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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:scHOT.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings scHOT_1.11.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/scHOT.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘scHOT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scHOT’ version ‘1.11.0’
* package encoding: UTF-8
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scHOT’ can be installed ... OK
* checking installed package size ... 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 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 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 ... 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘scHOT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scHOT_performPermutationTest
> ### Title: scHOT_performPermutationTest
> ### Aliases: scHOT_performPermutationTest
> 
> ### ** Examples
> 
>  data(MOB_subset)
>  sce_MOB_subset <- MOB_subset$sce_MOB_subset
>  scHOT_spatial <- scHOT_buildFromSCE(sce_MOB_subset,
+                                      assayName = "logcounts",
+                                     positionType = "spatial",
+                                      positionColData = c("x", "y"))
> pairs <- matrix(c("Arrb1", "Mtor", "Dnm1l", "Gucy1b3"), ncol = 2, byrow = TRUE)
> rownames(pairs) <- apply(pairs,1,paste0,collapse = "_")
> scHOT_spatial <- scHOT_addTestingScaffold(scHOT_spatial, pairs)
>  scHOT_spatial <- scHOT_setWeightMatrix(scHOT_spatial,
+                                        positionColData = c("x","y"),
+                                         positionType = "spatial",
+                                         nrow.out = NULL,
+                                         span = 0.05)
weightMatrix not provided, generating one using parameter settings...
> scHOT_spatial <- scHOT_calculateGlobalHigherOrderFunction(
+   scHOT_spatial,
+   higherOrderFunction = weightedSpearman,
+   higherOrderFunctionType = "weighted")
higherOrderFunctionType given will replace any stored param
higherOrderFunction given will replace any stored param
> scHOT_spatial <- scHOT_setPermutationScaffold(scHOT_spatial,
+                                               numberPermutations = 100)
numberScaffold set higher than the scaffold, setting permutation number for all tests
> scHOT_spatial <- scHOT_calculateHigherOrderTestStatistics(
+   scHOT_spatial,
+   higherOrderSummaryFunction = sd)
higherOrderSummaryFunction will replace any stored param
> 
> scHOT_spatial <- scHOT_performPermutationTest(
+   scHOT_spatial,
+   verbose = TRUE,
+   parallel = FALSE)
Permutation testing combination 1 of 2...
Permutation testing combination 2 of 2...
Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘scHOT.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘scHOT.Rmd’ using knitr
Killed

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/scHOT.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL scHOT
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘scHOT’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scHOT)