| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:33 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 HiCExperiment package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiCExperiment.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 914/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HiCExperiment 1.1.0 (landing page) Jacques Serizay
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: HiCExperiment |
| Version: 1.1.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:HiCExperiment.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings HiCExperiment_1.1.0.tar.gz |
| StartedAt: 2023-05-09 18:27:23 -0000 (Tue, 09 May 2023) |
| EndedAt: 2023-05-09 18:42:49 -0000 (Tue, 09 May 2023) |
| EllapsedTime: 926.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: HiCExperiment.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:HiCExperiment.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings HiCExperiment_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/HiCExperiment.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘HiCExperiment/DESCRIPTION’ ... OK
* this is package ‘HiCExperiment’ version ‘1.1.0’
* 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 ‘HiCExperiment’ 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
.Call("_H5Fis_hdf5", ..., PACKAGE = "rhdf5")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
File ‘HiCExperiment/R/zzz.R’:
.onLoad calls:
packageStartupMessage("Consider using the `HiContacts` package to perform advanced genomic operations \non `HiCExperiment` objects.\n\nRead \"Orchestrating Hi-C analysis with Bioconductor\" online book to learn more:\nhttps://js2264.github.io/OHCA/")
See section ‘Good practice’ in '?.onAttach'.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
import-methods 33.231 2.417 41.328
HiCExperiment 22.035 1.041 30.812
AggrHiCExperiment 15.740 1.215 20.752
HicproFile-class 5.726 0.701 13.431
HicFile-class 3.983 0.455 10.303
CoolFile-class 3.713 0.511 9.386
data 3.362 0.147 5.819
as 3.028 0.292 5.616
* 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 ...
‘HiCExperiment.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/HiCExperiment.Rcheck/00check.log’
for details.
HiCExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL HiCExperiment ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’ * installing *source* package ‘HiCExperiment’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (HiCExperiment)
HiCExperiment.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
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(HiCExperiment)
Consider using the `HiContacts` package to perform advanced genomic operations
on `HiCExperiment` objects.
Read "Orchestrating Hi-C analysis with Bioconductor" online book to learn more:
https://js2264.github.io/OHCA/
>
> test_check("HiCExperiment")
snapshotDate(): 2023-04-24
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
snapshotDate(): 2023-04-24
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
snapshotDate(): 2023-04-24
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
snapshotDate(): 2023-04-24
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
snapshotDate(): 2023-04-24
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
snapshotDate(): 2023-04-24
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
resolutions(1): 1000
resolutions(5): 1000 2000 4000 8000 16000
resolutions(1): 1000
resolutions(5): 1000 2000 4000 8000 16000
CoolFile object
.mcool file: /home/biocbuild/.cache/R/ExperimentHub/17ef0f2b2003a8_7751
resolution: 1000
pairs file:
metadata(0):
snapshotDate(): 2023-04-24
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
`HiCExperiment` object with 8,757,906 contacts over 763 regions
-------
fileName: "/home/biocbuild/.cache/R/ExperimentHub/17ef0f6df24b3d_7752"
focus: "II"
resolutions(5): 1000 2000 4000 8000 16000
active resolution: 16000
interactions: 267709
scores(3): count balanced test
topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0) centromeres(16) test(0)
pairsFile: /home/biocbuild/.cache/R/ExperimentHub/17ef0f4fa018e2_7753
metadata(1): test
resolutions(5): 1000 2000 4000 8000 16000
resolutions(5): 1000 2000 4000 8000 16000
HicFile object
.hic file: /home/biocbuild/.cache/R/ExperimentHub/2a925533ae41c1_7836
resolution: 1000
pairs file:
metadata(0):
HicproFile object
HiC-Pro files:
$ matrix: /home/biocbuild/.cache/R/ExperimentHub/2a92555b1db381_7837
$ regions: /home/biocbuild/.cache/R/ExperimentHub/2a925557f50ede_7838
resolution: 1000
pairs file:
metadata(0):
Going through preflight checklist...
Parsing the entire contact matrice as a sparse matrix...
Modeling distance decay...
Filtering for contacts within provided targets...
`AggrHiCExperiment` object over 2 targets
-------
fileName: "/home/biocbuild/.cache/R/ExperimentHub/17ef0f6df24b3d_7752"
focus: 2 targets
resolutions(5): 1000 2000 4000 8000 16000
active resolution: 8000
interactions: 10201
scores(4): count balanced expected detrended
slices(4): count balanced expected detrended
topologicalFeatures: targets(2)
pairsFile: N/A
metadata(0):
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 241 ]
>
> proc.time()
user system elapsed
241.972 11.352 252.901
HiCExperiment.Rcheck/HiCExperiment-Ex.timings
| name | user | system | elapsed | |
| AggrHiCExperiment | 15.740 | 1.215 | 20.752 | |
| CoolFile-class | 3.713 | 0.511 | 9.386 | |
| HiCExperiment | 22.035 | 1.041 | 30.812 | |
| HicFile-class | 3.983 | 0.455 | 10.303 | |
| HicproFile-class | 5.726 | 0.701 | 13.431 | |
| PairsFile-class | 1.880 | 0.103 | 4.281 | |
| as | 3.028 | 0.292 | 5.616 | |
| data | 3.362 | 0.147 | 5.819 | |
| import-methods | 33.231 | 2.417 | 41.328 | |