Back to Long Tests report for BioC 3.12

CHECK report for xcms on tokay1

This page was generated on 2021-05-08 14:20:33 -0400 (Sat, 08 May 2021).

To the developers/maintainers of the xcms package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 10/10HostnameOS / ArchCHECK
xcms 3.12.0  (landing page)
Steffen Neumann
Snapshot Date: 2021-05-08 09:00:02 -0400 (Sat, 08 May 2021)
URL: https://git.bioconductor.org/packages/xcms
Branch: RELEASE_3_12
Last Commit: 1518ef3
Last Changed Date: 2020-10-27 10:25:47 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  
tokay1Windows Server 2012 R2 Standard / x64  OK  
merida1macOS 10.14.6 Mojave / x86_64  OK  

Summary

Package: xcms
Version: 3.12.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no xcms_3.12.0.tar.gz
StartedAt: 2021-05-08 10:14:20 -0400 (Sat, 08 May 2021)
EndedAt: 2021-05-08 10:32:58 -0400 (Sat, 08 May 2021)
EllapsedTime: 1117.4 seconds
RetCode: 0
Status:   OK   
CheckDir: xcms.Rcheck
Warnings: 0

Tests output

xcms.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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

Welcome to Bioconductor

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

Loading required package: BiocParallel
Loading required package: MSnbase
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:base':

    expand.grid

Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.16.1 
  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 3.12.0 


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"))
> if (.Platform$OS.type == "unix") {
+     prm <- MulticoreParam(3)
+ } else {
+     prm <- SnowParam(3)
+ }
> register(bpstart(prm))
> ## 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)))

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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

Welcome to Bioconductor

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


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.16.1 
  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 3.12.0 


Attaching package: 'xcms'

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

    sigma

Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 87 found.

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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

Welcome to Bioconductor

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


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.16.1 
  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 3.12.0 


Attaching package: 'xcms'

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

    sigma

Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 100 found.

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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

Welcome to Bioconductor

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


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.16.1 
  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 3.12.0 


Attaching package: 'xcms'

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

    sigma

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 919 regions of interest ... OK: 61 found.
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.
> 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 515 regions of interest ... OK: 20 found.
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.
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
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko15.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko16.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko18.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko19.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko21.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko22.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt15.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt16.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt18.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt19.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt21.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt22.CDF 
method:  bin 
step:  0.1 
> 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
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko15.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko16.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko18.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko19.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt18.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt19.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt21.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt22.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko21.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko22.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt15.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt16.CDF 
method:  bin 
step:  0.1 
> 
> 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", 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 781 regions of interest ... OK: 46 found.
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.
> 
> 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 
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
== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 4 | SKIP 1 | PASS 637 ]
> 
> proc.time()
   user  system elapsed 
 300.09    7.29  393.39 

xcms.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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

Welcome to Bioconductor

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

Loading required package: BiocParallel
Loading required package: MSnbase
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:base':

    expand.grid

Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.16.1 
  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 3.12.0 


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"))
> if (.Platform$OS.type == "unix") {
+     prm <- MulticoreParam(3)
+ } else {
+     prm <- SnowParam(3)
+ }
> register(bpstart(prm))
> ## 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)))

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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

Welcome to Bioconductor

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


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.16.1 
  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 3.12.0 


Attaching package: 'xcms'

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

    sigma

Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 87 found.

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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

Welcome to Bioconductor

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


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.16.1 
  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 3.12.0 


Attaching package: 'xcms'

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

    sigma

Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 100 found.

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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

Welcome to Bioconductor

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


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.16.1 
  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 3.12.0 


Attaching package: 'xcms'

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

    sigma

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 919 regions of interest ... OK: 61 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 937 regions of interest ... OK: 87 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
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko21.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko22.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt15.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt16.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko15.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko16.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko18.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko19.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt18.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt19.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt21.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt22.CDF 
method:  bin 
step:  0.1 
> 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
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko21.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko22.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt15.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt16.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko15.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko16.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko18.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/KO/ko19.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt18.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt19.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt21.CDF 
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.12-bioc/R/library/faahKO/cdf/WT/wt22.CDF 
method:  bin 
step:  0.1 
> 
> 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", 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 781 regions of interest ... OK: 46 found.
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.
> 
> 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 
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
== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 4 | SKIP 1 | PASS 637 ]
> 
> proc.time()
   user  system elapsed 
 297.31    5.21  365.34 

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no xcms_3.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/xcms.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 '3.12.0'
* 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 whether package 'xcms' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   2.2Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... 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' '.get_closest_index' '.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
refineChromPeaks,XCMSnExp-FilterIntensityParam: warning in
  .split_by_file2(object, to_class = "XCMSnExp", msLevel = 1:10):
  partial argument match of 'msLevel' to 'msLevel.'
.split_by_file2: no visible global function definition for
  'featureData'
.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'
plotSurf,xcmsRaw: no visible global function definition for 'rgl.clear'
plotSurf,xcmsRaw: no visible global function definition for
  'rgl.surface'
plotSurf,xcmsRaw: no visible global function definition for
  'rgl.points'
plotSurf,xcmsRaw: no visible global function definition for 'rgl.bbox'
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:
  addChildren addEdge base64encode checkCluster checkForRemoteErrors
  edgemode<- featureData 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
  recvOneResult rgl.bbox rgl.clear rgl.points rgl.surface saveXML
  sendCall 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 tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* DONE

Status: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/xcms.Rcheck/00check.log'
for details.



Installation output

xcms.Rcheck/00install.out

* installing *source* package 'xcms' ...
** using staged installation
** libs

*** arch - i386
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c massifquant/Tracker.cpp -o massifquant/Tracker.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c massifquant/SegProc.cpp -o massifquant/SegProc.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c obiwarp/mat.cpp -o obiwarp/mat.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c obiwarp/vec.cpp -o obiwarp/vec.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -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]
   float bestscore;
         ^~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c xcms_obiwarp.cpp -o xcms_obiwarp.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c fastMatch.c -o fastMatch.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c mzROI.c -o mzROI.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c util.c -o util.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c xcms.c -o xcms.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c binners.c -o binners.o
binners.c: In function '_breaks_on_binSize':
binners.c:357:7: warning: unused variable 'idx' [-Wunused-variable]
   int idx = 0;
       ^~~
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o xcms.dll tmp.def 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 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/xcms.Rcheck/00LOCK-xcms/00new/xcms/libs/i386

*** arch - x64
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c massifquant/Tracker.cpp -o massifquant/Tracker.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c massifquant/SegProc.cpp -o massifquant/SegProc.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c obiwarp/mat.cpp -o obiwarp/mat.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c obiwarp/vec.cpp -o obiwarp/vec.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -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]
   float bestscore;
         ^~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c xcms_obiwarp.cpp -o xcms_obiwarp.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c fastMatch.c -o fastMatch.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c mzROI.c -o mzROI.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c util.c -o util.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c xcms.c -o xcms.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c binners.c -o binners.o
binners.c: In function '_breaks_on_binSize':
binners.c:357:7: warning: unused variable 'idx' [-Wunused-variable]
   int idx = 0;
       ^~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o xcms.dll tmp.def 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 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
C:\rtools40\mingw32\bin\nm.exe: C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/massifquant/xcms_massifquant.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/massifquant/TrMgr.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/massifquant/Tracker.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/massifquant/SegProc.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/massifquant/DataKeeper.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/massifquant/OpOverload.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/obiwarp/mat.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/obiwarp/vec.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/obiwarp/xcms_dynprog.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/obiwarp/xcms_lmat.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/xcms_obiwarp.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/fastMatch.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/mzClust_hclust.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/mzROI.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/util.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/xcms.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/binners.o: file format not recognized
There were 17 warnings (use warnings() to see them)
installing to C:/Users/biocbuild/bbs-3.12-bioc-longtests/meat/xcms.Rcheck/00LOCK-xcms/00new/xcms/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
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
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (xcms)