| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-06-06 11:00:40 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 regioneReloaded package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/regioneReloaded.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 1654/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| regioneReloaded 1.3.0 (landing page) Roberto Malinverni
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: regioneReloaded |
| Version: 1.3.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:regioneReloaded.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings regioneReloaded_1.3.0.tar.gz |
| StartedAt: 2023-06-06 05:07:19 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 05:17:03 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 584.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: regioneReloaded.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:regioneReloaded.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings regioneReloaded_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/regioneReloaded.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘regioneReloaded/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘regioneReloaded’ version ‘1.3.0’
* 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 ‘regioneReloaded’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
crosswisePermTest 23.634 0.143 23.821
multiLocalZscore 9.920 0.020 9.957
multiLocalZScore-class 5.160 0.016 5.186
* 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 ...
‘regioneReloaded.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
regioneReloaded.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL regioneReloaded ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘regioneReloaded’ ... ** using staged installation ** R ** data ** 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 (regioneReloaded)
regioneReloaded.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(regioneReloaded)
Loading required package: regioneR
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
>
> test_check("regioneReloaded")
[1] "method selected for hclustering: average"
complete average single ward.D2 median centroid mcquitty
0.7497654 0.7857181 0.6514804 0.7363304 0.3459672 0.4561003 0.7516609
[1] "method selected for hclustering: complete"
complete average single ward.D2 median centroid mcquitty
0.9098230 0.8541174 0.7986368 0.8320493 0.8348816 0.8510903 0.8475492
[1] "method selected for hclustering: average"
complete average single ward.D2 median centroid mcquitty
0.8909663 0.8944326 0.7892161 0.8311822 0.8813696 0.8857083 0.8784679
[1] "resampleRegions function need that universe parameters in not NULL universe will created using all the regions present in Blist"
[1] "resampleRegions function need that universe parameters in not NULL universe will created using all the regions present in Blist"
[1] "resampleRegions function need that universe parameters in not NULL universe will created using all the regions present in Blist"
[1] "resampleRegions function need that universe parameters in not NULL universe will created using all the regions present in Blist"
[1] "resampleRegions function need that universe parameters in not NULL universe will created using all the regions present in Blist"
[1] "resampleRegions function need that universe parameters in not NULL universe will created using all the regions present in Blist"
[1] "method selected for hclustering: average"
complete average single ward.D2 median centroid mcquitty
0.7515325 0.7716179 0.6542890 0.7136237 0.2223408 0.5618311 0.7245865
[1] "method selected for hclustering: average"
complete average single ward.D2 median centroid mcquitty
0.7497654 0.7857181 0.6514804 0.7363304 0.3459672 0.4561003 0.7516609
[1] "method selected for hclustering: complete"
complete average single ward.D2 median centroid mcquitty
0.9098230 0.8541174 0.7986368 0.8320493 0.8348816 0.8510903 0.8475492
[1] "method selected for hclustering: average"
complete average single ward.D2 median centroid mcquitty
0.8909663 0.8944326 0.7892161 0.8311822 0.8813696 0.8857083 0.8784679
[ FAIL 0 | WARN 132 | SKIP 6 | PASS 60 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (6)
[ FAIL 0 | WARN 132 | SKIP 6 | PASS 60 ]
>
> proc.time()
user system elapsed
248.231 21.734 169.444
regioneReloaded.Rcheck/regioneReloaded-Ex.timings
| name | user | system | elapsed | |
| chooseHclustMet | 0.009 | 0.000 | 0.009 | |
| createUniverse | 0.375 | 0.020 | 0.395 | |
| crosswisePermTest | 23.634 | 0.143 | 23.821 | |
| genoMatriXeR-class | 4.822 | 0.032 | 4.861 | |
| getHClust | 0.045 | 0.000 | 0.045 | |
| getMatrix | 0.077 | 0.014 | 0.091 | |
| getMultiEvaluation | 0.02 | 0.00 | 0.02 | |
| getParameters | 0.016 | 0.000 | 0.016 | |
| makeCrosswiseMatrix | 0.036 | 0.004 | 0.040 | |
| makeLZMatrix | 0.015 | 0.000 | 0.015 | |
| multiLocalZScore-class | 5.160 | 0.016 | 5.186 | |
| multiLocalZscore | 9.920 | 0.020 | 9.957 | |
| plotCrosswiseDimRed | 3.127 | 0.028 | 3.160 | |
| plotCrosswiseMatrix | 0.614 | 0.000 | 0.616 | |
| plotLocalZScoreMatrix | 0.015 | 0.000 | 0.014 | |
| plotSingleLZ | 0.617 | 0.020 | 0.639 | |
| plotSinglePT | 0.988 | 0.020 | 1.010 | |
| randomizeRegionsPerc | 0.394 | 0.004 | 0.398 | |
| similarRegionSet | 1.683 | 0.000 | 1.686 | |