Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 507/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
dcanr 1.22.0 (landing page) Dharmesh D. Bhuva
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the dcanr package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dcanr.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: dcanr |
Version: 1.22.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dcanr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dcanr_1.22.0.tar.gz |
StartedAt: 2024-12-20 16:58:30 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 16:59:37 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 66.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: dcanr.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dcanr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dcanr_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/dcanr.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘dcanr/DESCRIPTION’ ... OK * this is package ‘dcanr’ version ‘1.22.0’ * 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 ‘dcanr’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ...Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]], : It is recommended to use ‘given’ instead of ‘middle’. 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 ftgi.score: no visible binding for global variable ‘i’ ftgi.score: no visible binding for global variable ‘j’ Undefined global functions or variables: i j * 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-3.20-bioc/meat/dcanr.Rcheck/00check.log’ for details.
dcanr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL dcanr ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘dcanr’ ... ** using staged installation Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]], : It is recommended to use ‘given’ instead of ‘middle’. Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]], : It is recommended to use ‘given’ instead of ‘middle’. ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘dcScore’ with signature ‘"Matrix","ANY","ANY"’: no definition for class “Matrix” in method for ‘dcScore’ with signature ‘"ExpressionSet","ANY","ANY"’: no definition for class “ExpressionSet” in method for ‘dcScore’ with signature ‘"SummarizedExperiment","ANY","ANY"’: no definition for class “SummarizedExperiment” in method for ‘dcScore’ with signature ‘"DGEList","ANY","ANY"’: no definition for class “DGEList” ** 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 (dcanr)
dcanr.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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. > library(testthat) > library(dcanr) > > test_check("dcanr") Begin Phase I (Initial E-Step) ... Begin Phase II (M2-Step) ... Begin Phase III ([E M1] Cycle) ... Iteration: 1 Iteration: 2 One-Stepper Time: 0.00900000000000034 Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287 Estimating optimal shrinkage intensity lambda (correlation matrix): 1 Estimate (local) false discovery rates (partial correlations): Estimate (local) false discovery rates (partial correlations): Begin Phase I (Initial E-Step) ... Begin Phase II (M2-Step) ... Begin Phase III ([E M1] Cycle) ... Iteration: 1 Iteration: 2 One-Stepper Time: 0.00699999999999967 Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287 Estimating optimal shrinkage intensity lambda (correlation matrix): 1 Estimate (local) false discovery rates (partial correlations): Estimate (local) false discovery rates (partial correlations): Begin Phase I (Initial E-Step) ... Begin Phase II (M2-Step) ... Begin Phase III ([E M1] Cycle) ... Iteration: 1 Iteration: 2 One-Stepper Time: 0.00600000000000023 Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287 Estimating optimal shrinkage intensity lambda (correlation matrix): 1 Estimate (local) false discovery rates (partial correlations): Estimate (local) false discovery rates (partial correlations): Begin Phase I (Initial E-Step) ... Begin Phase II (M2-Step) ... Begin Phase III ([E M1] Cycle) ... Iteration: 1 Iteration: 2 One-Stepper Time: 0.0069999999999979 Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287 Estimating optimal shrinkage intensity lambda (correlation matrix): 1 Estimate (local) false discovery rates (partial correlations): Estimate (local) false discovery rates (partial correlations): Begin Phase I (Initial E-Step) ... Begin Phase II (M2-Step) ... Begin Phase III ([E M1] Cycle) ... Iteration: 1 Iteration: 2 One-Stepper Time: 0.00700000000000145 Begin Phase I (Initial E-Step) ... Begin Phase II (M2-Step) ... Begin Phase III ([E M1] Cycle) ... Iteration: 1 Iteration: 2 One-Stepper Time: 0.00700000000000145 Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287 Estimating optimal shrinkage intensity lambda (correlation matrix): 1 Estimate (local) false discovery rates (partial correlations): Estimate (local) false discovery rates (partial correlations): Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287 Estimating optimal shrinkage intensity lambda (correlation matrix): 1 Estimate (local) false discovery rates (partial correlations): Estimate (local) false discovery rates (partial correlations): Begin Phase I (Initial E-Step) ... Begin Phase II (M2-Step) ... Begin Phase III ([E M1] Cycle) ... Iteration: 1 Iteration: 2 One-Stepper Time: 0.00600000000000023 Begin Phase I (Initial E-Step) ... Begin Phase II (M2-Step) ... Begin Phase III ([E M1] Cycle) ... Iteration: 1 Iteration: 2 One-Stepper Time: 0.00600000000000023 [ FAIL 0 | WARN 316 | SKIP 0 | PASS 172 ] [ FAIL 0 | WARN 316 | SKIP 0 | PASS 172 ] > > proc.time() user system elapsed 19.278 0.883 20.178
dcanr.Rcheck/dcanr-Ex.timings
name | user | system | elapsed | |
cor.pairs | 0.002 | 0.000 | 0.002 | |
dcAdjust | 0.010 | 0.001 | 0.010 | |
dcEvaluate | 1.947 | 0.093 | 2.040 | |
dcMethods | 0.000 | 0.001 | 0.001 | |
dcNetwork | 0.096 | 0.004 | 0.100 | |
dcPipeline | 1.226 | 0.038 | 1.263 | |
dcScore | 0.002 | 0.000 | 0.002 | |
dcTest | 1.184 | 0.011 | 1.195 | |
dcZscore | 0.067 | 0.002 | 0.069 | |
getSimData | 0.146 | 0.008 | 0.153 | |
mi.ap | 0.110 | 0.001 | 0.110 | |
perfMethods | 0.000 | 0.000 | 0.001 | |
performanceMeasure | 0.001 | 0.000 | 0.001 | |
plotSimNetwork | 0.276 | 0.015 | 0.291 | |