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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scRepertoire.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scRepertoire_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/scRepertoire.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scRepertoire/DESCRIPTION’ ... OK
* this is package ‘scRepertoire’ version ‘1.12.0’
* 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 ‘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 startup messages can be suppressed ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
combineBCR            91.620  1.120  99.906
clonesizeDistribution 17.492  0.479  18.125
clusterTCR            17.358  0.339  17.887
alluvialClonotypes    11.887  0.369  12.391
clonalDiversity       11.410  0.257  11.803
combineTCR             9.650  1.975  11.746
abundanceContig        9.363  0.259   9.716
addVariable            8.567  0.165   8.805
quantContig            8.191  0.188   8.455
compareClonotypes      8.189  0.177   8.454
getCirclize            8.128  0.221   8.431
combineExpression      7.956  0.255   8.287
occupiedscRepertoire   8.014  0.181   8.281
clonalOverlay          7.876  0.177   8.131
vizGenes               7.771  0.214   8.060
lengthContig           7.655  0.206   7.989
expression2List        7.605  0.141   7.813
clonalProportion       7.474  0.159   7.700
highlightClonotypes    7.448  0.150   7.657
clonalHomeostasis      7.354  0.208   7.632
scatterClonotype       7.338  0.172   7.607
clonalOverlap          7.299  0.157   7.537
subsetContig           6.710  0.195   6.970
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/scRepertoire.Rcheck/00check.log’
for details.