Back to Long Tests report for BioC 3.23

This page was generated on 2026-04-25 23:55 -0400 (Sat, 25 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 RC (2026-04-17 r89917) -- "Because it was There" 4978
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 27/28HostnameOS / ArchCHECK
xcms 4.9.4  (landing page)
Steffen Neumann
Snapshot Date: 2026-04-25 09:55 -0400 (Sat, 25 Apr 2026)
git_url: https://git.bioconductor.org/packages/xcms
git_branch: devel
git_last_commit: 161fe37
git_last_commit_date: 2026-04-22 05:49:24 -0400 (Wed, 22 Apr 2026)
nebbiolo1Linux (Ubuntu 24.04.4 LTS) / x86_64  OK  

CHECK results for xcms on nebbiolo1

To the developers/maintainers of the xcms package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: xcms
Version: 4.9.4
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no xcms_4.9.4.tar.gz
StartedAt: 2026-04-25 16:25:36 -0400 (Sat, 25 Apr 2026)
EndedAt: 2026-04-25 16:40:22 -0400 (Sat, 25 Apr 2026)
EllapsedTime: 885.9 seconds
RetCode: 0
Status:   OK  
CheckDir: xcms.Rcheck
Warnings: 0

Tests output

xcms.Rcheck/tests/testthat.Rout


R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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)
> library(xcms)
Loading required package: BiocParallel

This is xcms version 4.9.4 

> library(MSnbase)
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: Biobase
Welcome to Bioconductor

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

Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

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: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.37.3 
  Visit https://lgatto.github.io/MSnbase/ to get started.
 Consider switching to the 'R for Mass Spectrometry'
 packages - see https://RforMassSpectrometry.org for details.


Attaching package: 'MSnbase'

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

    trimws

> library(faahKO)
> library(MsDataHub)
> 
> attr(faahko, "filepaths") <- sapply(
+     as.list(basename(attr(faahko, "filepaths"))),
+     function(x) system.file("cdf", if (length(grep("ko",x)) > 0) "KO" else "WT",
+                             x, package = "faahKO"))
> register(SerialParam())
> 
> ## Define test files:
> faahko_3_files <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
+                     system.file('cdf/KO/ko16.CDF', package = "faahKO"),
+                     system.file('cdf/KO/ko18.CDF', package = "faahKO"))
> fticrf <- c(MsDataHub::HAM004_641fE_14.11.07..Exp1.extracted.mzML(),
+             MsDataHub::HAM004_641fE_14.11.07..Exp2.extracted.mzML())
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
> 
> ## An xcmsRaw for the first file:
> faahko_xr_1 <- xcmsRaw(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
+                        profstep = 0)
> faahko_od <- readMSData(faahko_3_files, mode = "onDisk")
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
> faahko_xod <- findChromPeaks(
+     faahko_od, param = CentWaveParam(noise = 10000, snthresh = 40,
+                                      prefilter = c(3, 10000)))
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 87 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 100 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 61 found.
> faahko_xs <- xcmsSet(faahko_3_files, profparam = list(step = 0),
+                      method = "centWave", noise = 10000, snthresh = 40,
+                      prefilter = c(3, 10000))
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 87 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 100 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 61 found.
> faahko_xsg <- group(faahko_xs)
> ## Doing also the retention time correction etc
> od_x <- faahko_od
> mzr <- matrix(c(335, 335, 344, 344), ncol = 2, byrow = TRUE)
> od_chrs <- chromatogram(od_x, mz = mzr)
> xod_x <- faahko_xod
> pdp <- PeakDensityParam(sampleGroups = rep(1, 3))
> xod_xg <- groupChromPeaks(xod_x, param = pdp)
> xod_xgr <- adjustRtime(xod_xg, param = PeakGroupsParam(span = 0.4))
Performing retention time alignment using 19 anchor peaks.
Applying retention time adjustment to the identified chromatographic peaks ... OK
> xod_xgrg <- groupChromPeaks(xod_xgr, param = pdp)
> xod_r <- adjustRtime(as(od_x, "XCMSnExp"), param = ObiwarpParam())
Sample number 2 used as center sample.
Aligning ko15.CDF against ko16.CDF ... OK
Aligning ko18.CDF against ko16.CDF ... OK
> 
> xod_chr <- findChromPeaks(filterMz(filterRt(od_x, rt = c(2500, 3500)),
+                                    mz = c(334.9, 344.1)),
+                           param = CentWaveParam())
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 514 regions of interest ... OK: 23 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 551 regions of interest ... OK: 29 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 515 regions of interest ... OK: 20 found.
Warning message:
In .local(object, param, ...) :
  Your data appears to be not centroided! CentWave works best on data in centroid mode.
> 
> faahko_grouped_filled <- fillPeaks(group(faahko))
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko19.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko21.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko22.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt19.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt21.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt22.CDF 
method:  bin 
step:  0.1 
Warning message:
In .getPeaks_new(object, peakrange, step = step) :
  getPeaks: Peak  m/z:246.05-246.1,  RT:2501.378-2531.8945is out of retention time range for this sample (/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko18.CDF), using zero intensity value.

> faahko_grouped_retcor_filled <-
+     fillPeaks(group(retcor(group(updateObject(faahko)))))
Performing retention time alignment using 132 anchor peaks.
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko19.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko21.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko22.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt19.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt21.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt22.CDF 
method:  bin 
step:  0.1 
There were 35 warnings (use warnings() to see them)
> 
> ## Direct injection data:
> fticr <- readMSData(fticrf[1:2], msLevel. = 1, mode = "onDisk")
Warning message:
In .testReadMSDataInput(environment()) : Reading different file formats in.
This is untested and you are welcome to try it out.
Please report back!
> fticr_xod <- findChromPeaks(fticr, MSWParam(scales = c(1, 7),
+                                             peakThr = 80000, ampTh = 0.005,
+                                             SNR.method = "data.mean",
+                                             winSize.noise = 500))
> fticr_xs <- xcmsSet(method="MSW", files=fticrf[1:2], scales=c(1,7),
+                     SNR.method='data.mean' , winSize.noise=500,
+                     peakThr=80000,  amp.Th=0.005)
> 
> fs <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
+         system.file('cdf/KO/ko16.CDF', package = "faahKO"),
+         system.file('cdf/KO/ko18.CDF', package = "faahKO"),
+         system.file('cdf/KO/ko19.CDF', package = "faahKO"))
> xs_1 <- xcmsSet(fs, profparam = list(step = 0), method = "centWave",
+                 noise = 10000, snthresh = 50, prefilter = c(3, 10000))
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 75 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 79 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 41 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 781 regions of interest ... OK: 46 found.
> 
> test_check("xcms")
8.00  16.00  24.00  28.00  32.00  40.00  48.00  52.00  56.00  60.00  64.00  72.00  80.00  84.00  88.00  96.00  100.00  
8.00  16.00  28.00  32.00  40.00  64.00  80.00  96.00  100.00  
8.00  16.00  24.00  28.00  32.00  40.00  48.00  52.00  56.00  60.00  64.00  72.00  80.00  84.00  88.00  96.00  100.00  
center sample:  ko16 
Processing: ko15  ko18  
center sample:  ko18 
Processing: ko15  ko16  
center sample:  ko18 
Processing: ko15  ko16  
8.00  16.00  24.00  28.00  32.00  40.00  48.00  52.00  56.00  60.00  64.00  72.00  80.00  84.00  88.00  96.00  100.00  
8.00  16.00  24.00  28.00  32.00  40.00  48.00  52.00  56.00  60.00  64.00  72.00  80.00  84.00  88.00  96.00  100.00  
8.00  16.00  28.00  32.00  40.00  56.00  64.00  80.00  88.00  96.00  100.00  
8.00  16.00  28.00  32.00  40.00  56.00  64.00  80.00  88.00  96.00  100.00  
8.00  16.00  24.00  28.00  32.00  40.00  48.00  52.00  56.00  60.00  64.00  72.00  80.00  84.00  88.00  96.00  100.00  
8.00  16.00  24.00  28.00  32.00  40.00  48.00  52.00  56.00  60.00  64.00  72.00  80.00  84.00  88.00  96.00  100.00  
7fa3e396a90bd_10386 3b82e83a5ebdc8_10387 
method:  bin 
step:  0.1 
method:  bin 
step:  0.3 
method:  binlin 
step:  0.2 
method:  binlinbase 
step:  0.2 
method:  intlin 
step:  0.2 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko19.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko21.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko22.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt19.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt21.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt22.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko19.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko21.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko22.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt19.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt21.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt22.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko19.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko21.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko22.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt19.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt21.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/WT/wt22.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.23-bioc/R/site-library/faahKO/cdf/KO/ko18.CDF 
method:  bin 
step:  0.1 
center sample:  ko15 
Processing: ko16  
center sample:  ko16 
Processing: ko15  
center sample:  ko16 
Processing: ko15  
center sample:  ko16 
Processing: ko15  
center sample:  ko16 
Processing: ko15  
center sample:  ko16 
Processing: ko15  
center sample:  ko16 
Processing: ko15  
center sample:  ko16 
Processing: ko15  
Comparing peaks...OK
Comparing peaks...OK
Comparing peaks...OK
Comparing peak groups...OK
Comparing peaks...OK
Comparing peak groups...OK
Comparing peaks...OK
Comparing peak groups...OK
[ FAIL 0 | WARN 19 | SKIP 5 | PASS 608 ]

══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• empty test (5): 'test_old_functions-xcmsRaw.R:15:1',
  'test_old_methods-xcmsRaw.R:234:1', 'test_old_methods-xcmsSet.R:90:1',
  'test_old_methods-xcmsSet.R:170:1', 'test_old_methods-xcmsSet.R:184:1'

[ FAIL 0 | WARN 19 | SKIP 5 | PASS 608 ]
> 
> proc.time()
   user  system elapsed 
471.818   8.894 482.889

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no xcms_4.9.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc-longtests/meat/xcms.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-25 20:25:36 UTC
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘xcms/DESCRIPTION’ ... OK
* this is package ‘xcms’ version ‘4.9.4’
* 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:
  .BBSoptions
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 ‘xcms’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... INFO
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    help   1.0Mb
    libs   1.4Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL (>= 2) + file LICENSE
* 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
Unexported objects imported by ':::' calls:
  ‘MALDIquant:::.localMaxima’ ‘MSnbase:::.MSnExpReqFvarLabels’
  ‘MSnbase:::.plotXIC’ ‘MSnbase:::.vertical_sub_layout’
  ‘MSnbase:::formatFileSpectrumNames’ ‘Spectra:::.concatenate_spectra’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.copy_env’ ‘MSW.cwt’ ‘MSW.getLocalMaximumCWT’ ‘MSW.getRidge’
  ‘descendMin’ ‘descendMinTol’ ‘estimateChromNoise’
  ‘getLocalNoiseEstimate’ ‘na.flatfill’ ‘patternVsRowScore’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.xcmsFragments.plotTree: no visible global function definition for
  ‘edgemode<-’
.xcmsFragments.plotTree: no visible global function definition for
  ‘addEdge’
buildAnalysisSummary: no visible global function definition for
  ‘newXMLNode’
buildAssayList : <anonymous>: no visible global function definition for
  ‘newXMLNode’
buildAssayList: no visible global function definition for ‘newXMLNode’
buildAuditCollection: no visible global function definition for
  ‘newXMLNode’
buildCVlist: no visible global function definition for ‘newXMLNode’
buildCVlist: no visible global function definition for ‘addChildren’
buildCvParams : <anonymous>: no visible global function definition for
  ‘newXMLNode’
buildDataProcessingList: no visible global function definition for
  ‘newXMLNode’
buildFeatureList : <anonymous>: no visible global function definition
  for ‘newXMLNode’
buildInputFiles : <anonymous>: no visible global function definition
  for ‘newXMLNode’
buildInputFiles: no visible global function definition for ‘newXMLNode’
buildMzq: no visible global function definition for ‘xmlTree’
buildSmallMoleculeList : <anonymous>: no visible global function
  definition for ‘newXMLNode’
buildSmallMoleculeList: no visible global function definition for
  ‘newXMLNode’
buildSoftwareList: no visible global function definition for
  ‘newXMLNode’
buildStudyVariableList : <anonymous>: no visible global function
  definition for ‘newXMLNode’
buildStudyVariableList : <anonymous> : <anonymous>: no visible global
  function definition for ‘newXMLNode’
buildStudyVariableList: no visible global function definition for
  ‘newXMLNode’
running: multiple local function definitions for ‘funct’ with different
  formal arguments
verify.mzQuantML: no visible global function definition for
  ‘xmlTreeParse’
verify.mzQuantML: no visible global function definition for
  ‘xmlInternalTreeParse’
verify.mzQuantML: no visible global function definition for
  ‘xmlSchemaValidate’
xcmsClusterApply: no visible global function definition for
  ‘checkCluster’
xcmsClusterApply : submit: no visible global function definition for
  ‘sendCall’
xcmsClusterApply: no visible global function definition for
  ‘recvOneResult’
xcmsClusterApply: no visible global function definition for
  ‘checkForRemoteErrors’
xcmsPapply: no visible global function definition for ‘mpi.comm.size’
xcmsPapply: no visible global function definition for
  ‘mpi.spawn.Rslaves’
xcmsPapply: no visible global function definition for ‘mpi.comm.rank’
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for ‘mpi.send.Robj’
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for ‘mpi.recv.Robj’
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for ‘mpi.any.source’
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for ‘mpi.any.tag’
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for ‘mpi.get.sourcetag’
xcmsPapply: no visible global function definition for
  ‘mpi.bcast.Robj2slave’
xcmsPapply: no visible global function definition for ‘mpi.bcast.cmd’
xcmsPapply: no visible global function definition for ‘mpi.recv.Robj’
xcmsPapply: no visible global function definition for ‘mpi.any.source’
xcmsPapply: no visible global function definition for ‘mpi.any.tag’
xcmsPapply: no visible global function definition for
  ‘mpi.get.sourcetag’
xcmsPapply: no visible global function definition for ‘mpi.send.Robj’
xcmsParallelSetup: no visible global function definition for
  ‘mpi.spawn.Rslaves’
xcmsParallelSetup: no visible global function definition for
  ‘mpi.comm.size’
xcmsParallelSetup: no visible global function definition for
  ‘mpi.comm.rank’
xcmsParallelSetup: no visible global function definition for
  ‘makeCluster’
xcmsSet: no visible global function definition for ‘bpstopOnError’
xcmsSet: no visible global function definition for ‘bptry’
xcmsSet: no visible global function definition for ‘bpok’
plotSurf,xcmsRaw: no visible global function definition for ‘clear3d’
plotSurf,xcmsRaw: no visible global function definition for ‘surface3d’
plotSurf,xcmsRaw: no visible global function definition for ‘points3d’
plotSurf,xcmsRaw: no visible global function definition for ‘bbox3d’
plotTree,xcmsFragments: no visible global function definition for
  ‘edgemode<-’
plotTree,xcmsFragments: no visible global function definition for
  ‘addEdge’
write.cdf,xcmsRaw: no visible global function definition for
  ‘ncdim_def’
write.cdf,xcmsRaw: no visible global function definition for
  ‘ncvar_def’
write.cdf,xcmsRaw: no visible global function definition for
  ‘nc_create’
write.cdf,xcmsRaw: no visible global function definition for
  ‘ncvar_put’
write.cdf,xcmsRaw: no visible global function definition for
  ‘ncatt_put’
write.cdf,xcmsRaw: no visible global function definition for ‘nc_close’
write.mzQuantML,xcmsSet: no visible global function definition for
  ‘saveXML’
write.mzdata,xcmsRaw: no visible global function definition for
  ‘base64encode’
Undefined global functions or variables:
  addChildren addEdge base64encode bbox3d bpok bpstopOnError bptry
  checkCluster checkForRemoteErrors clear3d edgemode<- makeCluster
  mpi.any.source mpi.any.tag mpi.bcast.Robj2slave mpi.bcast.cmd
  mpi.comm.rank mpi.comm.size mpi.get.sourcetag mpi.recv.Robj
  mpi.send.Robj mpi.spawn.Rslaves nc_close nc_create ncatt_put
  ncdim_def ncvar_def ncvar_put newXMLNode points3d recvOneResult
  saveXML sendCall surface3d xmlInternalTreeParse xmlSchemaValidate
  xmlTree xmlTreeParse
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* 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 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 ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc-longtests/meat/xcms.Rcheck/00check.log’
for details.

Installation output

xcms.Rcheck/00install.out

* installing *source* package ‘xcms’ ...
** this is package ‘xcms’ version ‘4.9.4’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
rm -f massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o binners.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c massifquant/Tracker.cpp -o massifquant/Tracker.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c massifquant/SegProc.cpp -o massifquant/SegProc.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c obiwarp/mat.cpp -o obiwarp/mat.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c obiwarp/vec.cpp -o obiwarp/vec.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
obiwarp/xcms_dynprog.cpp: In member function ‘void DynProg::find_path(VEC::MatF&, VEC::VecF&, int, float, float, int, float)’:
obiwarp/xcms_dynprog.cpp:1113:9: warning: variable ‘bestscore’ set but not used [-Wunused-but-set-variable]
 1113 |   float bestscore;
      |         ^~~~~~~~~
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c xcms_obiwarp.cpp -o xcms_obiwarp.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c fastMatch.c -o fastMatch.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c mzClust_hclust.c -o mzClust_hclust.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c mzROI.c -o mzROI.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c util.c -o util.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c xcms.c -o xcms.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c binners.c -o binners.o
binners.c: In function ‘_breaks_on_binSize’:
binners.c:357:7: warning: unused variable ‘idx’ [-Wunused-variable]
  357 |   int idx = 0;
      |       ^~~
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o xcms.so massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o binners.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc-longtests/meat/xcms.Rcheck/00LOCK-xcms/00new/xcms/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘group’ in package ‘xcms’
Creating a new generic function for ‘sigma’ in package ‘xcms’
** help
*** installing help indices
*** copying figures
** 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 (xcms)