##############################################################################
##############################################################################
###
### Running command:
###
###   /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
###
##############################################################################
##############################################################################


* 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 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 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            137.805  0.390 126.185
clonesizeDistribution  24.090  0.016  24.147
clusterTCR             23.643  0.028  23.674
clonalDiversity        15.686  0.052  15.762
alluvialClonotypes     13.199  0.080  13.316
vizGenes               10.356  2.034  30.659
combineExpression      12.127  0.004  13.248
occupiedscRepertoire   11.538  0.004  12.090
combineTCR             10.640  0.706  13.426
abundanceContig        11.227  0.048  11.290
clonalOverlay          10.809  0.048  11.041
clonalOverlap          10.748  0.004  10.802
compareClonotypes      10.668  0.004  11.544
subsetContig           10.630  0.008  12.069
lengthContig           10.623  0.004  11.059
quantContig            10.133  0.491  15.613
getCirclize            10.603  0.012  11.136
addVariable            10.540  0.068  10.743
clonalHomeostasis      10.328  0.008  10.449
highlightClonotypes     9.909  0.395  13.690
expression2List        10.277  0.015  11.992
scatterClonotype       10.259  0.000  11.178
clonalProportion        9.949  0.000  10.006
* 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.
Killed

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

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/scRepertoire.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL scRepertoire
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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)