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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:EWCE.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings EWCE_1.9.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/EWCE.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘EWCE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EWCE’ version ‘1.9.3’
* 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 ‘EWCE’ 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 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                             user system elapsed
controlled_geneset_enrichment              30.566  0.826  36.820
merged_ewce                                24.559  0.817  28.221
generate_bootstrap_plots_for_transcriptome 18.398  0.332  21.201
filter_nonorthologs                        16.986  0.438  18.899
generate_bootstrap_plots                   16.433  0.315  18.939
filter_genes_without_1to1_homolog          15.986  0.333  17.696
sct_normalize                              13.444  0.308  15.280
bootstrap_enrichment_test                  13.162  0.200  17.055
ewce_expression_data                       12.900  0.424  15.668
check_ewce_genelist_inputs                 11.732  0.134  17.886
standardise_ctd                             9.785  0.203  11.496
merge_ctd                                   9.549  0.328  10.930
filter_ctd_genes                            8.255  0.251  10.529
add_res_to_merging_list                     6.938  0.260  18.903
merge_sce                                   6.914  0.215   8.597
fix_bad_mgi_symbols                         6.697  0.323   9.929
ctd_to_sce                                  5.635  0.125 943.959
generate_celltype_data                      5.394  0.234   8.664
bin_columns_into_quantiles                  5.341  0.120   6.456
bin_specificity_into_quantiles              5.353  0.108   7.852
plot_ctd                                    5.198  0.108   6.788
drop_uninformative_genes                    5.027  0.222   6.682
merge_two_expfiles                          4.053  0.315   5.876
get_celltype_table                          3.808  0.155   5.460
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    4.     └─ExperimentHub (local) .local(x, i, j = j, ...)
    5.       ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
    6.       │ └─base::eval(call, callEnv)
    7.       │   └─base::eval(call, callEnv)
    8.       └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
    9.         └─AnnotationHub (local) .local(x, i, j = j, ...)
   10.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
   11.             └─base::tryCatch(...)
   12.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   13.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   14.                   └─value[[3L]](cond)
  
  [ FAIL 3 | WARN 43 | SKIP 0 | PASS 112 ]
  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 ...
  ‘EWCE.Rmd’ using ‘UTF-8’... OK
  ‘extended.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ...