| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:13 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 metaMS package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metaMS.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1138/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| metaMS 1.35.0 (landing page) Yann Guitton
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: metaMS |
| Version: 1.35.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:metaMS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings metaMS_1.35.0.tar.gz |
| StartedAt: 2023-02-07 07:30:07 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 07:36:53 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 405.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: metaMS.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:metaMS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings metaMS_1.35.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/metaMS.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘metaMS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metaMS’ version ‘1.35.0’
* 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 ‘metaMS’ 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 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘runGC.Rnw’ using ‘UTF-8’... OK
‘runLC.Rnw’ using ‘UTF-8’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
metaMS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL metaMS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘metaMS’ ... ** 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 (metaMS)
metaMS.Rcheck/tests/runTests.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
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.
> BiocGenerics:::testPackage("metaMS")
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
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 2.25.1
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 3.21.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
< -------- Experiment of 4 samples ------------------------------------- >
< -------- Instrument: TSQXLS.QQQ.GC ----------------------------------- >
< -------- Annotation using database of 3 spectra ---------------------- >
< -------- Using xcmsSet object - only doing annotation ---------------- >
< -------- Removing artefacts (Bleeding, Plasticizers) ----------------- >
< -------- Matching with database of standards ------------------------- >
< -------- Matching unknowns across samples ---------------------------- >
< -------- Formatting results ------------------------------------------ >
< -------- Done! ------------------------------------------------------- >
< -------- Experiment of 4 samples ------------------------------------- >
< -------- Instrument: Synapt.QTOF.RP - polarity: positive ------------ >
< -------- Database of 4 compounds ------------------------------------- >
< -------- Using xcmsSet object - only doing annotation ---------------- >
< -------- Performing annotation --------------------------------------- >
Fixed mass tolerance 0.005
Feature-wise Annotation ...
< -------- Formatting the output --------------------------------------- >
< -------- Done ! ------------------------------------------------------ >
RUNIT TEST PROTOCOL -- Tue Feb 7 07:35:38 2023
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
metaMS RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
17.243 0.555 17.849
metaMS.Rcheck/metaMS-Ex.timings
| name | user | system | elapsed | |
| AnnotateTable | 0.044 | 0.012 | 0.057 | |
| FEMsettings | 0.001 | 0.000 | 0.001 | |
| addRI | 0.037 | 0.000 | 0.039 | |
| alignmentLC | 0.096 | 0.060 | 0.157 | |
| constructExpPseudoSpectra | 0.043 | 0.008 | 0.051 | |
| createSTDdbGC | 0.003 | 0.000 | 0.003 | |
| createSTDdbLC | 0.018 | 0.003 | 0.021 | |
| errf | 0.016 | 0.004 | 0.020 | |
| getAnnotationLC | 0.114 | 0.068 | 0.182 | |
| getAnnotationMat | 0.044 | 0.004 | 0.048 | |
| getFeatureInfo | 0.044 | 0.004 | 0.048 | |
| getPeakTable | 0.097 | 0.056 | 0.153 | |
| matchExpSpec | 0.019 | 0.000 | 0.020 | |
| matchSamples2DB | 0.000 | 0.003 | 0.003 | |
| matchSamples2Samples | 0.001 | 0.001 | 0.003 | |
| metaMSsettings-class | 0.001 | 0.000 | 0.002 | |
| metaSetting-methods | 0.000 | 0.000 | 0.001 | |
| msp | 0.002 | 0.000 | 0.002 | |
| peakDetection | 0.002 | 0.000 | 0.001 | |
| plotPseudoSpectrum | 0.021 | 0.000 | 0.021 | |
| processStandards | 0.048 | 0.000 | 0.048 | |
| readStdInfo | 0.023 | 0.000 | 0.023 | |
| runCAMERA | 0.089 | 0.064 | 0.152 | |
| runGC | 0.046 | 0.000 | 0.046 | |
| runLC | 0.027 | 0.000 | 0.026 | |
| threeStdsDB | 0.010 | 0.004 | 0.014 | |
| treat.DB | 0.004 | 0.000 | 0.005 | |