Stephanie C. Hicks
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/qsmooth |
| Branch: RELEASE_3_11 |
| Last Commit: f5ee169 |
| Last Changed Date: 2020-04-27 15:24:58 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:31 -0400 (Sat, 17 Oct 2020).
| 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 1394/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| qsmooth 1.4.0 Stephanie C. Hicks
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: qsmooth |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qsmooth.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings qsmooth_1.4.0.tar.gz |
| StartedAt: 2020-10-17 07:14:15 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 07:18:22 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 246.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: qsmooth.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qsmooth.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings qsmooth_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/qsmooth.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 'qsmooth/DESCRIPTION' ... OK * this is package 'qsmooth' version '1.4.0' * 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 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 * 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 ... 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 ... ** 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 'testthat.R' OK ** running tests for arch 'x64' ... 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
qsmooth.Rcheck/00install.out
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### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/qsmooth_1.4.0.tar.gz && rm -rf qsmooth.buildbin-libdir && mkdir qsmooth.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qsmooth.buildbin-libdir qsmooth_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL qsmooth_1.4.0.zip && rm qsmooth_1.4.0.tar.gz qsmooth_1.4.0.zip
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install for i386
* installing *source* package 'qsmooth' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'qsmooth'
finding HTML links ... done
qsmooth-class html
qsmooth html
qsmoothData html
qsmoothPlotWeights html
qsmoothWeights html
qstats html
** 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
install for x64
* installing *source* package 'qsmooth' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'qsmooth' as qsmooth_1.4.0.zip
* DONE (qsmooth)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'qsmooth' successfully unpacked and MD5 sums checked
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qsmooth.Rcheck/tests_i386/testthat.Rout
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(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_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)
+ })
>
> proc.time()
user system elapsed
8.23 0.68 8.90
|
qsmooth.Rcheck/tests_x64/testthat.Rout
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(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_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)
+ })
>
> proc.time()
user system elapsed
7.56 0.35 7.90
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qsmooth.Rcheck/examples_i386/qsmooth-Ex.timings
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qsmooth.Rcheck/examples_x64/qsmooth-Ex.timings
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