| Back to Long Tests report for BioC 3.14 |
This page was generated on 2022-04-09 21:00:03 -0400 (Sat, 09 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4322 |
| riesling1 | Windows Server 2019 Standard | x64 | 4.1.2 (2021-11-01) -- "Bird Hippie" | 4108 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4135 |
| 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 | ||||
|
To the developers/maintainers of the xcms package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 18/19 | Hostname | OS / Arch | CHECK | |||||||
| xcms 3.16.1 (landing page) Steffen Neumann
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | ERROR | |||||||
| riesling1 | Windows Server 2019 Standard / x64 | ERROR | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | ERROR | ||||||||
| Package: xcms |
| Version: 3.16.1 |
| Command: D:\biocbuild\bbs-3.14-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_3.16.1.tar.gz |
| StartedAt: 2022-04-09 08:09:00 -0400 (Sat, 09 Apr 2022) |
| EndedAt: 2022-04-09 08:14:44 -0400 (Sat, 09 Apr 2022) |
| EllapsedTime: 343.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: xcms.Rcheck |
| Warnings: NA |
|
xcms.Rcheck/tests_i386/testthat.Rout
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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: 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, 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 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 2.20.2
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 3.16.1
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: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 objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
This is MSnbase version 2.20.2
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 3.16.1
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: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 objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
This is MSnbase version 2.20.2
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 3.16.1
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.
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, 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 objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
This is MSnbase version 2.20.2
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 3.16.1
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.
> 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)
Error: BiocParallel errors
2 remote errors, element index: 2, 3
0 unevaluated and other errors
first remote error: cannot open the connection
Execution halted
There were 50 or more warnings (use warnings() to see the first 50)
Warning message:
In socketConnection(port = port, server = TRUE, blocking = TRUE, :
port 11195 cannot be opened
Warning message:
In socketConnection(port = port, server = TRUE, blocking = TRUE, :
port 11195 cannot be opened
|
xcms.Rcheck/tests_x64/testthat.Rout
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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: 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, 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 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 2.20.2
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 3.16.1
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: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 objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
This is MSnbase version 2.20.2
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 3.16.1
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: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 objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
This is MSnbase version 2.20.2
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 3.16.1
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: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 objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
This is MSnbase version 2.20.2
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 3.16.1
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)
Error: BiocParallel errors
2 remote errors, element index: 1, 3
0 unevaluated and other errors
first remote error: cannot open the connection
Execution halted
There were 50 or more warnings (use warnings() to see the first 50)
Warning message:
In socketConnection(port = port, server = TRUE, blocking = TRUE, :
port 11294 cannot be opened
Warning message:
In socketConnection(port = port, server = TRUE, blocking = TRUE, :
port 11294 cannot be opened
|
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.14-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_3.16.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.14-bioc-longtests/meat/xcms.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '3.16.1'
* 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 6.7Mb
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' '.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 '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:
List addChildren addEdge base64encode checkCluster
checkForRemoteErrors 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<- recvOneResult rgl.bbox rgl.clear
rgl.points rgl.surface sampleNames 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'
Warning message:
In file.rename(outfile, paste0(outfile, ".fail")) :
cannot rename file 'testthat.Rout' to 'testthat.Rout.fail', reason 'The process cannot access the file because it is being used by another process'
ERROR
** running tests for arch 'x64' ...
Running 'testthat.R'
Warning message:
In file.rename(outfile, paste0(outfile, ".fail")) :
cannot rename file 'testthat.Rout' to 'testthat.Rout.fail', reason 'The process cannot access the file because it is being used by another process'
ERROR
* DONE
Status: 2 ERRORs, 5 NOTEs
See
'D:/biocbuild/bbs-3.14-bioc-longtests/meat/xcms.Rcheck/00check.log'
for details.
xcms.Rcheck/00install.out
* installing *source* package 'xcms' ...
** using staged installation
** libs
*** arch - i386
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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 -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.14-bioc-longtests/meat/xcms.Rcheck/00LOCK-xcms/00new/xcms/libs/i386
*** arch - x64
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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"D:/biocbuild/bbs-3.14-bioc/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 -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lR
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-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: D:/biocbuild/bbs-3.14-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/massifquant/TrMgr.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/massifquant/Tracker.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/massifquant/SegProc.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/massifquant/DataKeeper.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/massifquant/OpOverload.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/obiwarp/mat.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/obiwarp/vec.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-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: D:/biocbuild/bbs-3.14-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: D:/biocbuild/bbs-3.14-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/xcms_obiwarp.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/fastMatch.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/mzClust_hclust.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/mzROI.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/util.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/xcms.Rcheck/00_pkg_src/xcms/src-x64/xcms.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-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 D:/biocbuild/bbs-3.14-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 '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
*** 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)