##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:MSstats.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings MSstats_4.11.1.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/MSstats.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘4.11.1’
* 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 ‘MSstats’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
* 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 ... 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘statmod’
  All declared Imports should be used.
Unexported object imported by a ':::' call: ‘MSstatsConvert:::.standardizeColnames’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.plotHeatmap : <anonymous>: no visible global function definition for
  ‘col2rgb’
.plotProfile: no visible binding for global variable ‘newABUNDANCE’
.savePlotlyPlotHTML: no visible global function definition for ‘zip’
.setCensoredByThreshold: no visible binding for global variable
  ‘any_censored’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘DetectionQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘LibPGQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘LibQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘GlobalPGQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘GlobalQValue’
MSstatsPrepareForSummarization: no visible binding for global variable
  ‘ref’
MSstatsPrepareForSummarization: no visible binding for global variable
  ‘LABEL’
MSstatsPrepareForSummarization: no visible binding for global variable
  ‘RUN’
SDRFtoAnnotation: no visible binding for global variable
  ‘..extract_cols’
extractSDRF: no visible binding for global variable ‘..extract_cols’
Undefined global functions or variables:
  ..extract_cols DetectionQValue GlobalPGQValue GlobalQValue LABEL
  LibPGQValue LibQValue RUN any_censored col2rgb newABUNDANCE ref zip
Consider adding
  importFrom("grDevices", "col2rgb")
  importFrom("utils", "zip")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) MSstatsSummarizationOutput.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MSstatsSummarizationOutput.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MSstatsSummarizationOutput.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘example_SDRF’
Undocumented data sets:
  ‘example_SDRF’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'dot-documentFunction.Rd':
  ‘removeFewMeasurements’ ‘useUniquePeptide’ ‘summaryforMultipleRows’
  ‘removeProtein_with1Feature’ ‘removeProtein_with1Peptide’
  ‘removeOxidationMpeptides’ ‘removeMpeptides’ ‘use_log_file’ ‘append’
  ‘verbose’ ‘log_file_path’

Documented arguments not in \usage in Rd file 'dot-getContrast.Rd':
  ‘contrast_matrix’

Documented arguments not in \usage in Rd file 'dot-getSingleProteinForProfile.Rd':
  ‘dataProcess’

Documented arguments not in \usage in Rd file 'dot-getWideTable.Rd':
  ‘vector’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MSstats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MSstatsGroupComparison
> ### Title: Group comparison
> ### Aliases: MSstatsGroupComparison
> 
> ### ** Examples
> 
> QuantData <- dataProcess(SRMRawData, use_log_file = FALSE)
INFO  [2024-03-28 07:39:28] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-28 07:39:28] ** Fractionation handled.
INFO  [2024-03-28 07:39:28] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-03-28 07:39:28] ** Log2 intensities under cutoff = 3.776  were considered as censored missing values.
INFO  [2024-03-28 07:39:28] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2024-03-28 07:39:28] ** Use all features that the dataset originally has.
INFO  [2024-03-28 07:39:28] 
 # proteins: 2
 # peptides per protein: 2-2
 # features per peptide: 3-3
INFO  [2024-03-28 07:39:28] 
                    1 2 3 4 5 6 7 8 9 10
             # runs 3 3 3 3 3 3 3 3 3  3
    # bioreplicates 3 3 3 3 3 3 3 3 3  3
 # tech. replicates 1 1 1 1 1 1 1 1 1  1
INFO  [2024-03-28 07:39:28]  == Start the summarization per subplot...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
INFO  [2024-03-28 07:39:28]  == Summarization is done.
> group_comparison_input = MSstatsPrepareForGroupComparison(QuantData)
> levels(QuantData$ProteinLevelData$GROUP)
 [1] "1"  "10" "2"  "3"  "4"  "5"  "6"  "7"  "8"  "9" 
> comparison <- matrix(c(-1,0,0,0,0,0,1,0,0,0),nrow=1)
> row.names(comparison) <- "T7-T1"
> groups = levels(QuantData$ProteinLevelData$GROUP)
> colnames(comparison) <- groups[order(as.numeric(groups))]
> samples_info = getSamplesInfo(QuantData)
> repeated = checkRepeatedDesign(QuantData)
> group_comparison = MSstatsGroupComparison(group_comparison_input, comparison,
+                                           FALSE, repeated, samples_info)

  |                                                                            
  |                                                                      |   0%
 *** caught segfault ***
address 0x40ff4000000000c4, cause 'memory not mapped'

Traceback:
 1: .Call(merPredDCreate, as(X, "matrix"), Lambdat, LamtUt, Lind,     RZX, Ut, Utr, V, VtV, Vtr, Xwts, Zt, beta0, delb, delu, theta,     u0)
 2: initializePtr()
 3: .Object$initialize(...)
 4: initialize(value, ...)
 5: initialize(value, ...)
 6: methods::new(def, ...)
 7: (new("refMethodDef", .Data = function (...) {    methods::new(def, ...)}, mayCall = c("methods", "new"), name = "new", refClassName = "refGeneratorSlot",     superClassMethod = ""))(Zt = new("dgCMatrix", i = c(0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L), p = 0:30, Dim = c(3L, 30L), Dimnames = list(c("ReplA", "ReplB", "ReplC"), c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "28", "29", "30")), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), theta = 1, Lambdat = new("dgCMatrix",     i = 0:2, p = 0:3, Dim = c(3L, 3L), Dimnames = list(NULL,         NULL), x = c(1, 1, 1), factors = list()), Lind = c(1L, 1L, 1L), n = 30L, X = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0))
 8: do.call(merPredD$new, c(reTrms[c("Zt", "theta", "Lambdat", "Lind")],     n = nrow(X), list(X = X)))
 9: (function (fr, X, reTrms, REML = TRUE, start = NULL, verbose = 0,     control = lmerControl(), ...) {    p <- ncol(X)    rho <- new.env(parent = parent.env(environment()))    rho$pp <- do.call(merPredD$new, c(reTrms[c("Zt", "theta",         "Lambdat", "Lind")], n = nrow(X), list(X = X)))    REMLpass <- if (REML)         p    else 0L    rho$resp <- if (missing(fr))         mkRespMod(REML = REMLpass, ...)    else mkRespMod(fr, REML = REMLpass)    pp <- resp <- NULL    rho$lmer_Deviance <- lmer_Deviance    devfun <- function(theta) .Call(lmer_Deviance, pp$ptr(),         resp$ptr(), as.double(theta))    environment(devfun) <- rho    if (is.null(start) && all(reTrms$cnms == "(Intercept)") &&         length(reTrms$flist) == length(reTrms$lower) && !is.null(y <- model.response(fr))) {        v <- sapply(reTrms$flist, function(f) var(ave(y, f)))        v.e <- var(y) - sum(v)        if (!is.na(v.e) && v.e > 0) {            v.rel <- v/v.e            if (all(v.rel >= reTrms$lower^2))                 rho$pp$setTheta(sqrt(v.rel))        }    }    if (length(rho$resp$y) > 0)         devfun(rho$pp$theta)    rho$lower <- reTrms$lower    devfun})(fr = list(ABUNDANCE = c(5.57704971964271, 6.81103421204961, 6.90909322304964, 6.3730693027354, 6.59574978924472, 6.34984275165681, 6.14037754568116, 6.60098109654682, 7.03394442072272, 6.79011582333719, 6.17493165813388, 7.31311548670605, 7.26021720237185, 7.20914079871192, 6.51945659596073, 9.65321855502201, 9.54278244667357, 9.55352713226583, 12.5563765883198, 12.6531040396988, 12.5508472937627, 12.7220414022688, 12.7828137645926, 12.8067582978909, 12.6638553883903, 12.7287281891049, 12.6668086382484, 12.7202902516363, 12.7764458468632, 12.7162868528541), GROUP = c(1L, 1L, 1L, 3L, 3L, 3L, 4L, 4L, 4L, 5L, 5L, 5L, 6L, 6L, 6L, 7L, 7L, 7L, 8L, 8L, 8L, 9L, 9L, 9L, 10L, 10L, 10L, 2L, 2L, 2L), SUBJECT = c(1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L)), X = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0), reTrms = list(    Zt = new("dgCMatrix", i = c(0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L,     2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L,     2L, 0L, 1L, 2L, 0L, 1L, 2L), p = 0:30, Dim = c(3L, 30L),         Dimnames = list(c("ReplA", "ReplB", "ReplC"), c("1",         "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12",         "13", "14", "15", "16", "17", "18", "19", "20", "21",         "22", "23", "24", "25", "26", "27", "28", "29", "30")),         x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,         1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()),     theta = 1, Lind = c(1L, 1L, 1L), Gp = c(0L, 3L), lower = 0,     Lambdat = new("dgCMatrix", i = 0:2, p = 0:3, Dim = c(3L,     3L), Dimnames = list(NULL, NULL), x = c(1, 1, 1), factors = list()),     flist = list(SUBJECT = c(1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L,     3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L,     3L, 1L, 2L, 3L, 1L, 2L, 3L)), cnms = list(SUBJECT = "(Intercept)"),     Ztlist = list(`1 | SUBJECT` = new("dgCMatrix", i = c(0L,     1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L,     1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L),         p = 0:30, Dim = c(3L, 30L), Dimnames = list(c("ReplA",         "ReplB", "ReplC"), c("1", "2", "3", "4", "5", "6", "7",         "8", "9", "10", "11", "12", "13", "14", "15", "16", "17",         "18", "19", "20", "21", "22", "23", "24", "25", "26",         "27", "28", "29", "30")), x = c(1, 1, 1, 1, 1, 1, 1,         1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,         1, 1, 1, 1, 1), factors = list())), nl = c(SUBJECT = 3L)),     REML = TRUE, wmsgs = character(0), start = NULL, verbose = 0L,     control = list(optimizer = "nloptwrap", restart_edge = TRUE,         boundary.tol = 1e-05, calc.derivs = TRUE, use.last.params = FALSE,         checkControl = list(check.nobs.vs.rankZ = "ignore", check.nobs.vs.nlev = "stop",             check.nlev.gtreq.5 = "ignore", check.nlev.gtr.1 = "stop",             check.nobs.vs.nRE = "stop", check.rankX = "message+drop.cols",             check.scaleX = "warning", check.formula.LHS = "stop"),         checkConv = list(check.conv.grad = list(action = "warning",             tol = 0.002, relTol = NULL), check.conv.singular = list(            action = "message", tol = 1e-04), check.conv.hess = list(            action = "warning", tol = 1e-06)), optCtrl = list()))
10: do.call(mkLmerDevfun, c(lmod, list(start = start, verbose = verbose,     control = control)))
11: lme4::lmer(ABUNDANCE ~ GROUP + (1 | SUBJECT), data = input)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
16: try(lme4::lmer(ABUNDANCE ~ GROUP + (1 | SUBJECT), data = input),     TRUE)
17: withCallingHandlers(expr, message = function(c) if (inherits(c,     classes)) tryInvokeRestart("muffleMessage"))
18: suppressMessages(try(lme4::lmer(ABUNDANCE ~ GROUP + (1 | SUBJECT),     data = input), TRUE))
19: .fitModelForGroupComparison(input, repeated, is_single_subject,     has_tech_replicates)
20: .fitModelSingleProtein(single_protein, contrast_matrix, has_tech_reps,     is_single_subject, repeated, groups, samples_info, save_fitted_models,     has_imputed)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
25: try(.fitModelSingleProtein(single_protein, contrast_matrix, has_tech_reps,     is_single_subject, repeated, groups, samples_info, save_fitted_models,     has_imputed), silent = TRUE)
26: MSstatsGroupComparisonSingleProtein(summarized_list[[i]], contrast_matrix,     repeated, groups, samples_info, save_fitted_models, has_imputed)
27: MSstatsGroupComparison(group_comparison_input, comparison, FALSE,     repeated, samples_info)
An irrecoverable exception occurred. R is aborting now ...
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.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 ERROR, 1 WARNING, 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/MSstats.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL MSstats
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘MSstats’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall  -c common.cpp -o common.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall  -c comparison_contrasts.cpp -o comparison_contrasts.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall  -c linear_summary.cpp -o linear_summary.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall  -c median_polish.cpp -o median_polish.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o MSstats.so RcppExports.o common.o comparison_contrasts.o linear_summary.o median_polish.o -fopenmp -lopenblas -lgfortran -lm -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/00LOCK-MSstats/00new/MSstats/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MSstats)

R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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Type 'license()' or 'licence()' for distribution details.

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> if ( requireNamespace("tinytest", quietly=TRUE) ){
+   tinytest::test_package("MSstats")
+ }

Attaching package: 'MSstats'

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

    savePlot


test_MSstatsdev.R.............    1 tests OK 55ms
2ms
All ok, 1 results (60ms)
> 
> proc.time()
   user  system elapsed 
  3.954   0.199   4.152