##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:hdxmsqc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings hdxmsqc_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/hdxmsqc.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hdxmsqc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘hdxmsqc’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘hdxmsqc’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
chargeCorrelationHdx: no visible global function definition for ‘assay’
chargeCorrelationHdx: no visible binding for global variable ‘x’
chargeCorrelationHdx: no visible binding for global variable ‘z’
chargeCorrelationHdx: no visible binding for global variable ‘peptide’
chargeCorrelationHdx: no visible binding for global variable ‘y’
compatibleUptake: no visible global function definition for ‘rowData’
compatibleUptake: no visible global function definition for ‘assay’
computeMassError: no visible global function definition for ‘rowData’
computeMassError: no visible global function definition for ‘assay’
computeMonotoneStats: no visible global function definition for ‘assay’
computeMonotoneStats: no visible binding for global variable ‘x’
computeMonotoneStats: no visible binding for global variable ‘y’
imTimeOutlier: no visible global function definition for ‘rowData’
imTimeOutlier: no visible global function definition for ‘rowMedians’
imTimeOutlier: no visible binding for global variable ‘Experiment’
imTimeOutlier: no visible binding for global variable ‘IMS_shift’
intensityOutliers: no visible global function definition for ‘rowData’
isMissingAtRandom: no visible global function definition for ‘assay’
isMissingAtRandom: no visible global function definition for ‘rowData’
plotImTimeOutlier: no visible binding for global variable ‘Experiment’
plotImTimeOutlier: no visible binding for global variable ‘IMS_shift’
plotImTimeOutlier: no visible global function definition for
  ‘brewer.pal’
plotIntensityOutliers: no visible binding for global variable ‘x’
plotIntensityOutliers: no visible binding for global variable ‘y’
plotIntensityOutliers: no visible binding for global variable ‘outlier’
plotIntensityOutliers: no visible global function definition for
  ‘brewer.pal’
plotMassError: no visible binding for global variable ‘x’
plotMassError: no visible binding for global variable ‘y’
plotMassError: no visible global function definition for ‘brewer.pal’
plotMissing: no visible global function definition for ‘assay’
plotMissing: no visible global function definition for ‘pheatmap’
plotMissing: no visible global function definition for ‘brewer.pal’
plotMonotoneStat : <anonymous>: no visible binding for global variable
  ‘x’
plotMonotoneStat : <anonymous>: no visible binding for global variable
  ‘y’
plotMonotoneStat : <anonymous>: no visible binding for global variable
  ‘outlier’
plotMonotoneStat : <anonymous>: no visible global function definition
  for ‘brewer.pal’
plotrTimeOutliers: no visible binding for global variable ‘Experiment’
plotrTimeOutliers: no visible binding for global variable ‘RT_shift’
plotrTimeOutliers: no visible global function definition for
  ‘brewer.pal’
processHDE: no visible binding for global variable ‘Deut.Time’
processHDE: no visible binding for global variable ‘Sequence’
processHDE: no visible binding for global variable ‘Protein.State’
processHDE: no visible binding for global variable ‘Charge’
qualityControl: no visible global function definition for ‘rowData’
rTimeOutliers: no visible global function definition for ‘rowData’
rTimeOutliers: no visible global function definition for ‘rowMedians’
rTimeOutliers: no visible binding for global variable ‘Experiment’
rTimeOutliers: no visible binding for global variable ‘RT_shift’
replicateCorrelation: no visible global function definition for ‘assay’
replicateCorrelation: no visible binding for global variable ‘x’
replicateCorrelation: no visible binding for global variable ‘y’
replicateOutlier: no visible global function definition for ‘assay’
replicateOutlier: no visible binding for global variable ‘x’
replicateOutlier: no visible binding for global variable ‘y’
spectraSimilarity: no visible global function definition for ‘bpparam’
spectraSimilarity: no visible binding for global variable ‘timepoints’
spectraSimilarity: no visible binding for global variable ‘Sequence’
spectraSimilarity: no visible global function definition for ‘bplapply’
spectraSimilarity: no visible global function definition for
  ‘spectraData’
spectraSimilarity: no visible binding for global variable ‘Charge’
spectraSimilarity: no visible binding for global variable ‘DeutTime’
Undefined global functions or variables:
  Charge Deut.Time DeutTime Experiment IMS_shift Protein.State RT_shift
  Sequence assay bplapply bpparam brewer.pal outlier peptide pheatmap
  rowData rowMedians spectraData timepoints x y z
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/hdxmsqc.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL hdxmsqc
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘hdxmsqc’ ...
** 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 (hdxmsqc)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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.

> # The setting of R_TESTS exists to work around an R bug. See
> # https://github.com/hadley/testthat/issues/144
> # We should remove it when the issue is resolved.
> Sys.setenv("R_TESTS" = "")
> 
> library("testthat")
> library("hdxmsqc")
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, saveRDS, setdiff, table,
    tapply, union, 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


Attaching package: 'QFeatures'

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

    longFormat

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

    sweep

Loading required package: Spectra
Loading required package: BiocParallel
> 
> test_check("hdxmsqc")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 13 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
  3.377   0.130   3.504