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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RNASeqPower.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RNASeqPower_1.46.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/RNASeqPower.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘RNASeqPower/DESCRIPTION’ ... OK
* this is package ‘RNASeqPower’ version ‘1.46.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 loading without being on the library search path ... 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 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/RNASeqPower.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL RNASeqPower
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
  0.142   0.033   0.163 

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