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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:scClassify.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings scClassify_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/scClassify.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 ‘scClassify/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scClassify’ 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 ‘scClassify’ 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘scClassify-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: runSampleCal
> ### Title: Run sample size calculation for pilot data for reference dataset
> ### Aliases: runSampleCal
> 
> ### ** Examples
> 
> data("scClassify_example")
> xin_cellTypes <- scClassify_example$xin_cellTypes
> exprsMat_xin_subset <- scClassify_example$exprsMat_xin_subset
> 
> exprsMat_xin_subset <- as(exprsMat_xin_subset, "dgCMatrix")
> set.seed(2019)
> accMat <- runSampleCal(exprsMat_xin_subset,
+ xin_cellTypes,
+ n_list = seq(20, 100, 20),
+ num_repeat = 5, BPPARAM = BiocParallel::SerialParam())
[1] "n= 20"
cellTypes_train
alpha  beta delta gamma 
    8     8     3     3 
cellTypes_train
alpha  beta delta gamma 
    8     8     3     3 
There are only 1 selected genes in reference data expressed in query data
cellTypes_train
alpha  beta delta gamma 
    8     8     3     3 
cellTypes_train
alpha  beta delta gamma 
    8     8     3     3 
cellTypes_train
alpha  beta delta gamma 
    8     8     3     3 
There are only 3 selected genes in reference data expressed in query data
                             [,1]        [,2]       [,3]        [,4]
correct                0.94938650 0.452453988 0.96932515 0.769938650
correctly unassigned   0.00000000 0.000000000 0.00000000 0.000000000
intermediate           0.02453988 0.374233129 0.00000000 0.000000000
incorrectly unassigned 0.01073620 0.170245399 0.01073620 0.225460123
error assigned         0.00000000 0.000000000 0.00000000 0.000000000
misclassified          0.01533742 0.003067485 0.01993865 0.004601227
                              [,5]
correct                0.527607362
correctly unassigned   0.000000000
intermediate           0.360429448
incorrectly unassigned 0.102760736
error assigned         0.000000000
misclassified          0.009202454
[1] "n= 40"
cellTypes_train
alpha  beta delta gamma 
   17    15     3     5 
Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘pretrainedModel.Rmd’ using ‘UTF-8’... OK
  ‘scClassify.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘pretrainedModel.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scClassify.Rcheck/vign_test/scClassify/vignettes/pretrainedModel_files/figure-html/unnamed-chunk-5-1.png" but not available.
--- finished re-building ‘pretrainedModel.Rmd’

--- re-building ‘scClassify.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scClassify.Rcheck/vign_test/scClassify/vignettes/scClassify_files/figure-html/unnamed-chunk-5-1.png" but not available.
Killed
SUMMARY: processing the following file failed:
  ‘scClassify.Rmd’

Error: Vignette re-building failed.
Execution halted

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

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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL scClassify
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘scClassify’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (scClassify)