Yann Guitton
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/metaMS |
| git_branch: master |
| git_last_commit: a2969d4 |
| git_last_commit_date: 2021-10-26 12:13:00 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:59 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1106/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| metaMS 1.31.0 (landing page) Yann Guitton
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: metaMS |
| Version: 1.31.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metaMS.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings metaMS_1.31.0.tar.gz |
| StartedAt: 2022-03-17 19:32:11 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:36:09 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 237.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: metaMS.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metaMS.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings metaMS_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/metaMS.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'metaMS/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'metaMS' version '1.31.0' * 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 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
metaMS.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL metaMS
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-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
converting help for package 'metaMS'
finding HTML links ... done
AnnotateTable html
FEMsettings html
finding level-2 HTML links ... done
GCresults html
LCDBtest html
LCresults html
addRI html
alignmentLC html
annotations2tab html
constructExpPseudoSpectra html
createSTDdbGC html
createSTDdbLC html
errf html
exptable html
getAnnotationLC html
getAnnotationMat html
getFeatureInfo html
getPeakTable html
match2ExtDB html
matchExpSpec html
matchSamples2DB html
matchSamples2Samples html
metaMS-package html
metaMSsettings-class html
metaSetting-methods html
msp html
peakDetection html
plotPseudoSpectrum html
printString html
processStandards html
readStdInfo html
removeDoubleMasses html
runCAMERA html
runGC html
runLC html
threeStdsDB html
treat.DB html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'MultiDataSet' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'spikeLI' is missing or broken
done
metaMS.Rcheck/tests/runTests.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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.
> 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, 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 2.21.6
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 3.17.3
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 -- Thu Mar 17 19:35:59 2022
***********************************************
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
11.98 1.09 13.07
metaMS.Rcheck/metaMS-Ex.timings
| name | user | system | elapsed | |
| AnnotateTable | 0.05 | 0.01 | 0.06 | |
| FEMsettings | 0 | 0 | 0 | |
| addRI | 0.03 | 0.00 | 0.04 | |
| alignmentLC | 0.11 | 0.13 | 0.24 | |
| constructExpPseudoSpectra | 0.75 | 0.01 | 0.76 | |
| createSTDdbGC | 0.02 | 0.00 | 0.02 | |
| createSTDdbLC | 0.02 | 0.00 | 0.01 | |
| errf | 0.00 | 0.02 | 0.02 | |
| getAnnotationLC | 0.10 | 0.08 | 0.19 | |
| getAnnotationMat | 0.05 | 0.02 | 0.06 | |
| getFeatureInfo | 0.02 | 0.01 | 0.04 | |
| getPeakTable | 0.12 | 0.05 | 0.17 | |
| matchExpSpec | 0.03 | 0.00 | 0.03 | |
| matchSamples2DB | 0 | 0 | 0 | |
| matchSamples2Samples | 0.00 | 0.02 | 0.01 | |
| metaMSsettings-class | 0 | 0 | 0 | |
| metaSetting-methods | 0 | 0 | 0 | |
| msp | 0 | 0 | 0 | |
| peakDetection | 0.00 | 0.01 | 0.02 | |
| plotPseudoSpectrum | 0.02 | 0.00 | 0.02 | |
| processStandards | 0.01 | 0.02 | 0.03 | |
| readStdInfo | 0.02 | 0.00 | 0.01 | |
| runCAMERA | 0.08 | 0.08 | 0.16 | |
| runGC | 0.01 | 0.03 | 0.05 | |
| runLC | 0.02 | 0.00 | 0.01 | |
| threeStdsDB | 0.03 | 0.00 | 0.03 | |
| treat.DB | 0 | 0 | 0 | |