Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 2070/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
statTarget 1.36.0 (landing page) Hemi Luan
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 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 | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the statTarget package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/statTarget.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: statTarget |
Version: 1.36.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:statTarget.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings statTarget_1.36.0.tar.gz |
StartedAt: 2024-11-20 03:08:16 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 03:12:39 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 263.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: statTarget.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:statTarget.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings statTarget_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/statTarget.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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘statTarget/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘statTarget’ version ‘1.36.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘statTarget’ 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 ComBat_qcFree: no visible global function definition for ‘model.matrix’ ComBat_qcFree: no visible binding for global variable ‘Beta.NA’ ComBat_qcFree: no visible global function definition for ‘dnorm’ ComBat_qcFree: no visible global function definition for ‘qqnorm’ ComBat_qcFree: no visible global function definition for ‘qqline’ oddRatio : logit_or: no visible global function definition for ‘relevel’ pvimPlot: no visible binding for global variable ‘GiniImportance’ pvimPlot: no visible binding for global variable ‘p.value’ shiftCor_dQC: no visible global function definition for ‘model.matrix’ statAnalysis: no visible global function definition for ‘read.delim2’ Undefined global functions or variables: Beta.NA GiniImportance dnorm model.matrix p.value qqline qqnorm read.delim2 relevel Consider adding importFrom("stats", "dnorm", "model.matrix", "qqline", "qqnorm", "relevel") importFrom("utils", "read.delim2") to your NAMESPACE file. * 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 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-3.20-bioc/meat/statTarget.Rcheck/00check.log’ for details.
statTarget.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL statTarget ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘statTarget’ ... ** using staged installation ** R ** 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 (statTarget)
statTarget.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(statTarget) > #library(statTarget) > datpath <- system.file("extdata",package = "statTarget") > samPeno <- paste(datpath,"MTBLS79_sampleList.csv", sep="/") > samFile <- paste(datpath,"MTBLS79.csv", sep="/") > file <- paste(datpath,"data_example_two_groups.csv", sep="/") > shiftCor(samPeno,samFile,Frule = 0.8,imputeM = "KNN") statTarget: Signal Correction Start... Time: Wed Nov 20 03:12:30 2024 * Step 1: Data File Checking Start..., Time: Wed Nov 20 03:12:30 2024 Data Link metaFile: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/statTarget/extdata/MTBLS79_sampleList.csv profileFile: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/statTarget/extdata/MTBLS79.csv 172 Meta Samples vs 172 Profile samples The Meta samples list (*NA, missing data from the Profile File) [1] "batch01_QC01" "batch01_QC02" "batch01_QC03" "batch01_C05" "batch01_S07" [6] "batch01_C10" "batch01_QC04" "batch01_S01" "batch01_C03" "batch01_S05" [11] "batch01_C07" "batch01_S06" "batch01_QC05" "batch01_C08" "batch01_C06" [16] "batch01_S02" "batch01_S09" "batch01_QC06" "batch01_S04" "batch01_C04" [21] "batch01_S10" "batch01_C09" "batch01_QC07" "batch02_C05" "batch02_S03" [26] "batch02_S07" "batch02_C01" "batch02_C10" "batch02_QC08" "batch02_S01" [31] "batch02_C03" "batch02_S05" "batch02_C07" "batch02_S06" "batch02_QC09" [36] "batch02_C08" "batch02_C06" "batch02_S02" "batch02_S09" "batch02_C02" [41] "batch02_QC10" "batch02_S04" "batch02_S08" "batch02_C04" "batch02_S10" [46] "batch02_C09" "batch02_QC11" "batch03_C05" "batch03_S03" "batch03_S07" [51] "batch03_C01" "batch03_C10" "batch03_QC12" "batch03_S01" "batch03_C03" [56] "batch03_S05" "batch03_C07" "batch03_S06" "batch03_QC13" "batch03_C08" [61] "batch03_C06" "batch03_S02" "batch03_S09" "batch03_C02" "batch03_QC14" [66] "batch03_S04" "batch03_S08" "batch03_C04" "batch03_S10" "batch03_C09" [71] "batch03_QC15" "batch04_C05" "batch04_S03" "batch04_S07" "batch04_C01" [76] "batch04_QC16" "batch04_S01" "batch04_S05" "batch04_C07" "batch04_S06" [81] "batch04_QC17" "batch04_C08" "batch04_C06" "batch04_S02" "batch04_S09" [86] "batch04_C02" "batch04_QC18" "batch04_S08" "batch04_C04" "batch04_S10" [91] "batch04_QC19" "batch05_QC20" "batch05_S03" "batch05_S07" "batch05_C01" [96] "batch05_C10" "batch05_QC21" "batch05_S01" "batch05_C03" "batch05_C07" [101] "batch05_QC22" "batch05_C06" "batch05_C02" "batch05_QC23" "batch05_S04" [106] "batch05_S08" "batch05_C04" "batch05_QC24" "batch06_QC25" "batch06_S03" [111] "batch06_C10" "batch06_QC26" "batch06_S01" "batch06_C03" "batch06_S05" [116] "batch06_C07" "batch06_S06" "batch06_QC27" "batch06_C08" "batch06_C06" [121] "batch06_S02" "batch06_C02" "batch06_QC28" "batch06_S04" "batch06_S08" [126] "batch06_C04" "batch06_C09" "batch06_QC29" "batch07_QC30" "batch07_C05" [131] "batch07_S03" "batch07_S07" "batch07_C01" "batch07_C10" "batch07_QC31" [136] "batch07_C03" "batch07_S05" "batch07_C07" "batch07_S06" "batch07_QC32" [141] "batch07_C08" "batch07_S02" "batch07_S09" "batch07_C02" "batch07_QC33" [146] "batch07_S04" "batch07_S08" "batch07_S10" "batch07_C09" "batch07_QC34" [151] "batch08_C05" "batch08_S03" "batch08_S07" "batch08_C01" "batch08_C10" [156] "batch08_QC36" "batch08_S01" "batch08_C03" "batch08_S05" "batch08_C07" [161] "batch08_S06" "batch08_QC37" "batch08_C08" "batch08_S02" "batch08_S09" [166] "batch08_QC38" "batch08_S04" "batch08_S08" "batch08_C04" "batch08_S10" [171] "batch08_C09" "batch08_QC39" Meta-information: Class No. 1 1 66 2 2 68 3 QC 38 Batch No. 1 1 91 2 2 17 3 3 20 4 4 44 Metabolic profile information: no. QC and samples 172 Metabolites 48 * Step 2: Evaluation of Missing Value... The number of missing value before QC based signal correction: 336 The number of filtered variables using the modified 80 % rule : 6 * Step 3: Imputation start... The imputation method was set at 'KNN' The number of missing value after imputation: 0 Imputation Finished! * Step 4: QC-based Signal Correction Start... Time: Wed Nov 20 03:12:30 2024 The Signal Correction method was set at QC-RFSC | | | 0% | |== | 2% | |=== | 5% | |===== | 7% | |======= | 10% | |========= | 12% | |========== | 15% | |============ | 17% | |============== | 20% | |=============== | 22% | |================= | 24% | |=================== | 27% | |==================== | 29% | |====================== | 32% | |======================== | 34% | |========================== | 37% | |=========================== | 39% | |============================= | 41% | |=============================== | 44% | |================================ | 46% | |================================== | 49% | |==================================== | 51% | |====================================== | 54% | |======================================= | 56% | |========================================= | 59% | |=========================================== | 61% | |============================================ | 63% | |============================================== | 66% | |================================================ | 68% | |================================================== | 71% | |=================================================== | 73% | |===================================================== | 76% | |======================================================= | 78% | |======================================================== | 80% | |========================================================== | 83% | |============================================================ | 85% | |============================================================= | 88% | |=============================================================== | 90% | |================================================================= | 93% | |=================================================================== | 95% | |==================================================================== | 98% | |======================================================================| 100% Calculation of CV distribution of raw peaks (QC)... CV<5% CV<10% CV<15% CV<20% CV<25% CV<30% CV<35% Batch_1 4.761905 50.00000 71.42857 78.57143 85.71429 92.85714 95.23810 Batch_2 21.428571 69.04762 80.95238 80.95238 92.85714 95.23810 95.23810 Batch_3 11.904762 45.23810 78.57143 83.33333 85.71429 92.85714 97.61905 Batch_4 7.142857 64.28571 78.57143 83.33333 92.85714 92.85714 95.23810 Total 0.000000 19.04762 38.09524 66.66667 69.04762 78.57143 80.95238 CV<40% CV<45% CV<50% CV<55% CV<60% CV<65% CV<70% CV<75% Batch_1 95.23810 97.61905 100.00000 100.00000 100.00000 100 100 100 Batch_2 95.23810 95.23810 97.61905 97.61905 97.61905 100 100 100 Batch_3 97.61905 100.00000 100.00000 100.00000 100.00000 100 100 100 Batch_4 100.00000 100.00000 100.00000 100.00000 100.00000 100 100 100 Total 80.95238 85.71429 88.09524 95.23810 100.00000 100 100 100 CV<80% CV<85% CV<90% CV<95% CV<100% Batch_1 100 100 100 100 100 Batch_2 100 100 100 100 100 Batch_3 100 100 100 100 100 Batch_4 100 100 100 100 100 Total 100 100 100 100 100 Calculation of CV distribution of corrected peaks (QC)... CV<5% CV<10% CV<15% CV<20% CV<25% CV<30% CV<35% Batch_1 45.23810 76.19048 85.71429 92.85714 95.2381 95.23810 100.00000 Batch_2 40.47619 78.57143 85.71429 92.85714 95.2381 95.23810 95.23810 Batch_3 11.90476 66.66667 80.95238 88.09524 95.2381 97.61905 97.61905 Batch_4 30.95238 73.80952 85.71429 97.61905 100.0000 100.00000 100.00000 Total 26.19048 73.80952 90.47619 95.23810 95.2381 97.61905 100.00000 CV<40% CV<45% CV<50% CV<55% CV<60% CV<65% CV<70% CV<75% CV<80% Batch_1 100.00000 100 100 100 100 100 100 100 100 Batch_2 97.61905 100 100 100 100 100 100 100 100 Batch_3 100.00000 100 100 100 100 100 100 100 100 Batch_4 100.00000 100 100 100 100 100 100 100 100 Total 100.00000 100 100 100 100 100 100 100 100 CV<85% CV<90% CV<95% CV<100% Batch_1 100 100 100 100 Batch_2 100 100 100 100 Batch_3 100 100 100 100 Batch_4 100 100 100 100 Total 100 100 100 100 * Step 5: Removal of the features (CV% > 30%) Wed Nov 20 03:12:32 2024 No. of removed features: 1 Feature name: 386.21715 Output Link: /Users/biocbuild/bbs-3.20-bioc/meat/statTarget.Rcheck/tests Correction Finished! Time: Wed Nov 20 03:12:32 2024 #################################### # Software Version: statTarget 2.0 + # # Email: hemi.luan@gmail.com # #################################### Warning message: In dir.create(dirout.w) : '/Users/biocbuild/bbs-3.20-bioc/meat/statTarget.Rcheck/tests/statTarget/shiftCor/RSDresult' already exists > > #test_check("statTarget") > > proc.time() user system elapsed 2.264 0.221 2.513
statTarget.Rcheck/statTarget-Ex.timings
name | user | system | elapsed | |
pvimPlot | 0.051 | 0.009 | 0.061 | |
rForest | 0.014 | 0.003 | 0.016 | |
shiftCor | 1.373 | 0.104 | 1.488 | |
shiftCor_dQC-open-paren-deprecated-close-paren | 0.095 | 0.013 | 0.109 | |
statAnalysis | 0.458 | 0.065 | 0.531 | |