Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-04 14:36:14 -0400 (Tue, 04 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
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 1743/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Rnits 1.39.0 (landing page) Dipen P. Sangurdekar
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
To the developers/maintainers of the Rnits package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rnits.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: Rnits |
Version: 1.39.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rnits.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rnits_1.39.0.tar.gz |
StartedAt: 2024-06-03 09:30:24 -0400 (Mon, 03 Jun 2024) |
EndedAt: 2024-06-03 09:33:10 -0400 (Mon, 03 Jun 2024) |
EllapsedTime: 166.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: Rnits.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rnits.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rnits_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rnits.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Rnits/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Rnits’ version ‘1.39.0’ * 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 ‘Rnits’ 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 build.Rnits: no visible global function definition for ‘median’ build.Rnits: no visible global function definition for ‘sd’ finds0: no visible global function definition for ‘rnorm’ finds0: no visible global function definition for ‘quantile’ finds0: no visible global function definition for ‘mad’ finds0 : <anonymous>: no visible global function definition for ‘sd’ modelfit: no visible global function definition for ‘hat’ ranknormalization: no visible binding for global variable ‘median’ ranknormalization: no visible global function definition for ‘smooth.spline’ ranknormalization: no visible global function definition for ‘predict’ ranknormalization: no visible global function definition for ‘par’ solvemat: no visible global function definition for ‘hat’ tsFit: no visible global function definition for ‘txtProgressBar’ tsFit: no visible global function definition for ‘setTxtProgressBar’ calculateGCV,Rnits: no visible global function definition for ‘glm’ calculateGCV,Rnits: no visible binding for global variable ‘gaussian’ fit,Rnits: no visible global function definition for ‘kmeans’ fit,Rnits : <anonymous>: no visible global function definition for ‘p.adjust’ fit,Rnits: no visible global function definition for ‘par’ fit,Rnits: no visible global function definition for ‘hist’ getCID,Rnits: no visible global function definition for ‘setNames’ getPval,Rnits: no visible global function definition for ‘setNames’ getStat,Rnits: no visible global function definition for ‘setNames’ plotResults,Rnits: no visible global function definition for ‘aes’ plotResults,Rnits: no visible binding for global variable ‘Time’ plotResults,Rnits: no visible binding for global variable ‘value’ plotResults,Rnits: no visible global function definition for ‘geom_point’ plotResults,Rnits: no visible binding for global variable ‘Sample’ plotResults,Rnits: no visible global function definition for ‘geom_smooth’ plotResults,Rnits: no visible global function definition for ‘ylab’ plotResults,Rnits: no visible global function definition for ‘theme_bw’ plotResults,Rnits: no visible global function definition for ‘theme’ plotResults,Rnits: no visible global function definition for ‘scale_color_brewer’ plotResults,Rnits: no visible global function definition for ‘facet_wrap’ plotResults,Rnits: no visible global function definition for ‘dev.off’ summary,Rnits: no visible global function definition for ‘hist’ timeAlign,Rnits: no visible global function definition for ‘quantile’ timeAlign,Rnits: no visible global function definition for ‘mvfft’ timeAlign,Rnits: no visible global function definition for ‘abline’ Undefined global functions or variables: Sample Time abline aes dev.off facet_wrap gaussian geom_point geom_smooth glm hat hist kmeans mad median mvfft p.adjust par predict quantile rnorm scale_color_brewer sd setNames setTxtProgressBar smooth.spline theme theme_bw txtProgressBar value ylab Consider adding importFrom("grDevices", "dev.off") importFrom("graphics", "abline", "hist", "par") importFrom("stats", "gaussian", "glm", "hat", "kmeans", "mad", "median", "mvfft", "p.adjust", "predict", "quantile", "rnorm", "sd", "setNames", "smooth.spline") importFrom("utils", "setTxtProgressBar", "txtProgressBar") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... NOTE Invalid package aliases in Rd file 'rnits.Rd': ‘rnits-package’ * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Documented arguments not in \usage in Rd file 'plotResults-methods.Rd': ‘...’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed calculateGCV-methods 10.405 0.24 12.947 * 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 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rnits.Rcheck/00check.log’ for details.
Rnits.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rnits ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘Rnits’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (Rnits)
Rnits.Rcheck/Rnits-Ex.timings
name | user | system | elapsed | |
build.Rnits | 0.862 | 0.083 | 1.075 | |
calculateGCV-methods | 10.405 | 0.240 | 12.947 | |
fit-methods | 0.463 | 0.021 | 0.596 | |
getCID-methods | 0.469 | 0.021 | 0.611 | |
getFitModel-methods | 0.476 | 0.022 | 0.620 | |
getLR-methods | 0.611 | 0.030 | 0.821 | |
getPval-methods | 0.453 | 0.020 | 0.579 | |
getStat-methods | 0.456 | 0.024 | 0.558 | |
plotResults-methods | 0.468 | 0.027 | 0.565 | |
summarizeProbes-methods | 0.461 | 0.021 | 0.575 | |
summary-methods | 0.460 | 0.022 | 0.580 | |
timeAlign-methods | 1.973 | 0.116 | 2.407 | |
topData-methods | 0.481 | 0.023 | 0.585 | |