Terry M Therneau
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/RNASeqPower |
| Branch: RELEASE_3_8 |
| Last Commit: 0ddd41e |
| Last Changed Date: 2019-01-04 13:47:26 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:56:48 -0400 (Tue, 16 Apr 2019).
| Package 1331/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RNASeqPower 1.22.1 Terry M Therneau
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: RNASeqPower |
| Version: 1.22.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RNASeqPower.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RNASeqPower_1.22.1.tar.gz |
| StartedAt: 2019-04-16 02:27:04 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 02:27:22 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 17.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RNASeqPower.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RNASeqPower.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RNASeqPower_1.22.1.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/RNASeqPower.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNASeqPower/DESCRIPTION’ ... OK
* this is package ‘RNASeqPower’ version ‘1.22.1’
* 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 R 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 in ‘inst/doc’ ... 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-3.8-bioc/meat/RNASeqPower.Rcheck/00check.log’
for details.
RNASeqPower.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RNASeqPower ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘RNASeqPower’ ... ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘samplesize.Rnw’ ** testing if installed package can be loaded * DONE (RNASeqPower)
RNASeqPower.Rcheck/tests/test1.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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
0.254 0.063 0.288
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 | 0.002 | 0.000 | 0.003 | |