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This page was generated on 2023-10-20 09:38:10 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 1747/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNASeqPower 1.40.0  (landing page)
Terry M Therneau
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/RNASeqPower
git_branch: RELEASE_3_17
git_last_commit: 7ea1d77
git_last_commit_date: 2023-04-25 10:26:10 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for RNASeqPower on kjohnson2


To the developers/maintainers of the RNASeqPower package:
- 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.

raw results


Summary

Package: RNASeqPower
Version: 1.40.0
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_1.40.0.tar.gz
StartedAt: 2023-10-18 20:03:50 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 20:04:30 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 40.5 seconds
RetCode: 0
Status:   OK  
CheckDir: RNASeqPower.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/RNASeqPower.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNASeqPower/DESCRIPTION’ ... OK
* this is package ‘RNASeqPower’ version ‘1.40.0’
* 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 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-3.17-bioc-mac-arm64/meat/RNASeqPower.Rcheck/00check.log’
for details.



Installation output

RNASeqPower.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RNASeqPower
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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)

Tests output

RNASeqPower.Rcheck/tests/test1.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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   0.067   0.386 

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 

Example timings

RNASeqPower.Rcheck/RNASeqPower-Ex.timings

nameusersystemelapsed
rnapower0.0020.0010.004