Olivier Cuvier
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/HicAggR |
| git_branch: RELEASE_3_20 |
| git_last_commit: bf7aff9 |
| git_last_commit_date: 2024-10-29 11:31:14 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 952/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HicAggR 1.2.0 (landing page) Olivier Cuvier
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
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: 1.2.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:HicAggR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings HicAggR_1.2.0.tar.gz |
| StartedAt: 2024-12-20 01:00:31 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 01:15:00 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 868.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: HicAggR.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:HicAggR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings HicAggR_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/HicAggR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘HicAggR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HicAggR’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 ‘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 ... OK
* 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 34.717 0.182 34.902
plotMultiAPA 18.447 0.166 18.613
Aggregation 8.762 0.303 9.065
PrepareMtxList 7.431 0.014 7.446
ggAPA 6.776 0.005 6.782
PlotAPA 6.156 0.115 6.271
* 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
See
‘/home/biocbuild/bbs-3.20-bioc/meat/HicAggR.Rcheck/00check.log’
for details.
HicAggR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL HicAggR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘HicAggR’ ... ** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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 1.2.0
>
> 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
119.097 37.671 124.082
HicAggR.Rcheck/HicAggR-Ex.timings
| name | user | system | elapsed | |
| Aggregation | 8.762 | 0.303 | 9.065 | |
| BalanceHiC | 1.588 | 0.021 | 1.609 | |
| Beaf32_Peaks.gnr | 0.021 | 0.000 | 0.021 | |
| BinGRanges | 0.156 | 0.005 | 0.161 | |
| CutHiC | 0.381 | 0.007 | 0.388 | |
| ExtractSubmatrix | 4.555 | 0.057 | 4.612 | |
| FilterInteractions | 4.215 | 0.078 | 4.295 | |
| GenomicSystem | 0.002 | 0.001 | 0.004 | |
| GetInfo | 0.028 | 0.001 | 0.032 | |
| GetQuantif | 4.684 | 0.090 | 4.774 | |
| HiC_Ctrl.cmx_lst | 0.040 | 0.001 | 0.040 | |
| HiC_HS.cmx_lst | 0.04 | 0.00 | 0.04 | |
| Hue | 0.002 | 0.000 | 0.003 | |
| ICEnorm | 0.075 | 0.002 | 0.077 | |
| ImportHiC | 0.930 | 0.111 | 1.043 | |
| IndexFeatures | 1.183 | 0.002 | 1.185 | |
| JoinHiC | 0.073 | 0.000 | 0.073 | |
| MergeGRanges | 0.122 | 0.000 | 0.122 | |
| OrientateMatrix | 4.518 | 0.024 | 4.543 | |
| OverExpectedHiC | 0.443 | 0.007 | 0.450 | |
| PlotAPA | 6.156 | 0.115 | 6.271 | |
| PrepareMtxList | 7.431 | 0.014 | 7.446 | |
| QtlThreshold | 0.002 | 0.000 | 0.003 | |
| SearchPairs | 2.977 | 0.003 | 2.980 | |
| SeqEnds | 0.009 | 0.000 | 0.009 | |
| StrToGRanges | 0.068 | 0.001 | 0.069 | |
| SwitchMatrix | 0.532 | 0.001 | 0.533 | |
| TADs_Domains.gnr | 0.013 | 0.001 | 0.014 | |
| TSS_Peaks.gnr | 0.012 | 0.000 | 0.012 | |
| VCnorm | 0.050 | 0.001 | 0.051 | |
| YlGnBu | 0.000 | 0.000 | 0.001 | |
| YlOrRd | 0.000 | 0.001 | 0.001 | |
| compareToBackground | 34.717 | 0.182 | 34.902 | |
| ggAPA | 6.776 | 0.005 | 6.782 | |
| plotMultiAPA | 18.447 | 0.166 | 18.613 | |
| preparePlotgardener | 0.073 | 0.002 | 0.075 | |
| viridis | 0.000 | 0.000 | 0.001 | |