| 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 MsQuality package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MsQuality.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 1296/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MsQuality 1.1.0 (landing page) Thomas Naake
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: MsQuality |
| Version: 1.1.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:MsQuality.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings MsQuality_1.1.0.tar.gz |
| StartedAt: 2023-06-06 02:43:20 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 02:50:22 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 422.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MsQuality.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:MsQuality.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings MsQuality_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MsQuality.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 ‘MsQuality/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MsQuality’ version ‘1.1.0’
* 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 ‘MsQuality’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 dependencies in R code ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
calculateMetricsFromMsExperiment 5.935 1.227 3.771
calculateMetricsFromOneSampleSpectra 5.375 0.637 3.073
calculateMetricsFromSpectra 4.234 0.896 3.445
plotMetric 3.464 0.809 5.113
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘MsQuality.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
MsQuality.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL MsQuality ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘MsQuality’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MsQuality)
MsQuality.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.
> library("testthat")
> library("MsQuality")
> library("Spectra")
Loading required package: S4Vectors
Loading required package: stats4
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
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: BiocParallel
Loading required package: ProtGenerics
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
> library("MsExperiment")
> library("msdata")
> library("S4Vectors")
>
> test_check("MsQuality")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 193 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 193 ]
>
> proc.time()
user system elapsed
70.594 18.870 60.092
MsQuality.Rcheck/MsQuality-Ex.timings
| name | user | system | elapsed | |
| MsQuality-package | 0 | 0 | 0 | |
| areaUnderTic | 3.253 | 0.240 | 3.501 | |
| areaUnderTicRtQuantiles | 0.218 | 0.000 | 0.218 | |
| calculateMetrics | 3.413 | 0.700 | 3.840 | |
| calculateMetricsFromMsExperiment | 5.935 | 1.227 | 3.771 | |
| calculateMetricsFromOneSampleSpectra | 5.375 | 0.637 | 3.073 | |
| calculateMetricsFromSpectra | 4.234 | 0.896 | 3.445 | |
| dot-rtOrderSpectra | 1.521 | 0.197 | 0.172 | |
| extentIdentifiedPrecursorIntensity | 0.134 | 0.004 | 0.138 | |
| meanCharge | 0.142 | 0.005 | 0.148 | |
| medianCharge | 0.129 | 0.016 | 0.145 | |
| medianPrecursorMz | 0.128 | 0.012 | 0.141 | |
| medianTicOfRtRange | 0.132 | 0.012 | 0.144 | |
| medianTicRtIqr | 0.142 | 0.004 | 0.147 | |
| msSignal10xChange | 0.142 | 0.008 | 0.151 | |
| mzAcquisitionRange | 0.136 | 0.024 | 0.159 | |
| numberSpectra | 0.123 | 0.020 | 0.143 | |
| plotMetric | 3.464 | 0.809 | 5.113 | |
| plotMetricTibble | 3.130 | 0.650 | 2.081 | |
| precursorIntensityMean | 0.131 | 0.024 | 0.156 | |
| precursorIntensityQuartiles | 0.147 | 0.005 | 0.153 | |
| precursorIntensityRange | 0.134 | 0.015 | 0.150 | |
| precursorIntensitySd | 0.139 | 0.025 | 0.163 | |
| qualityMetrics | 0.142 | 0.007 | 0.151 | |
| ratioCharge1over2 | 0.136 | 0.017 | 0.152 | |
| ratioCharge3over2 | 0.137 | 0.011 | 0.149 | |
| ratioCharge4over2 | 0.146 | 0.008 | 0.155 | |
| rtAcquisitionRange | 0.152 | 0.012 | 0.165 | |
| rtDuration | 0.141 | 0.004 | 0.145 | |
| rtIqr | 0.135 | 0.020 | 0.156 | |
| rtIqrRate | 0.149 | 0.008 | 0.157 | |
| rtOverMsQuarters | 0.146 | 0.010 | 0.156 | |
| rtOverTicQuantiles | 0.158 | 0.024 | 0.183 | |
| shinyMsQuality | 1.778 | 0.427 | 2.029 | |
| ticQuartileToQuartileLogRatio | 1.438 | 0.250 | 0.173 | |