##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:msqrob2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings msqrob2_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/msqrob2.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 ‘msqrob2/DESCRIPTION’ ... OK
* this is package ‘msqrob2’ version ‘1.7.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘msqrob2’ 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 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 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
msqrobLmer      24.424  4.697  13.548
msqrobAggregate 17.788  3.160   9.970
msqrob          17.737  3.094  12.478
msqrobQB         7.836  0.767   3.714
hypothesisTest   5.056  0.092   5.285
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘cptac.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘cptac.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/msqrob2.Rcheck/vign_test/msqrob2/vignettes/cptac_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/msqrob2.Rcheck/vign_test/msqrob2/vignettes/cptac_files/figure-html/unnamed-chunk-5-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/msqrob2.Rcheck/vign_test/msqrob2/vignettes/cptac_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/msqrob2.Rcheck/vign_test/msqrob2/vignettes/cptac_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/msqrob2.Rcheck/vign_test/msqrob2/vignettes/cptac_files/figure-html/unnamed-chunk-12-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/msqrob2.Rcheck/vign_test/msqrob2/vignettes/cptac_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/msqrob2.Rcheck/vign_test/msqrob2/vignettes/cptac_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/msqrob2.Rcheck/vign_test/msqrob2/vignettes/cptac_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/msqrob2.Rcheck/vign_test/msqrob2/vignettes/cptac_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/msqrob2.Rcheck/vign_test/msqrob2/vignettes/cptac_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/msqrob2.Rcheck/vign_test/msqrob2/vignettes/cptac_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/msqrob2.Rcheck/vign_test/msqrob2/vignettes/cptac_files/figure-html/unnamed-chunk-21-3.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/msqrob2.Rcheck/vign_test/msqrob2/vignettes/cptac_files/figure-html/unnamed-chunk-21-4.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/msqrob2.Rcheck/vign_test/msqrob2/vignettes/cptac_files/figure-html/unnamed-chunk-21-5.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/msqrob2.Rcheck/vign_test/msqrob2/vignettes/cptac_files/figure-html/unnamed-chunk-21-6.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/msqrob2.Rcheck/vign_test/msqrob2/vignettes/cptac_files/figure-html/unnamed-chunk-21-7.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/msqrob2.Rcheck/vign_test/msqrob2/vignettes/cptac_files/figure-html/unnamed-chunk-21-8.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/msqrob2.Rcheck/vign_test/msqrob2/vignettes/cptac_files/figure-html/unnamed-chunk-21-9.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/msqrob2.Rcheck/vign_test/msqrob2/vignettes/cptac_files/figure-html/unnamed-chunk-21-10.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/msqrob2.Rcheck/vign_test/msqrob2/vignettes/cptac_files/figure-html/unnamed-chunk-23-1.png" but not available.
Quitting from lines 407-419 (cptac.Rmd) 
Error: processing vignette 'cptac.Rmd' failed with diagnostics:
wrong args for environment subassignment
--- failed re-building ‘cptac.Rmd’

SUMMARY: processing the following file failed:
  ‘cptac.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/msqrob2.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL msqrob2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘msqrob2’ ...
** using staged installation
** R
** data
** 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 (msqrob2)

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.

> # setting R_TESTS to empty string because of
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> 
> library("testthat")
> library("msqrob2")
Loading required package: QFeatures
Loading required package: MultiAssayExperiment
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


Attaching package: 'QFeatures'

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

    longFormat

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

    sweep

> 
> test_check("msqrob2")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
 10.643   0.381  11.344