Back to Long Tests report for BioC 3.17

This page was generated on 2023-10-14 21:30:02 -0400 (Sat, 14 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 30/31HostnameOS / ArchCHECK
xcms 3.22.0  (landing page)
Steffen Neumann
Snapshot Date: 2023-10-14 09:55:02 -0400 (Sat, 14 Oct 2023)
git_url: https://git.bioconductor.org/packages/xcms
git_branch: RELEASE_3_17
git_last_commit: 75010ce
git_last_commit_date: 2023-04-25 09:41:50 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK  
palomino3Windows Server 2022 Datacenter / x64  OK  
merida1macOS 12.6.4 Monterey / 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: 3.22.0
Command: /home/biocbuild/bbs-3.17-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_3.22.0.tar.gz
StartedAt: 2023-10-14 11:42:05 -0400 (Sat, 14 Oct 2023)
EndedAt: 2023-10-14 11:53:07 -0400 (Sat, 14 Oct 2023)
EllapsedTime: 662.1 seconds
RetCode: 0
Status:   OK  
CheckDir: xcms.Rcheck
Warnings: 0

Tests output

xcms.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> library(testthat)
> library(xcms)
Loading required package: BiocParallel
Loading required package: MSnbase
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: 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 2.26.0 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    trimws


This is xcms version 3.22.0 


Attaching package: 'xcms'

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

    sigma

> library(faahKO)
> library(msdata)
> 
> 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())
> 
> ## Create some objects we can re-use in different tests:
> 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"))
> 
> ## 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)
Processing 2572 mz slices ... OK
> ## 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)
Processing 2572 mz slices ... OK
> xod_xgr <- adjustRtime(xod_xg, param = PeakGroupsParam(span = 0.4))
Performing retention time correction using 19 peak groups.
Applying retention time adjustment to the identified chromatographic peaks ... OK
> xod_xgrg <- groupChromPeaks(xod_xgr, param = pdp)
Processing 2572 mz slices ... OK
> 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))
Processing 3195 mz slices ... OK
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko19.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko21.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko22.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt19.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt21.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-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-3.17-bioc/R/site-library/faahKO/cdf/KO/ko18.CDF), using zero intensity value.

> faahko_grouped_retcor_filled <-
+     fillPeaks(group(retcor(group(updateObject(faahko)))))
Processing 3195 mz slices ... OK
Performing retention time correction using 132 peak groups.
Processing 3195 mz slices ... OK
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko19.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko21.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko22.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt19.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt21.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt22.CDF 
method:  bin 
step:  0.1 
There were 35 warnings (use warnings() to see them)
> 
> microtofq_fs <- c(system.file("microtofq/MM14.mzML", package = "msdata"),
+                   system.file("microtofq/MM8.mzML", package = "msdata"))
> microtofq_xr <- xcmsRaw(microtofq_fs[1], profstep = 0)
> microtofq_od <- readMSData(microtofq_fs, mode = "onDisk")
> 
> ## Direct injection data:
> fticrf <- list.files(system.file("fticr-mzML", package = "msdata"),
+                      recursive = TRUE, full.names = TRUE)
> fticr <- readMSData(fticrf[1:2], msLevel. = 1, mode = "onDisk")
> 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  
HAM004_641fE_14-11-07--Exp1.extracted HAM004_641fE_14-11-07--Exp2.extracted 
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-3.17-bioc/R/site-library/faahKO/cdf/KO/ko15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko19.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko21.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko22.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt19.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt21.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt22.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko19.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko21.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko22.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt19.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt21.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt22.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko19.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko21.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko22.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt19.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt21.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/WT/wt22.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-bioc/R/site-library/faahKO/cdf/KO/ko16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.17-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 18 | SKIP 4 | PASS 627 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• empty test (4): '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 18 | SKIP 4 | PASS 627 ]
> 
> proc.time()
   user  system elapsed 
360.129   5.599 365.846

'R CMD check' output

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### Running command:
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###   /home/biocbuild/bbs-3.17-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_3.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc-longtests/meat/xcms.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* 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 ‘3.22.0’
* 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 11.4.0-1ubuntu1~22.04) 11.4.0’
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    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 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 loading without being on the library search path ... OK
* checking 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’
  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’ ‘.getChromPeakData’ ‘.get_closest_index’
  ‘.spectra_for_peaks’ ‘.split_by_file2’ ‘.validChromPeaksMatrix’
  ‘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’
chromPeakSpectra: no visible global function definition for ‘List’
featureSpectra: no visible global function definition for ‘List’
plotQC: no visible global function definition for ‘sampleNames’
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’
[,XChromatograms-ANY-ANY-ANY: no visible global function definition for
  ‘pData<-’
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’
refineChromPeaks,XCMSnExp-FilterIntensityParam: no visible binding for
  global variable ‘value’
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:
  List addChildren addEdge base64encode bbox3d 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 pData<- points3d recvOneResult sampleNames
  saveXML sendCall surface3d value 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc-longtests/meat/xcms.Rcheck/00check.log’
for details.

Installation output

xcms.Rcheck/00install.out

* installing *source* package ‘xcms’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
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++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c massifquant/Tracker.cpp -o massifquant/Tracker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c massifquant/SegProc.cpp -o massifquant/SegProc.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c obiwarp/mat.cpp -o obiwarp/mat.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c obiwarp/vec.cpp -o obiwarp/vec.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -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++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c xcms_obiwarp.cpp -o xcms_obiwarp.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c fastMatch.c -o fastMatch.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c mzClust_hclust.c -o mzClust_hclust.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c mzROI.c -o mzROI.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c util.c -o util.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c xcms.c -o xcms.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -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++17 -shared -L/home/biocbuild/bbs-3.17-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-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-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’
Creating a generic function from function ‘hasFilledChromPeaks’ in package ‘xcms’
** 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 (xcms)