Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:44 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 1606/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
qmtools 1.9.0 (landing page) Jaehyun Joo
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the qmtools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/qmtools.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: qmtools |
Version: 1.9.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:qmtools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings qmtools_1.9.0.tar.gz |
StartedAt: 2024-08-26 22:40:20 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 22:44:07 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 227.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: qmtools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:qmtools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings qmtools_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/qmtools.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-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 Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘qmtools/DESCRIPTION’ ... OK * this is package ‘qmtools’ version ‘1.9.0’ * 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 ‘qmtools’ 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 ... 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotMiss 6.575 0.069 6.673 plotCorr 5.213 0.123 5.369 * 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: OK
qmtools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL qmtools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘qmtools’ ... ** 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 (qmtools)
qmtools.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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. > library(testthat) > library(qmtools) 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 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, table, tapply, union, 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 > > test_check("qmtools") Contrast: WT - KO Contrast: WT - KO Imputing along margin 1 (features/rows). Imputing along margin 1 (features/rows). Imputing along margin 1 (features/rows). Imputing along margin 2 (samples/columns). Imputing along margin 2 (samples/columns). Imputing along margin 2 (samples/columns). Imputing along margin 2 (samples/columns). Imputing along margin 2 (samples/columns). Imputing along margin 2 (samples/columns). Imputing along margin 2 (samples/columns). [1] 325618.6 Imputing along margin 2 (samples/columns). [1] 325618.6 Imputing along margin 2 (samples/columns). [1] 325618.6 Imputing along margin 1 (features/rows). Missing value(s) in 'x'. 12% of values are missing. Please consider missing value imputation. Performing NIPALS PCA... Missing value(s) in 'x'. 12% of values are missing. Please consider missing value imputation. Performing NIPALS PCA... Calculating ICC... | | | 0% | |= | 2% | |=== | 4% | |==== | 6% | |====== | 8% | |======= | 10% | |========= | 12% | |========== | 14% | |=========== | 16% | |============= | 18% | |============== | 20% | |================ | 22% | |================= | 24% | |=================== | 27% | |==================== | 29% | |===================== | 31% | |======================= | 33% | |======================== | 35% | |========================== | 37% | |=========================== | 39% | |============================= | 41% | |============================== | 43% | |=============================== | 45% | |================================= | 47% | |================================== | 49% | |==================================== | 51% | |===================================== | 53% | |======================================= | 55% | |======================================== | 57% | |========================================= | 59% | |=========================================== | 61% | |============================================ | 63% | |============================================== | 65% | |=============================================== | 67% | |================================================= | 69% | |================================================== | 71% | |=================================================== | 73% | |===================================================== | 76% | |====================================================== | 78% | |======================================================== | 80% | |========================================================= | 82% | |=========================================================== | 84% | |============================================================ | 86% | |============================================================= | 88% | |=============================================================== | 90% | |================================================================ | 92% | |================================================================== | 94% | |=================================================================== | 96% | |===================================================================== | 98% | |======================================================================| 100% Calculating ICC... | | | 0% | |= | 2% | |=== | 4% | |==== | 6% | |====== | 8% | |======= | 10% | |========= | 12% | |========== | 14% | |=========== | 16% | |============= | 18% | |============== | 20% | |================ | 22% | |================= | 24% | |=================== | 27% | |==================== | 29% | |===================== | 31% | |======================= | 33% | |======================== | 35% | |========================== | 37% | |=========================== | 39% | |============================= | 41% | |============================== | 43% | |=============================== | 45% | |================================= | 47% | |================================== | 49% | |==================================== | 51% | |===================================== | 53% | |======================================= | 55% | |======================================== | 57% | |========================================= | 59% | |=========================================== | 61% | |============================================ | 63% | |============================================== | 65% | |=============================================== | 67% | |================================================= | 69% | |================================================== | 71% | |=================================================== | 73% | |===================================================== | 76% | |====================================================== | 78% | |======================================================== | 80% | |========================================================= | 82% | |=========================================================== | 84% | |============================================================ | 86% | |============================================================= | 88% | |=============================================================== | 90% | |================================================================ | 92% | |================================================================== | 94% | |=================================================================== | 96% | |===================================================================== | 98% | |======================================================================| 100% [ FAIL 0 | WARN 0 | SKIP 0 | PASS 200 ] > > proc.time() user system elapsed 20.554 1.000 21.696
qmtools.Rcheck/qmtools-Ex.timings
name | user | system | elapsed | |
clusterFeatures | 0.250 | 0.024 | 0.276 | |
compareSamples | 0.084 | 0.005 | 0.090 | |
faahko_se | 0.016 | 0.003 | 0.019 | |
imputeIntensity | 1.592 | 0.072 | 1.675 | |
imputeKNN | 0.314 | 0.016 | 0.332 | |
normalizeIntensity | 0.050 | 0.015 | 0.065 | |
normalizePQN | 0.034 | 0.013 | 0.048 | |
plotBox | 1.039 | 0.066 | 1.111 | |
plotCorr | 5.213 | 0.123 | 5.369 | |
plotMiss | 6.575 | 0.069 | 6.673 | |
plotRTgroup | 0.320 | 0.020 | 0.342 | |
plotReduced | 0.350 | 0.008 | 0.360 | |
reduceFeatures | 0.048 | 0.005 | 0.053 | |
reducePCA | 0.018 | 0.002 | 0.021 | |
reducePLSDA | 0.025 | 0.002 | 0.027 | |
reduceTSNE | 0.038 | 0.004 | 0.043 | |
removeBlankRatio | 0.005 | 0.002 | 0.008 | |
removeFeatures | 0.044 | 0.008 | 0.052 | |
removeICC | 0.603 | 0.023 | 0.629 | |
removeMiss | 0.027 | 0.021 | 0.048 | |
removeRSD | 0.003 | 0.005 | 0.008 | |
scaleCols | 0.026 | 0.015 | 0.041 | |
scaleRows | 0.029 | 0.015 | 0.044 | |