Build/check report for BioC 3.17 - CHECK results for scRepertoire on kunpeng1

Hostname	OS	Arch (*)	R version	Installed pkgs
kunpeng1	Linux (Ubuntu 22.04.1 LTS)	aarch64	R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"	4021
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*
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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:scRepertoire.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings scRepertoire_1.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.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 ‘scRepertoire/DESCRIPTION’ ... OK
* this is package ‘scRepertoire’ version ‘1.9.0’
* 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 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 ... WARNING
Error in library(scRepertoire, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") : 
  there is no package called ‘scRepertoire’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* 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 ... SKIPPED
* 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’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘vignette.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-11-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-13-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-14-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-14-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-15-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-16-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-16-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-17-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-18-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-19-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-19-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-20-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-20-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-21-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-21-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-22-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-23-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-24-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-25-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-26-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-26-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-30-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-31-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-32-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-33-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-33-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-34-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-35-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-35-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-36-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-36-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-37-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-38-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-40-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-41-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-43-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/vign_test/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-43-2.png" but not available.
Killed

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

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/00check.log’
for details.
CHECK results for scRepertoire on kunpeng1

Summary

Command output

Installation output

Tests output

Example timings
