Multiple platform build/check report for BioC 3.11 - CHECK report for RNASeqPower on tokay2

Package: RNASeqPower

Version: 1.28.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RNASeqPower.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings RNASeqPower_1.28.0.tar.gz

StartedAt: 2020-10-17 07:41:30 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 07:42:16 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 45.7 seconds

RetCode: 0

Status: OK

CheckDir: RNASeqPower.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RNASeqPower.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings RNASeqPower_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/RNASeqPower.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RNASeqPower/DESCRIPTION' ... OK
* this is package 'RNASeqPower' version '1.28.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test1.R'
  Comparing 'test1.Rout' to 'test1.Rout.save' ... OK
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/RNASeqPower.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/RNASeqPower_1.28.0.tar.gz && rm -rf RNASeqPower.buildbin-libdir && mkdir RNASeqPower.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RNASeqPower.buildbin-libdir RNASeqPower_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL RNASeqPower_1.28.0.zip && rm RNASeqPower_1.28.0.tar.gz RNASeqPower_1.28.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  8164  100  8164    0     0   121k      0 --:--:-- --:--:-- --:--:--  135k

install for i386

* installing *source* package 'RNASeqPower' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RNASeqPower'
    finding HTML links ... done
    rnapower                                html  
** building package indices
** installing vignettes
   'samplesize.Rnw' 
** 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

install for x64

* installing *source* package 'RNASeqPower' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RNASeqPower' as RNASeqPower_1.28.0.zip
* DONE (RNASeqPower)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'RNASeqPower' successfully unpacked and MD5 sums checked


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


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


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
   0.32    0.01    0.32


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   0.28    0.03    0.29

name	user	system	elapsed
rnapower	0	0	0

name	user	system	elapsed
rnapower	0	0	0

CHECK report for RNASeqPower on tokay2

Summary

Command output

Installation output

Tests output

Example timings