Vivek Bhardwaj
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/icetea |
| Branch: RELEASE_3_9 |
| Last Commit: 833adaf |
| Last Changed Date: 2019-05-02 11:54:12 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:02:44 -0400 (Wed, 16 Oct 2019).
| Package 787/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| icetea 1.2.0 Vivek Bhardwaj
| 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: icetea |
| Version: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:icetea.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings icetea_1.2.0.tar.gz |
| StartedAt: 2019-10-16 03:44:41 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:53:04 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 502.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: icetea.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:icetea.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings icetea_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/icetea.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 ‘icetea/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘icetea’ version ‘1.2.0’ * 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 ‘icetea’ 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 ... NOTE diffQCplots: no visible binding for global variable ‘design’ detectTSS,CapSet :: no visible global function definition for ‘aggregate’ detectTSS,CapSet : : no visible binding for global variable ‘filter’ Undefined global functions or variables: aggregate design filter Consider adding importFrom("stats", "aggregate", "filter") 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed detectTSS 22.505 4.474 25.554 annotateTSS 14.336 0.921 15.665 getNormFactors 4.019 1.597 4.108 plotTSSprecision 4.790 0.751 5.488 * 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 NOTE See ‘/Users/biocbuild/bbs-3.9-bioc/meat/icetea.Rcheck/00check.log’ for details.
icetea.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL icetea ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘icetea’ ... ** 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 (icetea)
icetea.Rcheck/tests/testthat.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(testthat)
> library(icetea)
>
> test_check("icetea")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 17 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 0 ]
>
> proc.time()
user system elapsed
59.178 6.222 63.955
icetea.Rcheck/icetea-Ex.timings
| name | user | system | elapsed | |
| annotateTSS | 14.336 | 0.921 | 15.665 | |
| demultiplexFASTQ | 2.649 | 0.214 | 2.894 | |
| detectDiffTSS | 0.001 | 0.001 | 0.002 | |
| detectTSS | 22.505 | 4.474 | 25.554 | |
| exampleCSobject | 0.222 | 0.058 | 0.279 | |
| exportTSS | 0.285 | 0.055 | 0.339 | |
| filterDuplicates | 2.114 | 0.581 | 2.696 | |
| fitDiffTSS | 0.000 | 0.000 | 0.001 | |
| getGeneCounts | 3.454 | 0.272 | 3.726 | |
| getNormFactors | 4.019 | 1.597 | 4.108 | |
| mapCaps | 0.001 | 0.000 | 0.001 | |
| newCapSet | 0.144 | 0.041 | 0.186 | |
| plotReadStats | 0.940 | 0.154 | 1.094 | |
| plotTSSprecision | 4.790 | 0.751 | 5.488 | |
| sampleInfo | 0.113 | 0.006 | 0.119 | |
| splitBAM_byIndex | 0.253 | 0.021 | 0.275 | |
| splitBAM_byRepindex | 0.299 | 0.016 | 0.316 | |