Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 13:04:22 -0400 (Wed, 16 Oct 2019).
Package 461/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
doseR 1.0.0 ake.vastermark
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: doseR |
Version: 1.0.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:doseR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings doseR_1.0.0.tar.gz |
StartedAt: 2019-10-16 02:22:12 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 02:26:28 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 255.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: doseR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:doseR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings doseR_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/doseR.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘doseR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘doseR’ version ‘1.0.0’ * 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 ‘doseR’ 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 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 ‘1.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
doseR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL doseR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘doseR’ ... ** 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 (doseR)
doseR.Rcheck/tests/1.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (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(doseR) > > data(hmel.se) > f_se <- quantFilter(se, lo.bound = 0.4, hi.bound = 0.5) Filtering removed 12660 (92.96%) of 13619 total loci. > dm <- se.DM(f_se) > temp <- glSeq(dm, "-1 + replicate") > > RUnit::checkEqualsNumeric(round(temp@optinfo$val[4], 1), round(6.008, 1)) [1] TRUE > RUnit::checkEqualsNumeric(round(temp@optinfo$val[5], 1), round(5.840, 1)) [1] TRUE > > proc.time() user system elapsed 13.385 1.125 14.459
doseR.Rcheck/doseR-Ex.timings
name | user | system | elapsed | |
dafs | 3.736 | 0.318 | 4.058 | |
dafsFilter | 2.845 | 0.244 | 3.089 | |
generateStats | 0.169 | 0.012 | 0.181 | |
getLibsizes3 | 0.107 | 0.008 | 0.115 | |
glSeq | 3.854 | 0.164 | 4.019 | |
iqrxFilter | 0.120 | 0.004 | 0.124 | |
make_RPKM | 0.139 | 0.007 | 0.145 | |
plotExpr | 0.198 | 0.016 | 0.214 | |
plotMA.se | 0.126 | 0.010 | 0.137 | |
plotRatioBoxes | 0.093 | 0.005 | 0.099 | |
plotRatioDensity | 0.140 | 0.012 | 0.153 | |
quantFilter | 0.072 | 0.007 | 0.078 | |
se.DM | 0.379 | 0.020 | 0.399 | |
simpleFilter | 0.343 | 0.009 | 0.352 | |
test_diffs | 0.188 | 0.007 | 0.195 | |