, we recommend using `tree_method` parameter instead.
  [11:26:47] WARNING: amalgamation/../src/gbm/gbtree.cc:82: DANGER AHEAD: You have manually specified `updater` parameter. The `tree_method` parameter will be ignored. Incorrect sequence of updaters will produce undefined behavior. For common uses, we recommend using `tree_method` parameter instead.
  [11:26:47] WARNING: amalgamation/../src/gbm/gbtree.cc:82: DANGER AHEAD: You have manually specified `updater` parameter. The `tree_method` parameter will be ignored. Incorrect sequence of updaters will produce undefined behavior. For common uses, we recommend using `tree_method` parameter instead.
  
  | |        19 | update trees in an existing model                               
  v |        22 | update trees in an existing model [0.5s]
  
  == Results =====================================================================
  Duration: 51.2 s
  
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 583 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... NONE
  'discoverYourData.Rmd' using 'UTF-8'... OK
  'xgboostPresentation.Rmd' using 'UTF-8'... OK
  'xgboostfromJSON.Rmd' using 'UTF-8'... OK
  'xgboost.Rnw'... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building 'discoverYourData.Rmd' using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  no png support in this version of R
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Loading required package: xgboost
Loading required package: Matrix
Loading required package: data.table
Loading required package: vcd
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'vcd'
Installing package into '/scratch/th798/data.table-revdeps/2022-11-12/tasks/1294/xgboost.Rcheck'
(as 'lib' is unspecified)
Quitting from lines 28-32 (discoverYourData.Rmd) 
Error: processing vignette 'discoverYourData.Rmd' failed with diagnostics:
trying to use CRAN without setting a mirror
--- failed re-building 'discoverYourData.Rmd'

--- re-building 'xgboostPresentation.Rmd' using rmarkdown
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning in xgb.load(rawVec) :
  The support for loading raw booster with `xgb.load` will be  discontinued in upcoming release. Use `xgb.load.raw` or  `xgb.unserialize` instead. 
--- finished re-building 'xgboostPresentation.Rmd'

--- re-building 'xgboostfromJSON.Rmd' using rmarkdown
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Warning: The device 'svg' is not operational; falling back to 'jpeg'.
Quitting from lines 115-122 (xgboostfromJSON.Rmd) 
Error: processing vignette 'xgboostfromJSON.Rmd' failed with diagnostics:
could not find function "fl"
--- failed re-building 'xgboostfromJSON.Rmd'

--- re-building 'xgboost.Rnw' using knitr
Loading required package: knitr
--- finished re-building 'xgboost.Rnw'

SUMMARY: processing the following files failed:
  'discoverYourData.Rmd' 'xgboostfromJSON.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE
Status: 3 ERRORs, 4 NOTEs