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This page was generated on 2021-10-15 15:06:17 -0400 (Fri, 15 Oct 2021).
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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 1474/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| qPLEXanalyzer 1.10.0 (landing page) Ashley Sawle
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: qPLEXanalyzer |
| Version: 1.10.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qPLEXanalyzer.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings qPLEXanalyzer_1.10.0.tar.gz |
| StartedAt: 2021-10-15 03:58:41 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 04:03:13 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 272.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: qPLEXanalyzer.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qPLEXanalyzer.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings qPLEXanalyzer_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/qPLEXanalyzer.Rcheck' * using R version 4.1.1 (2021-08-10) * 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 '1.10.0' * 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 '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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... 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 'C:/Users/biocbuild/bbs-3.13-bioc/meat/qPLEXanalyzer.Rcheck/00check.log' for details.
qPLEXanalyzer.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/qPLEXanalyzer_1.10.0.tar.gz && rm -rf qPLEXanalyzer.buildbin-libdir && mkdir qPLEXanalyzer.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qPLEXanalyzer.buildbin-libdir qPLEXanalyzer_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL qPLEXanalyzer_1.10.0.zip && rm qPLEXanalyzer_1.10.0.tar.gz qPLEXanalyzer_1.10.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
30 3890k 30 1190k 0 0 2460k 0 0:00:01 --:--:-- 0:00:01 2459k
100 3890k 100 3890k 0 0 3745k 0 0:00:01 0:00:01 --:--:-- 3748k
install for i386
* 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
install for x64
* installing *source* package 'qPLEXanalyzer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'qPLEXanalyzer' as qPLEXanalyzer_1.10.0.zip
* DONE (qPLEXanalyzer)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'qPLEXanalyzer' successfully unpacked and MD5 sums checked
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qPLEXanalyzer.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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 2.18.0
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")
== Skipped tests ===============================================================
* On CRAN (11)
[ FAIL 0 | WARN 10 | SKIP 11 | PASS 156 ]
>
> proc.time()
user system elapsed
20.70 1.14 21.84
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qPLEXanalyzer.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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 2.18.0
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")
== Skipped tests ===============================================================
* On CRAN (11)
[ FAIL 0 | WARN 10 | SKIP 11 | PASS 156 ]
>
> proc.time()
user system elapsed
22.51 0.67 23.39
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qPLEXanalyzer.Rcheck/examples_i386/qPLEXanalyzer-Ex.timings
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qPLEXanalyzer.Rcheck/examples_x64/qPLEXanalyzer-Ex.timings
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