Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:45 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 |
Package 934/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
hdxmsqc 1.3.0 (landing page) Oliver M. Crook
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the hdxmsqc package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hdxmsqc.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: hdxmsqc |
Version: 1.3.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:hdxmsqc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings hdxmsqc_1.3.0.tar.gz |
StartedAt: 2024-12-22 19:42:03 -0500 (Sun, 22 Dec 2024) |
EndedAt: 2024-12-22 19:43:34 -0500 (Sun, 22 Dec 2024) |
EllapsedTime: 91.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: hdxmsqc.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:hdxmsqc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings hdxmsqc_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/hdxmsqc.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘hdxmsqc/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘hdxmsqc’ version ‘1.3.0’ * 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 ‘hdxmsqc’ 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 code 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 chargeCorrelationHdx: no visible global function definition for ‘assay’ chargeCorrelationHdx: no visible binding for global variable ‘x’ chargeCorrelationHdx: no visible binding for global variable ‘z’ chargeCorrelationHdx: no visible binding for global variable ‘peptide’ chargeCorrelationHdx: no visible binding for global variable ‘y’ compatibleUptake: no visible global function definition for ‘rowData’ compatibleUptake: no visible global function definition for ‘assay’ computeMassError: no visible global function definition for ‘rowData’ computeMassError: no visible global function definition for ‘assay’ computeMonotoneStats: no visible global function definition for ‘assay’ computeMonotoneStats: no visible binding for global variable ‘x’ computeMonotoneStats: no visible binding for global variable ‘y’ imTimeOutlier: no visible global function definition for ‘rowData’ imTimeOutlier: no visible global function definition for ‘rowMedians’ imTimeOutlier: no visible binding for global variable ‘Experiment’ imTimeOutlier: no visible binding for global variable ‘IMS_shift’ intensityOutliers: no visible global function definition for ‘rowData’ isMissingAtRandom: no visible global function definition for ‘assay’ isMissingAtRandom: no visible global function definition for ‘rowData’ plotImTimeOutlier: no visible binding for global variable ‘Experiment’ plotImTimeOutlier: no visible binding for global variable ‘IMS_shift’ plotImTimeOutlier: no visible global function definition for ‘brewer.pal’ plotIntensityOutliers: no visible binding for global variable ‘x’ plotIntensityOutliers: no visible binding for global variable ‘y’ plotIntensityOutliers: no visible binding for global variable ‘outlier’ plotIntensityOutliers: no visible global function definition for ‘brewer.pal’ plotMassError: no visible binding for global variable ‘x’ plotMassError: no visible binding for global variable ‘y’ plotMassError: no visible global function definition for ‘brewer.pal’ plotMissing: no visible global function definition for ‘assay’ plotMissing: no visible global function definition for ‘pheatmap’ plotMissing: no visible global function definition for ‘brewer.pal’ plotMonotoneStat : <anonymous>: no visible binding for global variable ‘x’ plotMonotoneStat : <anonymous>: no visible binding for global variable ‘y’ plotMonotoneStat : <anonymous>: no visible binding for global variable ‘outlier’ plotMonotoneStat : <anonymous>: no visible global function definition for ‘brewer.pal’ plotrTimeOutliers: no visible binding for global variable ‘Experiment’ plotrTimeOutliers: no visible binding for global variable ‘RT_shift’ plotrTimeOutliers: no visible global function definition for ‘brewer.pal’ processHDE: no visible binding for global variable ‘Deut.Time’ processHDE: no visible binding for global variable ‘Sequence’ processHDE: no visible binding for global variable ‘Protein.State’ processHDE: no visible binding for global variable ‘Charge’ qualityControl: no visible global function definition for ‘rowData’ rTimeOutliers: no visible global function definition for ‘rowData’ rTimeOutliers: no visible global function definition for ‘rowMedians’ rTimeOutliers: no visible binding for global variable ‘Experiment’ rTimeOutliers: no visible binding for global variable ‘RT_shift’ replicateCorrelation: no visible global function definition for ‘assay’ replicateCorrelation: no visible binding for global variable ‘x’ replicateCorrelation: no visible binding for global variable ‘y’ replicateOutlier: no visible global function definition for ‘assay’ replicateOutlier: no visible binding for global variable ‘x’ replicateOutlier: no visible binding for global variable ‘y’ spectraSimilarity: no visible global function definition for ‘bpparam’ spectraSimilarity: no visible binding for global variable ‘timepoints’ spectraSimilarity: no visible binding for global variable ‘Sequence’ spectraSimilarity: no visible global function definition for ‘bplapply’ spectraSimilarity: no visible global function definition for ‘spectraData’ spectraSimilarity: no visible binding for global variable ‘Charge’ spectraSimilarity: no visible binding for global variable ‘DeutTime’ Undefined global functions or variables: Charge Deut.Time DeutTime Experiment IMS_shift Protein.State RT_shift Sequence assay bplapply bpparam brewer.pal outlier peptide pheatmap rowData rowMedians spectraData timepoints x y z * 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 ... 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 ‘/Users/biocbuild/bbs-3.21-bioc/meat/hdxmsqc.Rcheck/00check.log’ for details.
hdxmsqc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL hdxmsqc ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘hdxmsqc’ ... ** 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 (hdxmsqc)
hdxmsqc.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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. > # The setting of R_TESTS exists to work around an R bug. See > # https://github.com/hadley/testthat/issues/144 > # We should remove it when the issue is resolved. > Sys.setenv("R_TESTS" = "") > > library("testthat") > library("hdxmsqc") Loading required package: QFeatures Loading required package: MultiAssayExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors 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: IRanges Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Attaching package: 'QFeatures' The following object is masked from 'package:base': sweep Loading required package: Spectra Loading required package: BiocParallel > > test_check("hdxmsqc") [ FAIL 0 | WARN 1 | SKIP 0 | PASS 13 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 13 ] > > proc.time() user system elapsed 4.107 0.169 4.272
hdxmsqc.Rcheck/hdxmsqc-Ex.timings
name | user | system | elapsed | |
chargeCorrelationHdx | 0.520 | 0.008 | 0.533 | |
compatibleUptake | 0.025 | 0.001 | 0.027 | |
computeMassError | 0.016 | 0.001 | 0.017 | |
computeMonotoneStats | 0.029 | 0.001 | 0.031 | |
fourierIsotope | 0.001 | 0.000 | 0.001 | |
generateSpectra | 0.020 | 0.001 | 0.021 | |
hdx-distributions | 0 | 0 | 0 | |
imTimeOutlier | 0.137 | 0.011 | 0.149 | |
intensityOutliers | 0.035 | 0.004 | 0.039 | |
isotopicDistributionHDXfourier | 0.005 | 0.001 | 0.005 | |
plotImTimeOutlier | 0.476 | 0.010 | 0.485 | |
plotIntensityOutliers | 0.117 | 0.003 | 0.120 | |
plotMassError | 0.024 | 0.001 | 0.026 | |
plotMissing | 0.052 | 0.004 | 0.056 | |
plotMonotoneStat | 0.965 | 0.004 | 0.973 | |
plotrTimeOutliers | 0.399 | 0.007 | 0.432 | |
processHDE | 0.023 | 0.001 | 0.025 | |
rTimeOutliers | 0.065 | 0.002 | 0.068 | |
replicateCorrelation | 0.833 | 0.003 | 0.854 | |
replicateOutlier | 0.874 | 0.004 | 0.878 | |