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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MAST.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MAST_1.25.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MAST.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 ‘MAST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MAST’ version ‘1.25.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MAST’ 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 ... 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 loading without being on the library search path ... WARNING
Error in library(MAST, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") : 
  there is no package called ‘MAST’
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 ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [ FAIL 1 | WARN 26 | SKIP 5 | PASS 292 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • empty test (5)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-lrtest.R:25'): LRT and zlm are equivalent ────────────────────
  all(lrout$lrstat[smallDOF] >= lrout2[smallDOF, 3, 1]) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 26 | SKIP 5 | PASS 292 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘MAITAnalysis.Rmd’ using ‘UTF-8’... OK
  ‘MAST-Intro.Rmd’ using ‘UTF-8’... OK
  ‘MAST-interoperability.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘MAITAnalysis.Rmd’ using rmarkdown
Warning: code chunks must not depend on the uncached chunk "data"
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAITAnalysis_files/figure-html/heatmap-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAITAnalysis_files/figure-html/pca-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAITAnalysis_files/figure-html/unnamed-chunk-1-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAITAnalysis_files/figure-html/pcaFilter-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAITAnalysis_files/figure-html/distribution-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAITAnalysis_files/figure-html/threshold-1.png" but not available.
Warning: code chunks must not depend on the uncached chunk "zlm"
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAITAnalysis_files/figure-html/unnamed-chunk-4-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAITAnalysis_files/figure-html/unnamed-chunk-5-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAITAnalysis_files/figure-html/unnamed-chunk-6-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAITAnalysis_files/figure-html/unnamed-chunk-7-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAITAnalysis_files/figure-html/addResiduals-1.png" but not available.
Warning: code chunks must not depend on the uncached chunk "boots"
Killed
--- re-building ‘MAST-Intro.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAST-Intro_files/figure-html/splitbyncells-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAST-Intro_files/figure-html/burdenOfFiltering-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAST-Intro_files/figure-html/zlmExample-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAST-Intro_files/figure-html/tests-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAST-Intro_files/figure-html/advancedArmExample-1.png" but not available.
--- finished re-building ‘MAST-Intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MAST
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘MAST’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** 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 (MAST)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> test_check("MAST")
Loading required package: MAST
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Error : number of levels of each grouping factor must be < number of observations (problems: Subject.ID)
(0.0426,0.354]  (0.354,0.757]   (0.757,1.28]    (1.28,1.96]    (1.96,2.84] 
      2.258200       2.258200       2.258200       2.258200       2.258200 
   (2.84,3.99]    (3.99,13.2] 
      2.258200       3.313588 
(0.0602,0.436]   (0.436,0.67]   (0.67,0.944]   (0.944,1.26]    (1.26,1.63] 
      1.967142       1.967142       1.967142       2.003488       2.003488 
   (1.63,2.06]    (2.06,2.56]    (2.56,3.83] 
      2.600202       2.600202       2.600202 
    (0.03,1.56]     (1.56,5.36]     (5.36,14.8] (14.8,9.25e+03] 
       238.2279        238.2279        238.2279       4525.1912 
Error : grouping factors must have > 1 sampled level
NULL
NULL
NULL
Error in (function (x, y, weights = rep.int(1, nobs), start = NULL, etastart = NULL,  : 
  NAs in V(mu)
[ FAIL 1 | WARN 26 | SKIP 5 | PASS 292 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (5)

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-lrtest.R:25'): LRT and zlm are equivalent ────────────────────
all(lrout$lrstat[smallDOF] >= lrout2[smallDOF, 3, 1]) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

[ FAIL 1 | WARN 26 | SKIP 5 | PASS 292 ]
Error: Test failures
Execution halted