Raymond G. Cavalcante
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/chipenrich |
| Branch: RELEASE_3_10 |
| Last Commit: 38187ca |
| Last Changed Date: 2019-10-29 13:08:46 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:08:01 -0400 (Wed, 15 Apr 2020).
| Package 272/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| chipenrich 2.10.0 Raymond G. Cavalcante
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: chipenrich |
| Version: 2.10.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:chipenrich.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings chipenrich_2.10.0.tar.gz |
| StartedAt: 2020-04-15 01:51:22 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:59:39 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 497.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: chipenrich.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:chipenrich.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings chipenrich_2.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/chipenrich.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chipenrich/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chipenrich’ version ‘2.10.0’
* 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 ‘chipenrich’ 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
proxReg: no visible global function definition for ‘lm’
Undefined global functions or variables:
lm
Consider adding
importFrom("stats", "lm")
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
broadenrich 8.360 0.040 8.590
polyenrich 7.816 0.048 7.881
* 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
‘/home/biocbuild/bbs-3.10-bioc/meat/chipenrich.Rcheck/00check.log’
for details.
chipenrich.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL chipenrich ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘chipenrich’ ... ** 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 (chipenrich)
chipenrich.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(chipenrich)
>
> test_check("chipenrich")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 194 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
208.984 1.008 215.291
chipenrich.Rcheck/chipenrich-Ex.timings
| name | user | system | elapsed | |
| assign_peak_segments | 0.316 | 0.000 | 0.446 | |
| assign_peaks | 0.808 | 0.040 | 0.864 | |
| broadenrich | 8.36 | 0.04 | 8.59 | |
| calc_peak_gene_overlap | 0.316 | 0.000 | 0.316 | |
| chipenrich | 1.976 | 0.008 | 2.002 | |
| load_peaks | 0.068 | 0.000 | 0.068 | |
| num_peaks_per_gene | 0.736 | 0.004 | 0.743 | |
| peaks2genes | 0.728 | 0.004 | 0.732 | |
| plot_chipenrich_spline | 2.164 | 0.028 | 2.212 | |
| plot_dist_to_tss | 0.412 | 0.004 | 0.416 | |
| plot_gene_coverage | 1.312 | 0.004 | 1.318 | |
| plot_polyenrich_spline | 3.600 | 0.024 | 3.631 | |
| polyenrich | 7.816 | 0.048 | 7.881 | |
| proxReg | 0.704 | 0.012 | 0.719 | |
| read_bed | 0.364 | 0.000 | 0.377 | |
| supported_genesets | 0.008 | 0.000 | 0.009 | |
| supported_genomes | 0.004 | 0.000 | 0.003 | |
| supported_locusdefs | 0.008 | 0.004 | 0.009 | |
| supported_methods | 0.000 | 0.000 | 0.002 | |
| supported_read_lengths | 0.004 | 0.004 | 0.009 | |