Ashley Sawle
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/qPLEXanalyzer |
| git_branch: master |
| git_last_commit: 679a682 |
| git_last_commit_date: 2022-03-16 10:29:42 -0400 (Wed, 16 Mar 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:23 -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 qPLEXanalyzer package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/qPLEXanalyzer.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 1507/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| qPLEXanalyzer 1.13.1 (landing page) Ashley Sawle
| 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: qPLEXanalyzer |
| Version: 1.13.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:qPLEXanalyzer.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings qPLEXanalyzer_1.13.1.tar.gz |
| StartedAt: 2022-03-17 19:58:05 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:00:53 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 168.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: qPLEXanalyzer.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:qPLEXanalyzer.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings qPLEXanalyzer_1.13.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/qPLEXanalyzer.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 'qPLEXanalyzer/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'qPLEXanalyzer' version '1.13.1' * 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 'qPLEXanalyzer' 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 ... NOTE convertToMSnset: no visible binding for global variable 'SampleName' corrPlot: no visible binding for global variable 'X' corrPlot: no visible binding for global variable 'AddValues' corrPlot: no visible binding for global variable 'Cor' corrPlot: no visible binding for global variable 'Y' corrPlot: no visible binding for global variable 'CorTxt' coveragePlot: no visible binding for global variable 'Accessions' coveragePlot: no visible binding for global variable 'Sequences' getContrastResults: no visible binding for global variable 'B' getContrastResults: no visible binding for global variable 'AveExpr' getContrastResults: no visible binding for global variable 'logFC' groupScaling: no visible binding for global variable 'sInt' groupScaling: no visible binding for global variable 'meanscaledIntensity' hierarchicalPlot: no visible binding for global variable 'x' hierarchicalPlot: no visible binding for global variable 'y' hierarchicalPlot: no visible binding for global variable 'xend' hierarchicalPlot: no visible binding for global variable 'yend' hierarchicalPlot: no visible binding for global variable 'SampleName' intensityBoxplot: no visible binding for global variable 'Intensity' intensityBoxplot: no visible binding for global variable 'logInt' intensityBoxplot: no visible binding for global variable 'SampleName' intensityPlot: no visible binding for global variable 'Intensity' intensityPlot: no visible binding for global variable 'SampleName' maVolPlot: no visible binding for global variable 'group' maVolPlot: no visible binding for global variable 'adj.P.Val' maVolPlot: no visible binding for global variable 'GeneSymbol' maVolPlot: no visible binding for global variable 'SymbolLab' mergePeptides: no visible binding for global variable 'Accessions' mergePeptides: no visible binding for global variable 'Sequences' mergePeptides: no visible binding for global variable 'phosseqid' mergePeptides: no visible global function definition for 'where' mergePeptides: no visible binding for global variable 'Count' peptideIntensityPlot: no visible binding for global variable 'PeptideID' peptideIntensityPlot: no visible binding for global variable 'Intensity' peptideIntensityPlot: no visible binding for global variable 'Accessions' peptideIntensityPlot: no visible binding for global variable 'SampleName' peptideIntensityPlot: no visible binding for global variable 'logIntensity' peptideIntensityPlot: no visible binding for global variable 'Sequences' peptideIntensityPlot: no visible binding for global variable 'Modifications' plotMeanVar: no visible binding for global variable 'x' plotMeanVar: no visible binding for global variable 'y' plotMeanVar: no visible binding for global variable 'Mean' plotMeanVar: no visible binding for global variable 'Variance' rliPlot: no visible binding for global variable 'RowID' rliPlot: no visible binding for global variable 'Intensity' rliPlot: no visible binding for global variable 'logInt' rliPlot: no visible binding for global variable 'medianLogInt' rliPlot: no visible binding for global variable 'SampleName' rliPlot: no visible binding for global variable 'RLI' summarizeIntensities: no visible binding for global variable 'Accessions' summarizeIntensities: no visible binding for global variable 'Sequences' summarizeIntensities: no visible global function definition for 'where' summarizeIntensities: no visible binding for global variable 'Count' Undefined global functions or variables: Accessions AddValues AveExpr B Cor CorTxt Count GeneSymbol Intensity Mean Modifications PeptideID RLI RowID SampleName Sequences SymbolLab Variance X Y adj.P.Val group logFC logInt logIntensity meanscaledIntensity medianLogInt phosseqid sInt where x xend y yend * 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 'testthat.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: 1 NOTE See 'D:/biocbuild/bbs-3.15-bioc/meat/qPLEXanalyzer.Rcheck/00check.log' for details.
qPLEXanalyzer.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL qPLEXanalyzer
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'qPLEXanalyzer' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to '=='
Note: wrong number of arguments to '=='
** help
*** installing help indices
converting help for package 'qPLEXanalyzer'
finding HTML links ... done
ER_ARID1A_KO_MCF7 html
IRSnorm html
finding level-2 HTML links ... done
assignColours html
computeDiffStats html
convertToMSnset html
corrPlot html
coveragePlot html
exp2_Xlink html
exp3_OHT_ESR1 html
getContrastResults html
groupScaling html
hierarchicalPlot html
human_anno html
intensityBoxplot html
intensityPlot html
maVolPlot html
mergePeptides html
mouse_anno html
normalizeQuantiles html
normalizeScaling html
pcaPlot html
peptideIntensityPlot html
plotMeanVar html
qPLEXanalyzer-package html
regressIntensity html
rliPlot html
rowScaling html
summarizeIntensities 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 (qPLEXanalyzer)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'sesame' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'SingleCellSignalR' is missing or broken
done
qPLEXanalyzer.Rcheck/tests/testthat.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.
> library(testthat)
> library(vdiffr)
> library(qPLEXanalyzer)
Loading required package: Biobase
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: MSnbase
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 2.21.6
Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:base':
trimws
>
> options(lifecycle_verbosity = "warning")
> test_check("qPLEXanalyzer")
[ FAIL 0 | WARN 10 | SKIP 11 | PASS 156 ]
== Skipped tests ===============================================================
* On CRAN (11)
[ FAIL 0 | WARN 10 | SKIP 11 | PASS 156 ]
>
> proc.time()
user system elapsed
17.89 0.84 18.75
qPLEXanalyzer.Rcheck/qPLEXanalyzer-Ex.timings
| name | user | system | elapsed | |
| IRSnorm | 4.50 | 0.02 | 4.52 | |
| assignColours | 0.28 | 0.01 | 0.30 | |
| computeDiffStats | 0.50 | 0.03 | 0.53 | |
| convertToMSnset | 0.18 | 0.02 | 0.18 | |
| corrPlot | 0.65 | 0.01 | 0.68 | |
| coveragePlot | 0.92 | 0.02 | 0.94 | |
| getContrastResults | 0.36 | 0.06 | 0.42 | |
| groupScaling | 0.22 | 0.02 | 0.24 | |
| hierarchicalPlot | 0.23 | 0.01 | 0.25 | |
| intensityBoxplot | 0.72 | 0.10 | 0.81 | |
| intensityPlot | 0.72 | 0.04 | 0.76 | |
| maVolPlot | 1.16 | 0.15 | 1.30 | |
| mergePeptides | 0.45 | 0.00 | 0.45 | |
| normalizeQuantiles | 0.19 | 0.01 | 0.21 | |
| normalizeScaling | 0.15 | 0.05 | 0.20 | |
| pcaPlot | 0.63 | 0.03 | 0.66 | |
| peptideIntensityPlot | 0.50 | 0.01 | 0.51 | |
| plotMeanVar | 0.54 | 0.02 | 0.56 | |
| regressIntensity | 2.43 | 0.03 | 2.46 | |
| rliPlot | 1.34 | 0.08 | 1.42 | |
| rowScaling | 0.41 | 0.05 | 0.45 | |
| summarizeIntensities | 0.28 | 0.01 | 0.30 | |