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 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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 1780/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RNASeqPower 1.46.0 (landing page) Terry M Therneau
| 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 RNASeqPower package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RNASeqPower.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: RNASeqPower |
Version: 1.46.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RNASeqPower.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RNASeqPower_1.46.0.tar.gz |
StartedAt: 2024-12-20 08:43:13 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 08:43:50 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 36.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RNASeqPower.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RNASeqPower.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RNASeqPower_1.46.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RNASeqPower.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘RNASeqPower/DESCRIPTION’ ... OK * this is package ‘RNASeqPower’ version ‘1.46.0’ * 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 ‘RNASeqPower’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 rnapower: no visible global function definition for ‘qnorm’ rnapower: no visible global function definition for ‘pnorm’ Undefined global functions or variables: pnorm qnorm Consider adding importFrom("stats", "pnorm", "qnorm") 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test1.R’ Comparing ‘test1.Rout’ to ‘test1.Rout.save’ ... OK 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/RNASeqPower.Rcheck/00check.log’ for details.
RNASeqPower.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RNASeqPower ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘RNASeqPower’ ... ** 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 (RNASeqPower)
RNASeqPower.Rcheck/tests/test1.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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(RNASeqPower) > > # Error message: "missing depth" > #rnapower(n=10, cv=.1, effect=2, alpha=.05, power=.9) > > rnapower(10, cv=.5, effect=c(1.5, 1.75, 2), alpha=.05, power=c(.8, .9)) 0.8 0.9 1.5 33.41941 44.73910 1.75 17.54389 23.48629 2 11.43549 15.30888 > rnapower(10, n=20 , effect=c(1.5, 1.75, 2), alpha=.05, power=c(.8, .9)) 0.8 0.9 1.5 0.3308461 0.2376188 1.75 0.5468084 0.4450239 2 0.7156322 0.5977048 > rnapower(10, n= c(10,20), cv=.5, alpha=.05, power=c(.8, .9)) 0.8 0.9 10 2.098515 2.357553 20 1.688986 1.833876 > rnapower(10, n= c(10,20), cv=.5, effect=1.5, power=c(.8, .9)) 0.8 0.9 10 0.4896329 0.8018431 20 0.1849454 0.3757519 > rnapower(10, n= c(10,20), cv=.5, effect=c(1.5,2), alpha=.05) 1.5 2 10 0.3345258 0.7453365 20 0.5821271 0.9595131 > > > # More formal tests: cv and n > t1 <- rnapower(15, n=20, effect=1.5, alpha=.05, power=.8) > t2 <- rnapower(15, effect=1.5, alpha=.05, power=.8, cv=t1) > all.equal(t2, 20) [1] TRUE > > > # effect and n > t3 <- rnapower(15, n=20, cv=.5, alpha=.05, power=.8) > t4 <- rnapower(15, cv=.5, alpha=.05, power=.8, effect=t3) > all.equal(t4, 20) [1] TRUE > > # power and n > t5 <- rnapower(15, n=20, effect=1.5, cv=.5, alpha=.05) > t6 <- rnapower(15, effect=1.5, cv=.5, alpha=.05, power=t5) > all.equal(t6, 20) [1] TRUE > > # alpha and n > t7 <- rnapower(15, n=20, effect=1.5, cv=.5, power=.8) > t8 <- rnapower(15, effect=1.5, cv=.5, power=.8, alpha=t7) > all.equal(t8, 20) [1] TRUE > > > proc.time() user system elapsed 0.369 0.123 0.466
RNASeqPower.Rcheck/tests/test1.Rout.save
R version 2.15.0 (2012-03-30) Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-unknown-linux-gnu (64-bit) 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(RNASeqPower) > > # Error message: "missing depth" > #rnapower(n=10, cv=.1, effect=2, alpha=.05, power=.9) > > rnapower(10, cv=.5, effect=c(1.5, 1.75, 2), alpha=.05, power=c(.8, .9)) 0.8 0.9 1.5 33.41941 44.73910 1.75 17.54389 23.48629 2 11.43549 15.30888 > rnapower(10, n=20 , effect=c(1.5, 1.75, 2), alpha=.05, power=c(.8, .9)) 0.8 0.9 1.5 0.3308461 0.2376188 1.75 0.5468084 0.4450239 2 0.7156322 0.5977048 > rnapower(10, n= c(10,20), cv=.5, alpha=.05, power=c(.8, .9)) 0.8 0.9 10 2.098515 2.357553 20 1.688986 1.833876 > rnapower(10, n= c(10,20), cv=.5, effect=1.5, power=c(.8, .9)) 0.8 0.9 10 0.4896329 0.8018431 20 0.1849454 0.3757519 > rnapower(10, n= c(10,20), cv=.5, effect=c(1.5,2), alpha=.05) 1.5 2 10 0.3345258 0.7453365 20 0.5821271 0.9595131 > > > # More formal tests: cv and n > t1 <- rnapower(15, n=20, effect=1.5, alpha=.05, power=.8) > t2 <- rnapower(15, effect=1.5, alpha=.05, power=.8, cv=t1) > all.equal(t2, 20) [1] TRUE > > > # effect and n > t3 <- rnapower(15, n=20, cv=.5, alpha=.05, power=.8) > t4 <- rnapower(15, cv=.5, alpha=.05, power=.8, effect=t3) > all.equal(t4, 20) [1] TRUE > > # power and n > t5 <- rnapower(15, n=20, effect=1.5, cv=.5, alpha=.05) > t6 <- rnapower(15, effect=1.5, cv=.5, alpha=.05, power=t5) > all.equal(t6, 20) [1] TRUE > > # alpha and n > t7 <- rnapower(15, n=20, effect=1.5, cv=.5, power=.8) > t8 <- rnapower(15, effect=1.5, cv=.5, power=.8, alpha=t7) > all.equal(t8, 20) [1] TRUE > > > proc.time() user system elapsed 0.220 0.051 0.297
RNASeqPower.Rcheck/RNASeqPower-Ex.timings
name | user | system | elapsed | |
rnapower | 0.003 | 0.002 | 0.006 | |