Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:28 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the annotatr package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/annotatr.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. |
Package 69/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
annotatr 1.18.1 (landing page) Raymond G. Cavalcante
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: annotatr |
Version: 1.18.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:annotatr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings annotatr_1.18.1.tar.gz |
StartedAt: 2021-10-14 16:16:51 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 16:23:43 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 411.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: annotatr.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:annotatr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings annotatr_1.18.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/annotatr.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘annotatr/DESCRIPTION’ ... OK * this is package ‘annotatr’ version ‘1.18.1’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘annotatr’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘AnnotationHub::hubUrl’ by ‘rtracklayer::hubUrl’ when loading ‘annotatr’ See ‘/Users/biocbuild/bbs-3.13-bioc/meat/annotatr.Rcheck/00install.out’ for details. * 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 plot_coannotations: no visible binding for global variable ‘.’ plot_numerical_coannotations: no visible binding for global variable ‘.’ Undefined global functions or variables: . * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed build_ah_annots 7.412 0.426 9.522 build_annotations 6.037 0.144 6.188 * 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, 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/annotatr.Rcheck/00check.log’ for details.
annotatr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL annotatr ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘annotatr’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘AnnotationHub::hubUrl’ by ‘rtracklayer::hubUrl’ when loading ‘annotatr’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘AnnotationHub::hubUrl’ by ‘rtracklayer::hubUrl’ when loading ‘annotatr’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘AnnotationHub::hubUrl’ by ‘rtracklayer::hubUrl’ when loading ‘annotatr’ ** testing if installed package keeps a record of temporary installation path * DONE (annotatr)
annotatr.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" 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) > library(annotatr) Warning message: replacing previous import 'AnnotationHub::hubUrl' by 'rtracklayer::hubUrl' when loading 'annotatr' > > test_check("annotatr") [ FAIL 0 | WARN 6 | SKIP 0 | PASS 72 ] > > proc.time() user system elapsed 52.832 2.024 72.550
annotatr.Rcheck/annotatr-Ex.timings
name | user | system | elapsed | |
annotate_regions | 0.520 | 0.014 | 0.537 | |
annotatr_cache | 2.191 | 0.461 | 2.654 | |
build_ah_annots | 7.412 | 0.426 | 9.522 | |
build_annotations | 6.037 | 0.144 | 6.188 | |
builtin_annotations | 0.011 | 0.008 | 0.019 | |
builtin_genomes | 0.000 | 0.001 | 0.001 | |
plot_annotation | 4.347 | 0.161 | 4.517 | |
plot_categorical | 4.404 | 0.091 | 4.497 | |
plot_coannotations | 1.016 | 0.006 | 1.022 | |
plot_numerical | 0.571 | 0.007 | 0.578 | |
plot_numerical_coannotations | 0.764 | 0.011 | 0.776 | |
randomize_regions | 3.768 | 0.033 | 3.806 | |
read_annotations | 0.560 | 0.012 | 0.572 | |
read_regions | 0.484 | 0.016 | 0.501 | |
summarize_annotations | 3.953 | 0.033 | 3.987 | |
summarize_categorical | 0.560 | 0.014 | 0.574 | |
summarize_numerical | 0.679 | 0.018 | 0.698 | |