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CHECK report for qsmooth on merida1

This page was generated on 2021-05-06 12:36:16 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the qsmooth package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1430/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qsmooth 1.6.0  (landing page)
Stephanie C. Hicks
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/qsmooth
Branch: RELEASE_3_12
Last Commit: 06aebf4
Last Changed Date: 2020-10-27 11:44:06 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: qsmooth
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:qsmooth.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings qsmooth_1.6.0.tar.gz
StartedAt: 2021-05-06 05:05:07 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:08:27 -0400 (Thu, 06 May 2021)
EllapsedTime: 200.0 seconds
RetCode: 0
Status:   OK  
CheckDir: qsmooth.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:qsmooth.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings qsmooth_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/qsmooth.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qsmooth/DESCRIPTION’ ... OK
* this is package ‘qsmooth’ version ‘1.6.0’
* package encoding: UTF-8
* 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 ‘qsmooth’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: OK


Installation output

qsmooth.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL qsmooth
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘qsmooth’ ...
** 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 (qsmooth)

Tests output

qsmooth.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(testthat)
> context("checking the qsmooth function")
> 
> library(qsmooth)
> 
> test_that("checking dimensions of qsmooth object", {
+   n_genes <- 1000
+   n_samples <- 10
+   set.seed(1234)
+   x <- matrix(rnorm(n_genes*n_samples), n_genes, n_samples)
+   group_factor <- rep(c(1,2),each=5)
+   qs_norm <- qsmooth(object = x, 
+                     group_factor = group_factor)
+   
+   expect_equal(length(qsmoothWeights(qs_norm)), n_genes)
+   expect_equal(nrow(qsmoothData(qs_norm)), n_genes)
+   expect_equal(ncol(qsmoothData(qs_norm)), n_samples)
+ })
Test passed 🥇
> 
> test_that("checking qsmooth normalized data", {
+   n_genes <- 1000
+   n_samples <- 10
+   set.seed(1234)
+   x <- matrix(rnorm(n_genes*n_samples), n_genes, n_samples)
+   group_factor <- rep(c(1,2),each=5)
+   qs_norm <- qsmooth(object = x, group_factor = group_factor)
+   expect_equal(qsmoothData(qs_norm)[1,1], -1.25856, tolerance = .0001)
+   expect_equal(qsmoothWeights(qs_norm)[1], 0.97495, tolerance = .0001)
+ })
Test passed 🥇
> 
> proc.time()
   user  system elapsed 
 10.139   0.470  10.596 

Example timings

qsmooth.Rcheck/qsmooth-Ex.timings

nameusersystemelapsed
qsmooth-class0.0110.0010.011
qsmooth0.0060.0000.006
qsmoothData0.0110.0160.027
qsmoothPlotWeights0.0090.0010.010
qsmoothWeights0.0080.0010.009
qstats0.0030.0000.004