Olivier Cuvier
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/HicAggR |
| git_branch: RELEASE_3_21 |
| git_last_commit: bcacfde |
| git_last_commit_date: 2025-04-15 13:35:49 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 | ||||
| Package 969/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HicAggR 1.4.0 (landing page) Olivier Cuvier
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the HicAggR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HicAggR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: HicAggR |
| Version: 1.4.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HicAggR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HicAggR_1.4.0.tar.gz |
| StartedAt: 2025-10-15 00:18:59 -0400 (Wed, 15 Oct 2025) |
| EndedAt: 2025-10-15 00:27:48 -0400 (Wed, 15 Oct 2025) |
| EllapsedTime: 529.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: HicAggR.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HicAggR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HicAggR_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/HicAggR.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HicAggR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HicAggR’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ‘HicAggR’ 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 code 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 whether 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 ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
ExtractSubmatrix.Rd: GRanges
ImportHiC.Rd: GRanges
IndexFeatures.Rd: GRanges
MergeGRanges.Rd: GRanges
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘ImportLoops’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
compareToBackground 42.772 0.835 43.982
plotMultiAPA 28.467 0.240 28.778
Aggregation 11.611 0.405 12.149
ggAPA 9.662 0.153 9.839
PrepareMtxList 9.414 0.169 9.605
PlotAPA 7.214 0.106 7.348
ExtractSubmatrix 5.227 0.076 5.353
OrientateMatrix 5.133 0.140 5.326
FilterInteractions 5.017 0.101 5.159
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 1 NOTE
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/HicAggR.Rcheck/00check.log’
for details.
HicAggR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HicAggR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘HicAggR’ ... ** this is package ‘HicAggR’ version ‘1.4.0’ ** 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 (HicAggR)
HicAggR.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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(HicAggR)
Package 'HicAggR' version 1.4.0
>
> test_check("HicAggR")
hicLst is already o/e.
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extracted : 23 Matrices on 2L_2L
extracted : 22 Matrices on 2R_2R
FILTERED extracted submat: 45
TOTAL extracted submat: 45
extracted : 23 Matrices on 2L_2L
extracted : 22 Matrices on 2R_2R
FILTERED extracted submat: 45
TOTAL extracted submat: 45
extracted : 1 Matrices on 2R_2R
FILTERED extracted submat: 1
TOTAL extracted submat: 1
24 matrices are oriented
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 24 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
141.718 40.340 151.032
HicAggR.Rcheck/HicAggR-Ex.timings
| name | user | system | elapsed | |
| Aggregation | 11.611 | 0.405 | 12.149 | |
| BalanceHiC | 1.980 | 0.080 | 2.079 | |
| Beaf32_Peaks.gnr | 0.024 | 0.003 | 0.027 | |
| BinGRanges | 0.193 | 0.007 | 0.203 | |
| CutHiC | 0.458 | 0.027 | 0.492 | |
| ExtractSubmatrix | 5.227 | 0.076 | 5.353 | |
| FilterInteractions | 5.017 | 0.101 | 5.159 | |
| GenomicSystem | 0.003 | 0.000 | 0.003 | |
| GetInfo | 0.037 | 0.010 | 0.183 | |
| GetQuantif | 4.463 | 0.057 | 4.524 | |
| HiC_Ctrl.cmx_lst | 0.053 | 0.006 | 0.059 | |
| HiC_HS.cmx_lst | 0.053 | 0.005 | 0.057 | |
| Hue | 0.003 | 0.000 | 0.003 | |
| ICEnorm | 0.120 | 0.009 | 0.128 | |
| ImportHiC | 0.442 | 0.053 | 0.497 | |
| IndexFeatures | 2.190 | 0.038 | 2.230 | |
| JoinHiC | 0.099 | 0.010 | 0.109 | |
| MergeGRanges | 0.143 | 0.008 | 0.151 | |
| OrientateMatrix | 5.133 | 0.140 | 5.326 | |
| OverExpectedHiC | 0.658 | 0.024 | 0.687 | |
| PlotAPA | 7.214 | 0.106 | 7.348 | |
| PrepareMtxList | 9.414 | 0.169 | 9.605 | |
| QtlThreshold | 0.003 | 0.001 | 0.004 | |
| SearchPairs | 3.478 | 0.060 | 3.562 | |
| SeqEnds | 0.011 | 0.001 | 0.011 | |
| StrToGRanges | 0.102 | 0.003 | 0.105 | |
| SwitchMatrix | 0.737 | 0.025 | 0.763 | |
| TADs_Domains.gnr | 0.014 | 0.003 | 0.018 | |
| TSS_Peaks.gnr | 0.014 | 0.003 | 0.017 | |
| VCnorm | 0.062 | 0.005 | 0.067 | |
| YlGnBu | 0.001 | 0.001 | 0.001 | |
| YlOrRd | 0.001 | 0.000 | 0.001 | |
| compareToBackground | 42.772 | 0.835 | 43.982 | |
| ggAPA | 9.662 | 0.153 | 9.839 | |
| plotMultiAPA | 28.467 | 0.240 | 28.778 | |
| preparePlotgardener | 0.098 | 0.009 | 0.108 | |
| viridis | 0.001 | 0.001 | 0.001 | |