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### Running command:
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###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:scRepertoire.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings scRepertoire_1.11.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/scRepertoire.Rcheck’
* using R version 4.3.0 (2023-04-21)
* 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 ‘scRepertoire/DESCRIPTION’ ... OK
* this is package ‘scRepertoire’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  download from 'https://CRAN.R-project.org/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES' failed
 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 ‘scRepertoire’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    CHANGES IN VERSION 1.3.2
    # This is the new numbering scheme apologies - we are all up-to-date now and now cell ranger >= 5 will # work on bioconductor, so let's all just take that as a win.
    * added dot.size parameter to scatterClonotype
    * filteringMulti now subsets clonotypes with contains >=2, to prevent 2 of the same chains
    * changed how coldata is added to SCE objects using merge instead of union
    * Can now add BCR and TCR simultaneously by making large list
    * scatter plotting code is not so ugly and allows for user to select dot.size as a variable on the x or y axis
    * Removed regressClonotype function - too many dependencies required, adding an additional vignette to go through the process
    * Added chain option to visualizations and combineExpression to allow users to facilitate single chains - removed chain option from combineTCR/BCR/TRUST4 (the combined object will have both chains no matter what)
    * Added NA filter to combineTCR/BCR/TRUST4 for cell barcodes with only NA values
    * Added NA filter to expression2List() for cells with NA clonotypes.
    * Updated VizGene to order the genes automatically by highest to lowest variance
    * Updated VizGene to pull the correct genes based on selection
    * Updated parse method - old version had issue with place V-->J-->D in the TRB/Heavy chains 
    * Simplified the clonalDiversity() to allow for more options in organizing plot and box plots. 
    * CombineExpression() adds the groupBy variable to Frequency, allowing for multiple calculations to be saved in the meta data. 
    * Default color scheme now uses viridis plasma, because it I am on transfusion medicine.
  Cannot process chunk/lines:
    CHANGES IN VERSION 1.2.2
    # Working on renumbering versions for consistency - this is the new current dev branch
    # The below have not been implemented into the master branch or the bioconductor version
    * added the combineTRUST4 function to parse contigs from TUST4 pipeline
    * added the filter of contigs by chain in the combineTCR, combineBCR, and combineTRUST4 functions
    * no longer require the ID in the combineTCR/BCR/TRUST4 functions
    * added jaccard index for overlap analysis
    * replaced vizVgene with vizGene - allowing users to look at any gene in the combinedContig object
    * Fixed coloring scale on the overlap analysis
    * Added regressClonotype function using harmony to remove the clonotype effect on feature space
    * allowed occupiedRepertoire to use proportion.
    * added scatterClonotype function to Viz.R
  Cannot process chunk/lines:
    The first version of scRepertoire submitted to Bioconductor.
* 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 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 ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘vignette.Rmd’ using ‘UTF-8’... failed to complete the test
 ERROR
Errors in running code in vignettes:
when running code in ‘vignette.Rmd’
  ...
> proc.time()
   user  system elapsed 
  0.165   0.036   0.196 

... incomplete output.  Crash?

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
* checking PDF version of manual without index ... ERROR
* DONE

Status: 2 ERRORs, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/scRepertoire.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL scRepertoire
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘scRepertoire’ ...
** 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 (scRepertoire)