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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MAST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MAST_1.33.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MAST.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MAST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MAST’ version ‘1.33.0’
* 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 ... 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 installed package size ... 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 code 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 ... WARNING
Missing or unexported object: ‘gdata::xls2csv’
* 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 ... NOTE
checkRd: (-1) GSEATests-class.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{\code{tests}}{array: gene sets X {discrete,continuous} X {stat, variance, degrees of freedom, avg correlation} X {test, null}}
       |                                        ^
checkRd: (-1) GSEATests-class.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{\code{tests}}{array: gene sets X {discrete,continuous} X {stat, variance, degrees of freedom, avg correlation} X {test, null}}
       |                                                                ^
checkRd: (-1) GSEATests-class.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{\code{tests}}{array: gene sets X {discrete,continuous} X {stat, variance, degrees of freedom, avg correlation} X {test, null}}
       |                                                                                                                        ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MAST-defunct.Rd: colData, mcols, assay
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
* 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:
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • empty test (5): 'test-GSEA-by-boot.R:99:1', 'test-SingleCellAssay.R:298:1',
    'test-lmWrapper-glmer.R:8:1', 'test-sparsematrix.R:18:1',
    'test-sparsematrix.R:26:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-lrtest.R:25:5'): LRT and zlm are equivalent ──────────────────
  all(lrout$lrstat[smallDOF] >= lrout2[smallDOF, 3, 1]) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 49 | SKIP 5 | PASS 292 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/MAST.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MAST
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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 49 | SKIP 5 | PASS 292 ]

══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• empty test (5): 'test-GSEA-by-boot.R:99:1', 'test-SingleCellAssay.R:298:1',
  'test-lmWrapper-glmer.R:8:1', 'test-sparsematrix.R:18:1',
  'test-sparsematrix.R:26:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-lrtest.R:25:5'): LRT and zlm are equivalent ──────────────────
all(lrout$lrstat[smallDOF] >= lrout2[smallDOF, 3, 1]) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

[ FAIL 1 | WARN 49 | SKIP 5 | PASS 292 ]
Error: Test failures
Execution halted