Olivier Cuvier
| Snapshot Date: 2025-11-05 13:40 -0500 (Wed, 05 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/HicAggR |
| git_branch: devel |
| git_last_commit: 7e29b61 |
| git_last_commit_date: 2025-10-29 11:30:21 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-06 11:32 -0500 (Thu, 06 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4818 |
| 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 963/2323 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HicAggR 1.7.0 (landing page) Olivier Cuvier
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | 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: 1.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:HicAggR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings HicAggR_1.7.0.tar.gz |
| StartedAt: 2025-11-06 00:16:53 -0500 (Thu, 06 Nov 2025) |
| EndedAt: 2025-11-06 00:30:21 -0500 (Thu, 06 Nov 2025) |
| EllapsedTime: 808.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: HicAggR.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:HicAggR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings HicAggR_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/HicAggR.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘HicAggR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HicAggR’ version ‘1.7.0’
* 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 loading without being on the library search path ... 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 58.687 0.455 59.147
plotMultiAPA 25.325 0.040 25.372
Aggregation 13.794 0.263 14.057
PrepareMtxList 11.531 0.158 11.690
PlotAPA 9.778 0.387 10.168
ggAPA 9.638 0.175 9.816
OrientateMatrix 6.735 0.310 7.078
FilterInteractions 6.906 0.100 7.007
ExtractSubmatrix 6.207 0.051 6.263
GetQuantif 5.587 0.024 5.611
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/HicAggR.Rcheck/00check.log’
for details.
HicAggR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL HicAggR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘HicAggR’ ... ** this is package ‘HicAggR’ version ‘1.7.0’ ** 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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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 1.7.0
>
> 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
139.984 41.061 145.224
HicAggR.Rcheck/HicAggR-Ex.timings
| name | user | system | elapsed | |
| Aggregation | 13.794 | 0.263 | 14.057 | |
| BalanceHiC | 2.312 | 0.033 | 2.344 | |
| Beaf32_Peaks.gnr | 0.036 | 0.005 | 0.041 | |
| BinGRanges | 0.275 | 0.001 | 0.276 | |
| CutHiC | 0.525 | 0.003 | 0.528 | |
| ExtractSubmatrix | 6.207 | 0.051 | 6.263 | |
| FilterInteractions | 6.906 | 0.100 | 7.007 | |
| GenomicSystem | 0.005 | 0.000 | 0.005 | |
| GetInfo | 0.045 | 0.004 | 0.055 | |
| GetQuantif | 5.587 | 0.024 | 5.611 | |
| HiC_Ctrl.cmx_lst | 0.056 | 0.003 | 0.059 | |
| HiC_HS.cmx_lst | 0.056 | 0.001 | 0.058 | |
| Hue | 0.003 | 0.001 | 0.003 | |
| ICEnorm | 0.098 | 0.003 | 0.100 | |
| ImportHiC | 1.560 | 0.071 | 1.637 | |
| IndexFeatures | 1.659 | 0.024 | 1.683 | |
| JoinHiC | 0.123 | 0.009 | 0.132 | |
| MergeGRanges | 0.203 | 0.005 | 0.207 | |
| OrientateMatrix | 6.735 | 0.310 | 7.078 | |
| OverExpectedHiC | 0.868 | 0.026 | 0.895 | |
| PlotAPA | 9.778 | 0.387 | 10.168 | |
| PrepareMtxList | 11.531 | 0.158 | 11.690 | |
| QtlThreshold | 0.004 | 0.002 | 0.006 | |
| SearchPairs | 3.918 | 0.065 | 3.984 | |
| SeqEnds | 0.012 | 0.000 | 0.011 | |
| StrToGRanges | 0.091 | 0.000 | 0.091 | |
| SwitchMatrix | 0.759 | 0.013 | 0.773 | |
| TADs_Domains.gnr | 0.02 | 0.00 | 0.02 | |
| TSS_Peaks.gnr | 0.015 | 0.002 | 0.017 | |
| VCnorm | 0.059 | 0.006 | 0.064 | |
| YlGnBu | 0.000 | 0.000 | 0.001 | |
| YlOrRd | 0.000 | 0.001 | 0.001 | |
| compareToBackground | 58.687 | 0.455 | 59.147 | |
| ggAPA | 9.638 | 0.175 | 9.816 | |
| plotMultiAPA | 25.325 | 0.040 | 25.372 | |
| preparePlotgardener | 0.081 | 0.000 | 0.081 | |
| viridis | 0.000 | 0.000 | 0.001 | |