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 12:06 -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: /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_1.2.0.tar.gz |
| StartedAt: 2024-12-20 04:32:48 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 04:49:47 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 1018.3 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/HicAggR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HicAggR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HicAggR’ version ‘1.2.0’
* 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 ‘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 ... 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 83.689 0.838 87.823
plotMultiAPA 35.760 0.261 37.711
Aggregation 21.070 0.482 23.395
ggAPA 18.450 0.171 18.891
PrepareMtxList 18.000 0.171 18.383
PlotAPA 15.707 0.132 16.035
ExtractSubmatrix 14.000 0.097 14.814
OrientateMatrix 13.724 0.118 13.954
GetQuantif 12.962 0.107 13.490
FilterInteractions 12.748 0.078 13.261
SearchPairs 9.503 0.062 9.691
* 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
See
‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/Resources/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-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 1.2.0
>
> 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
321.950 61.163 327.359
HicAggR.Rcheck/HicAggR-Ex.timings
| name | user | system | elapsed | |
| Aggregation | 21.070 | 0.482 | 23.395 | |
| BalanceHiC | 4.400 | 0.058 | 4.695 | |
| Beaf32_Peaks.gnr | 0.056 | 0.003 | 0.060 | |
| BinGRanges | 0.413 | 0.015 | 0.470 | |
| CutHiC | 1.007 | 0.040 | 1.111 | |
| ExtractSubmatrix | 14.000 | 0.097 | 14.814 | |
| FilterInteractions | 12.748 | 0.078 | 13.261 | |
| GenomicSystem | 0.008 | 0.001 | 0.009 | |
| GetInfo | 0.065 | 0.009 | 0.669 | |
| GetQuantif | 12.962 | 0.107 | 13.490 | |
| HiC_Ctrl.cmx_lst | 0.081 | 0.005 | 0.086 | |
| HiC_HS.cmx_lst | 0.080 | 0.004 | 0.084 | |
| Hue | 0.007 | 0.000 | 0.008 | |
| ICEnorm | 0.161 | 0.004 | 0.166 | |
| ImportHiC | 1.517 | 0.105 | 1.699 | |
| IndexFeatures | 3.230 | 0.033 | 3.380 | |
| JoinHiC | 0.157 | 0.010 | 0.168 | |
| MergeGRanges | 0.333 | 0.007 | 0.341 | |
| OrientateMatrix | 13.724 | 0.118 | 13.954 | |
| OverExpectedHiC | 1.006 | 0.019 | 1.028 | |
| PlotAPA | 15.707 | 0.132 | 16.035 | |
| PrepareMtxList | 18.000 | 0.171 | 18.383 | |
| QtlThreshold | 0.006 | 0.002 | 0.009 | |
| SearchPairs | 9.503 | 0.062 | 9.691 | |
| SeqEnds | 0.025 | 0.001 | 0.026 | |
| StrToGRanges | 0.189 | 0.002 | 0.192 | |
| SwitchMatrix | 1.270 | 0.015 | 1.293 | |
| TADs_Domains.gnr | 0.027 | 0.004 | 0.031 | |
| TSS_Peaks.gnr | 0.025 | 0.003 | 0.028 | |
| VCnorm | 0.091 | 0.004 | 0.098 | |
| YlGnBu | 0.002 | 0.000 | 0.002 | |
| YlOrRd | 0.001 | 0.001 | 0.002 | |
| compareToBackground | 83.689 | 0.838 | 87.823 | |
| ggAPA | 18.450 | 0.171 | 18.891 | |
| plotMultiAPA | 35.760 | 0.261 | 37.711 | |
| preparePlotgardener | 0.137 | 0.007 | 0.145 | |
| viridis | 0.002 | 0.000 | 0.003 | |