| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:36 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
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To the developers/maintainers of the MSnbase package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSnbase.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1291/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSnbase 2.27.0 (landing page) Laurent Gatto
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | TIMEOUT | |||||||||
| Package: MSnbase |
| Version: 2.27.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:MSnbase.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings MSnbase_2.27.0.tar.gz |
| StartedAt: 2023-06-06 02:41:28 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 03:21:29 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 2400.7 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: MSnbase.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:MSnbase.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings MSnbase_2.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MSnbase.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘MSnbase/DESCRIPTION’ ... OK
* this is package ‘MSnbase’ version ‘2.27.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSnbase’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 6.5Mb
sub-directories of 1Mb or more:
R 1.7Mb
data 1.9Mb
libs 1.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives more than one person with maintainer role:
Laurent Gatto <laurent.gatto@uclouvain.be> [aut, cre] (<https://orcid.org/0000-0002-1520-2268>)
Johannes Rainer <Johannes.Rainer@eurac.edu> [aut, cre] (<https://orcid.org/0000-0002-6977-7147>)
Sebastian Gibb <mail@sebastiangibb.de> [aut, cre] (<https://orcid.org/0000-0001-7406-4443>)
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
':::' calls which should be '::':
‘S4Vectors:::makeClassinfoRowForCompactPrinting’
‘S4Vectors:::makePrettyMatrixForCompactPrinting’
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
‘Biobase:::.showAnnotatedDataFrame’ ‘MALDIquant:::.estimateNoise’
‘MALDIquant:::.localMaxima’ ‘MALDIquant:::.movingAverage’
‘MALDIquant:::.savitzkyGolay’ ‘mzR:::.hasChromatograms’
‘mzR:::.hasSpectra’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
chromatogram-MSnExp-method 15.771 0.403 16.205
MSnSet-class 12.536 0.307 12.869
OnDiskMSnExp-class 10.233 0.248 10.538
averageMSnSet 7.466 0.138 7.643
estimateMzResolution 5.755 0.143 5.910
aggvar 5.840 0.052 5.906
combineSpectra 5.179 0.144 5.333
plot-methods 4.933 0.100 5.042
MzTab-class 0.544 0.064 10.656
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
MSnbase.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL MSnbase ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘MSnbase’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c Spectrum1_class.c -o Spectrum1_class.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c Spectrum2_class.c -o Spectrum2_class.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c utils.c -o utils.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o MSnbase.so RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-MSnbase/00new/MSnbase/libs ** R ** data *** moving datasets to lazyload DB Creating a new generic function for ‘trimws’ in package ‘MSnbase’ in method for ‘coerce’ with signature ‘"MSnSet","SummarizedExperiment"’: no definition for class “SummarizedExperiment” in method for ‘coerce’ with signature ‘"SummarizedExperiment","MSnSet"’: no definition for class “SummarizedExperiment” in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra” in method for ‘plotMzDelta’ with signature ‘"mzRramp"’: no definition for class “mzRramp” ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘trimws’ in package ‘MSnbase’ in method for ‘coerce’ with signature ‘"MSnSet","SummarizedExperiment"’: no definition for class “SummarizedExperiment” in method for ‘coerce’ with signature ‘"SummarizedExperiment","MSnSet"’: no definition for class “SummarizedExperiment” in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra” in method for ‘plotMzDelta’ with signature ‘"mzRramp"’: no definition for class “mzRramp” ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MSnbase)
MSnbase.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # setting R_TESTS to empty string because of
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> library("testthat")
> library("MSnbase")
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: ProtGenerics
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
This is MSnbase version 2.27.0
Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:base':
trimws
> setMSnbaseVerbose(FALSE)
> ## register(SerialParam()) ## see issue 205
>
> ## Erwinia
> f <- msdata::proteomics(full.names = TRUE,
+ pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")
> tmt_erwinia_in_mem_ms1 <- readMSData(f, msLevel = 1)
> tmt_erwinia_in_mem_ms2 <- readMSData(f, msLevel = 2)
> tmt_erwinia_on_disk <- readMSData(f, mode = "onDisk")
> tmt_erwinia_on_disk_ms1 <- readMSData(f, msLevel = 1, mode = "onDisk")
> tmt_erwinia_on_disk_ms2 <- readMSData(f, msLevel = 2, mode = "onDisk")
> ## subset by rt
> tmt_im_ms1_sub <- filterRt(tmt_erwinia_in_mem_ms1, c(1200, 1250))
> tmt_im_ms2_sub <- filterRt(tmt_erwinia_in_mem_ms2, c(1200, 1250))
> tmt_od_sub <- filterRt(tmt_erwinia_on_disk, c(1200, 1250))
> tmt_od_ms1_sub <- filterRt(tmt_erwinia_on_disk_ms1, c(1200, 1250))
> tmt_od_ms2_sub <- filterRt(tmt_erwinia_on_disk_ms2, c(1200, 1250))
>
> ## microtofq
> f <- c(system.file("microtofq/MM14.mzML", package = "msdata"),
+ system.file("microtofq/MM8.mzML", package = "msdata"))
> microtofq_in_mem_ms1 <- readMSData(f, msLevel = 1)
> microtofq_on_disk_ms1 <- readMSData(f, msLevel = 1, mode = "onDisk")
> microtofq_on_disk <- readMSData(f, mode = "onDisk")
>
> ## extdata mzML
> f <- dir(system.file(package = "MSnbase", dir = "extdata"),
+ full.name = TRUE, pattern = "mzXML$")
> extdata_mzXML_in_mem_ms2 <- readMSData(f, verbose = FALSE, centroided. = FALSE)
> extdata_mzXML_on_disk <- readMSData(f, centroided. = FALSE, mode = "onDisk")
> extdata_mzXML_on_disk_ms2 <- readMSData(f, msLevel = 2, centroided. = FALSE, mode = "onDisk")
>
> sf <- dir(system.file("sciex", package = "msdata"), full.names = TRUE)
> sciex <- readMSData(sf, mode = "onDisk")
>
> test_check("MSnbase")
Experiment data
Experimenter name: Laurent Gatto
Laboratory: Cambridge Centre for Proteomics (CCP)
Contact information: Laurent Gatto
Contact email: lg390@cam.ac.uk
Title: Example 'MSnExp' data set
URL:
PMIDs:
No abstract available.
Instrument :
Model: test (1)
Manufacturer:
Customisations:
Use 'msInfo(object)' for more MIAPE-MS information.
Experiment data
Experimenter name: Laurent Gatto
Laboratory: Cambridge Centre for Proteomics (CCP)
Contact information: Laurent Gatto
Contact email: lg390@cam.ac.uk
Title: Example 'MSnExp' data set
URL:
PMIDs:
No abstract available.
notes:
Note1:
First note
MIAPE-MS information:
1. General features:
Date stamp:
Contact: Laurent Gatto
Name: Laurent Gatto
Laboratory: Cambridge Centre for Proteomics (CCP)
Instument model: test
Manufacturer:
Customisations:
Software:
Version:
Switching:
Param file:
2. Ion source
Source:
Source details:
3. Post-source componentry
Analyzer:
Analyzer details:
Collision gas:
Pressure: bars
Energy:
Detector type:
Sensitivity:
MSnbase.Rcheck/MSnbase-Ex.timings
| name | user | system | elapsed | |
| Chromatogram-class | 0.107 | 0.012 | 0.119 | |
| FeatComp-class | 0.254 | 0.012 | 0.277 | |
| FeaturesOfInterest-class | 0.082 | 0.000 | 0.081 | |
| MChromatograms-class | 0.196 | 0.000 | 0.196 | |
| MSmap-class | 0.001 | 0.000 | 0.001 | |
| MSnExp-class | 0.754 | 0.004 | 0.761 | |
| MSnProcess-class | 0.001 | 0.000 | 0.001 | |
| MSnSet-class | 12.536 | 0.307 | 12.869 | |
| MSnSetList-class | 2.219 | 0.111 | 2.336 | |
| MSpectra | 0.119 | 0.008 | 0.128 | |
| MzTab-class | 0.544 | 0.064 | 10.656 | |
| OnDiskMSnExp-class | 10.233 | 0.248 | 10.538 | |
| ProcessingStep-class | 0.003 | 0.000 | 0.002 | |
| ReporterIons-class | 0.014 | 0.000 | 0.013 | |
| TMT6 | 0.009 | 0.000 | 0.009 | |
| addIdentificationData-methods | 1.099 | 0.007 | 1.110 | |
| aggvar | 5.840 | 0.052 | 5.906 | |
| averageMSnSet | 7.466 | 0.138 | 7.643 | |
| bin-methods | 0.334 | 0.032 | 0.366 | |
| calculateFragments-methods | 1.369 | 0.016 | 1.388 | |
| chromatogram-MSnExp-method | 15.771 | 0.403 | 16.205 | |
| clean-methods | 0.176 | 0.004 | 0.181 | |
| combineFeatures | 1.376 | 0.004 | 1.383 | |
| combineSpectra | 5.179 | 0.144 | 5.333 | |
| combineSpectraMovingWindow | 3.521 | 0.028 | 3.555 | |
| commonFeatureNames | 0.363 | 0.000 | 0.363 | |
| compareSpectra-methods | 0.248 | 0.000 | 0.248 | |
| consensusSpectrum | 0.041 | 0.000 | 0.041 | |
| estimateMzResolution | 5.755 | 0.143 | 5.910 | |
| estimateMzScattering | 1.798 | 0.084 | 1.885 | |
| estimateNoise-method | 0.013 | 0.000 | 0.013 | |
| extractPrecSpectra-methods | 1.347 | 0.052 | 1.401 | |
| extractSpectraData | 2.502 | 0.072 | 2.672 | |
| fData-utils | 0.412 | 0.016 | 0.429 | |
| factorsAsStrings | 0.011 | 0.004 | 0.014 | |
| featureCV | 0.023 | 0.004 | 0.028 | |
| fillUp | 0.004 | 0.000 | 0.004 | |
| formatRt | 0.000 | 0.000 | 0.001 | |
| get.amino.acids | 0.004 | 0.000 | 0.003 | |
| get.atomic.mass | 0.001 | 0.000 | 0.000 | |
| getVariableName | 0.004 | 0.000 | 0.004 | |
| hasSpectraOrChromatograms | 0.379 | 0.024 | 0.412 | |
| iPQF | 0.354 | 0.004 | 0.359 | |
| iTRAQ4 | 0.015 | 0.000 | 0.016 | |
| imageNA2 | 4.243 | 0.040 | 4.294 | |
| impute | 1.871 | 0.032 | 1.906 | |
| isCentroidedFromFile | 2.537 | 0.099 | 2.634 | |
| itraqdata | 0.062 | 0.000 | 0.062 | |
| listOf | 0.001 | 0.000 | 0.001 | |
| makeCamelCase | 0.001 | 0.000 | 0.001 | |
| makeNaData | 0.704 | 0.004 | 0.709 | |
| meanMzInts | 0.047 | 0.004 | 0.051 | |
| missing-data | 3.927 | 0.004 | 3.939 | |
| mzRident2dfr | 0.037 | 0.000 | 0.036 | |
| nFeatures | 0.498 | 0.016 | 0.514 | |
| nQuants | 0.155 | 0.000 | 0.155 | |
| naplot | 0.074 | 0.000 | 0.074 | |
| navMS | 3.267 | 0.140 | 3.490 | |
| normToReference | 0.221 | 0.007 | 0.229 | |
| normalise-methods | 0.013 | 0.004 | 0.017 | |
| npcv | 0.001 | 0.004 | 0.005 | |
| pSet-class | 0.001 | 0.000 | 0.001 | |
| pickPeaks-method | 0.442 | 0.008 | 0.451 | |
| plot-methods | 4.933 | 0.100 | 5.042 | |
| plot2d-methods | 0.737 | 0.008 | 0.747 | |
| plotDensity-methods | 0.918 | 0.004 | 0.924 | |
| plotMzDelta-methods | 1.169 | 0.000 | 1.172 | |
| plotNA-methods | 0.568 | 0.000 | 0.570 | |
| plotSpectrumSpectrum-methods | 1.836 | 0.000 | 1.838 | |
| precSelection | 0.01 | 0.00 | 0.01 | |
| purityCorrect-methods | 0.021 | 0.000 | 0.023 | |
| quantify-methods | 3.783 | 0.004 | 3.794 | |
| readMSData | 2.541 | 0.044 | 2.590 | |
| readMSnSet | 0.101 | 0.000 | 0.103 | |
| readMgfData | 2.026 | 0.028 | 2.059 | |
| readMzIdData | 0.682 | 0.231 | 0.927 | |
| readMzTabData | 1.099 | 0.039 | 2.481 | |
| readMzTabData_v0.9 | 0.163 | 0.012 | 1.027 | |
| readSRMData | 1.435 | 0.072 | 1.510 | |
| reduce-data.frame-method | 0.019 | 0.000 | 0.020 | |
| removeNoId-methods | 1.490 | 0.164 | 1.657 | |
| removePeaks-methods | 0.745 | 0.008 | 0.754 | |
| removeReporters-methods | 0.639 | 0.000 | 0.640 | |
| selectFeatureData | 1.411 | 0.016 | 1.430 | |
| smooth-methods | 0.272 | 0.000 | 0.273 | |
| trimMz-methods | 0.189 | 0.000 | 0.190 | |
| writeMgfData-methods | 1.893 | 0.016 | 1.912 | |