Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (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 952/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HicAggR 1.2.0  (landing page)
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)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for HicAggR on palomino8

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.

raw results


Summary

Package: HicAggR
Version: 1.2.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HicAggR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings HicAggR_1.2.0.tar.gz
StartedAt: 2024-12-20 02:24:41 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 02:33:53 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 552.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: HicAggR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HicAggR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings HicAggR_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/HicAggR.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 49.97   1.38   51.36
plotMultiAPA        24.53   0.35   24.90
Aggregation         12.70   0.30   13.17
PrepareMtxList      10.55   0.11   10.66
ggAPA                8.56   0.25    8.81
OrientateMatrix      7.99   0.25    8.25
PlotAPA              7.83   0.25    8.09
GetQuantif           6.21   0.10    6.32
ExtractSubmatrix     5.99   0.22    6.21
FilterInteractions   6.01   0.08    6.09
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/HicAggR.Rcheck/00check.log'
for details.


Installation output

HicAggR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL HicAggR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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)

Tests output

HicAggR.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
 150.68    1.90  152.75 

Example timings

HicAggR.Rcheck/HicAggR-Ex.timings

nameusersystemelapsed
Aggregation12.70 0.3013.17
BalanceHiC2.520.072.59
Beaf32_Peaks.gnr0.040.000.03
BinGRanges0.250.000.25
CutHiC0.540.020.56
ExtractSubmatrix5.990.226.21
FilterInteractions6.010.086.09
GenomicSystem000
GetInfo0.030.010.09
GetQuantif6.210.106.32
HiC_Ctrl.cmx_lst0.040.010.06
HiC_HS.cmx_lst0.080.000.08
Hue000
ICEnorm0.110.020.14
ImportHiC1.220.061.29
IndexFeatures1.670.061.74
JoinHiC0.090.030.13
MergeGRanges0.170.000.17
OrientateMatrix7.990.258.25
OverExpectedHiC0.450.020.47
PlotAPA7.830.258.09
PrepareMtxList10.55 0.1110.66
QtlThreshold000
SearchPairs3.930.084.02
SeqEnds0.020.000.01
StrToGRanges0.090.000.09
SwitchMatrix0.830.030.86
TADs_Domains.gnr0.020.010.04
TSS_Peaks.gnr0.010.020.03
VCnorm0.110.030.14
YlGnBu0.020.000.01
YlOrRd000
compareToBackground49.97 1.3851.36
ggAPA8.560.258.81
plotMultiAPA24.53 0.3524.90
preparePlotgardener0.120.000.12
viridis000