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This page was generated on 2021-11-25 14:05:42 -0500 (Thu, 25 Nov 2021).

CHECK results for qsmooth on merida1

To the developers/maintainers of the qsmooth package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/qsmooth.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1491/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qsmooth 1.11.0  (landing page)
Stephanie C. Hicks
Snapshot Date: 2021-11-24 14:50:13 -0500 (Wed, 24 Nov 2021)
git_url: https://git.bioconductor.org/packages/qsmooth
git_branch: master
git_last_commit: 88ec22a
git_last_commit_date: 2021-10-26 12:50:25 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: qsmooth
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:qsmooth.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings qsmooth_1.11.0.tar.gz
StartedAt: 2021-11-25 06:51:45 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 06:56:51 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 305.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: qsmooth.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:qsmooth.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings qsmooth_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/qsmooth.Rcheck’
* using R Under development (unstable) (2021-11-01 r81125)
* 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 ‘1.11.0’
* 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 ... WARNING
Undocumented data sets:
  ‘gc’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/qsmooth.Rcheck/00check.log’
for details.



Installation output

qsmooth.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘qsmooth’ ...
** using staged installation
** R
** data
** 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 Under development (unstable) (2021-11-01 r81125) -- "Unsuffered Consequences"
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 🥇
> 
> 
> test_that("checking qsmoothGC normalized data", {
+   n_genes <- 1000
+   n_samples <- 10
+   set.seed(1234)
+   x <- matrix(rpois(n_genes*n_samples, lambda=12), n_genes, n_samples)
+   group_factor <- rep(c(1,2),each=5)
+   gc <- runif(n=n_genes, min=0.2, max=0.9)
+   ## one group should be same as qsmooth
+   qs_norm <- qsmooth(object = x, group_factor = group_factor)
+   qs_normGC <- qsmoothGC(object = x, 
+                          gc = gc, 
+                          group_factor = group_factor, 
+                          nGroups = 1,
+                          round = FALSE)
+   expect_equal(qsmoothData(qs_norm), qsmoothData(qs_normGC), tolerance = .001)
+ })
Test passed 🥇
> 
> proc.time()
   user  system elapsed 
 15.959   0.703  16.679 

Example timings

qsmooth.Rcheck/qsmooth-Ex.timings

nameusersystemelapsed
qsmooth-class0.6700.0030.675
qsmooth0.0080.0000.009
qsmoothData0.0140.0080.022
qsmoothGC0.3100.0020.314
qsmoothPlotWeights0.0130.0010.014
qsmoothWeights0.0080.0000.009
qstats0.0050.0000.005