| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:37 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the HiContacts package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiContacts.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 922/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HiContacts 1.1.3 (landing page) Jacques Serizay
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: HiContacts |
| Version: 1.1.3 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:HiContacts.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings HiContacts_1.1.3.tar.gz |
| StartedAt: 2023-04-12 06:48:14 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 07:04:39 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 985.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: HiContacts.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:HiContacts.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings HiContacts_1.1.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/HiContacts.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘HiContacts/DESCRIPTION’ ... OK
* this is package ‘HiContacts’ version ‘1.1.3’
* 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 ‘HiContacts’ 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 loading without being on the library search path ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
arithmetics 57.166 3.123 59.799
getCompartments 16.849 2.935 13.817
Contacts 18.325 0.847 20.001
plotMatrix 12.241 0.668 13.275
plotScalogram 11.858 0.980 16.463
plotPs 10.325 0.848 12.170
scalogram 7.869 0.572 8.774
getDiamondInsulation 5.771 2.480 6.508
cisTransRatio 4.976 0.048 5.343
* 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 ...
‘HiContacts.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
HiContacts.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL HiContacts ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘HiContacts’ ... ** 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 (HiContacts)
HiContacts.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 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.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(HiContacts)
Loading required package: HiCExperiment
Attaching package: 'HiContacts'
The following object is masked from 'package:base':
merge
>
> test_check("HiContacts")
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[ FAIL 0 | WARN 1 | SKIP 0 | PASS 51 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 51 ]
>
> proc.time()
user system elapsed
167.053 24.445 185.417
HiContacts.Rcheck/HiContacts-Ex.timings
| name | user | system | elapsed | |
| Contacts | 18.325 | 0.847 | 20.001 | |
| Ps | 4.315 | 0.104 | 4.744 | |
| arithmetics | 57.166 | 3.123 | 59.799 | |
| cisTransRatio | 4.976 | 0.048 | 5.343 | |
| getCompartments | 16.849 | 2.935 | 13.817 | |
| getDiamondInsulation | 5.771 | 2.480 | 6.508 | |
| palettes | 0.001 | 0.000 | 0.001 | |
| plot4C | 3.592 | 0.536 | 4.436 | |
| plotMatrix | 12.241 | 0.668 | 13.275 | |
| plotPs | 10.325 | 0.848 | 12.170 | |
| plotScalogram | 11.858 | 0.980 | 16.463 | |
| scalogram | 7.869 | 0.572 | 8.774 | |
| virtual4C | 3.062 | 0.220 | 3.645 | |