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This page was generated on 2025-08-04 12:12 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4536
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4517
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 1391/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MultiRNAflow 1.7.0  (landing page)
Rodolphe Loubaton
Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 2025)
git_url: https://git.bioconductor.org/packages/MultiRNAflow
git_branch: devel
git_last_commit: 0a56bc3
git_last_commit_date: 2025-04-15 13:20:02 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for MultiRNAflow on taishan

To the developers/maintainers of the MultiRNAflow package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MultiRNAflow.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: MultiRNAflow
Version: 1.7.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:MultiRNAflow.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MultiRNAflow_1.7.0.tar.gz
StartedAt: 2025-08-01 08:52:37 -0000 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 09:04:51 -0000 (Fri, 01 Aug 2025)
EllapsedTime: 734.2 seconds
RetCode: 0
Status:   OK  
CheckDir: MultiRNAflow.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:MultiRNAflow.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MultiRNAflow_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MultiRNAflow.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MultiRNAflow/DESCRIPTION’ ... OK
* this is package ‘MultiRNAflow’ version ‘1.7.0’
* 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 ‘MultiRNAflow’ 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 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:
  DEplotAlluvial.Rd: ggplot2
  DEplotBarplot.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* 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
PCAanalysis            14.659  0.719  15.426
DEanalysisTimeAndGroup 13.114  1.141  14.284
DEplotHeatmaps         11.875  1.599  13.700
PCAgraphics             7.773  0.446   8.242
DEanalysisTime          6.493  0.761   7.268
DEresultGroupPerTime    5.526  0.598   6.137
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/MultiRNAflow.Rcheck/00check.log’
for details.


Installation output

MultiRNAflow.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL MultiRNAflow
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘MultiRNAflow’ ...
** this is package ‘MultiRNAflow’ version ‘1.7.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (MultiRNAflow)

Tests output

MultiRNAflow.Rcheck/tests/testthat.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(MultiRNAflow)
Loading required package: Mfuzz
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: e1071

Attaching package: 'e1071'

The following object is masked from 'package:generics':

    interpolate


Attaching package: 'DynDoc'

The following object is masked from 'package:BiocGenerics':

    path

> 
> test_check("MultiRNAflow")
[1] "3 genes deleted."
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
[1] "3 genes deleted."
[1] "Preprocessing"
[1] "Differential expression step with DESeq2::DESeq()"
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
[1] "Case 1 analysis : Biological conditions only"
[1] "Preprocessing"
[1] "Differential expression step with DESeq2::DESeq()"
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
[1] "Case 2 analysis : Time only"
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
[1] "DE time analysis for each biological condition."
[1] "DE group analysis for each time measurement."
[1] "Combined time and group results."
[1] "DE time analysis for each biological condition."
[1] "DE group analysis for each time measurement."
[1] "Combined time and group results."
[1] "DE time analysis for each biological condition."
[1] "DE group analysis for each time measurement."
[1] "Combined time and group results."
[1] "DE time analysis for each biological condition."
[1] "DE group analysis for each time measurement."
[1] "Combined time and group results."
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
converting counts to integer mode
converting counts to integer mode
0 genes excluded.
0 genes excluded.
0 genes excluded.
0 genes excluded.
0 genes excluded.
0 genes excluded.
0 genes excluded.
0 genes excluded.
0 genes excluded.
0 genes excluded.
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 324 ]

[ FAIL 0 | WARN 11 | SKIP 0 | PASS 324 ]
> 
> proc.time()
   user  system elapsed 
279.309  28.478 318.324 

Example timings

MultiRNAflow.Rcheck/MultiRNAflow-Ex.timings

nameusersystemelapsed
CharacterNumbers0.0010.0000.001
ColnamesToFactors0.0190.0000.019
DATAnormalization2.2310.2372.509
DATAplotBoxplotSamples1.0860.2751.363
DATAplotExpression1Gene1.0450.1551.203
DATAplotExpressionGenes1.8260.1922.022
DATAprepSE0.3330.0480.381
DEanalysisGlobal3.9180.6114.536
DEanalysisGroup3.6080.4834.098
DEanalysisSubData0.8930.1121.006
DEanalysisTime6.4930.7617.268
DEanalysisTimeAndGroup13.114 1.14114.284
DEplotAlluvial0.9540.0801.036
DEplotBarplot0.4950.0360.532
DEplotBarplotFacetGrid1.3150.1281.447
DEplotBarplotTime0.4040.0130.428
DEplotHeatmaps11.875 1.59913.700
DEplotVennBarplotGroup2.0780.1762.261
DEplotVennBarplotTime1.5100.0711.584
DEplotVolcanoMA4.3090.5264.846
DEresultGroup3.3260.4563.789
DEresultGroupPerTime5.5260.5986.137
GSEAQuickAnalysis0.3060.0400.347
GSEApreprocessing4.3910.5714.973
HCPCanalysis4.3410.3474.698
MFUZZanalysis2.7610.2353.002
MFUZZclustersNumber1.2710.1201.394
PCAanalysis14.659 0.71915.426
PCAgraphics7.7730.4468.242
PCApreprocessing0.8490.1721.023
PCArealization0.9870.1511.141
RawCountsSimulation0.0540.0160.070
RawCounts_Antoszewski2022_MOUSEsub5000.0040.0000.003
RawCounts_Leong2014_FISSIONsub500wt0.0050.0000.006
RawCounts_Schleiss2021_CLLsub5000.010.000.01
RawCounts_Weger2021_MOUSEsub5000.0170.0000.018
Results_DEanalysis_sub5000.090.000.09
Transcript_HomoSapiens_Database0.0850.0000.084