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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1372/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MultiRNAflow 1.4.0  (landing page)
Rodolphe Loubaton
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/MultiRNAflow
git_branch: RELEASE_3_20
git_last_commit: 2b38b98
git_last_commit_date: 2024-10-29 11:23:15 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for MultiRNAflow on lconway

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.

raw results


Summary

Package: MultiRNAflow
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MultiRNAflow.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MultiRNAflow_1.4.0.tar.gz
StartedAt: 2024-11-20 00:28:34 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 00:41:21 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 766.8 seconds
RetCode: 0
Status:   OK  
CheckDir: MultiRNAflow.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MultiRNAflow.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MultiRNAflow_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MultiRNAflow.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘MultiRNAflow/DESCRIPTION’ ... OK
* this is package ‘MultiRNAflow’ version ‘1.4.0’
* 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 ‘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 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
DEplotHeatmaps         8.115  2.295  10.313
DEanalysisTimeAndGroup 8.315  1.794  10.034
PCAanalysis            8.771  0.715   9.461
PCAgraphics            4.725  0.446   5.169
DEanalysisTime         4.049  0.985   4.980
* 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: OK


Installation output

MultiRNAflow.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MultiRNAflow
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘MultiRNAflow’ ...
** 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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(MultiRNAflow)
Loading required package: Mfuzz
Loading required package: Biobase
Loading required package: BiocGenerics

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, 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: '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 
191.351  40.297 230.658 

Example timings

MultiRNAflow.Rcheck/MultiRNAflow-Ex.timings

nameusersystemelapsed
CharacterNumbers0.0010.0010.001
ColnamesToFactors0.0140.0050.019
DATAnormalization1.0530.2531.298
DATAplotBoxplotSamples0.6910.1670.844
DATAplotExpression1Gene0.6000.1450.739
DATAplotExpressionGenes1.0210.2201.223
DATAprepSE0.2020.0630.260
DEanalysisGlobal2.6930.7383.380
DEanalysisGroup2.6230.7733.349
DEanalysisSubData1.1380.1841.311
DEanalysisTime4.0490.9854.980
DEanalysisTimeAndGroup 8.315 1.79410.034
DEplotAlluvial0.5350.0590.590
DEplotBarplot0.2740.0310.303
DEplotBarplotFacetGrid0.7170.0800.796
DEplotBarplotTime0.2130.0220.234
DEplotHeatmaps 8.115 2.29510.313
DEplotVennBarplotGroup0.8680.0920.963
DEplotVennBarplotTime0.9450.0991.045
DEplotVolcanoMA3.6940.8334.493
DEresultGroup2.5080.7763.253
DEresultGroupPerTime3.7861.1404.889
GSEAQuickAnalysis0.2350.0730.304
GSEApreprocessing3.3370.9514.256
HCPCanalysis2.8480.5093.369
MFUZZanalysis1.9020.3572.251
MFUZZclustersNumber0.8920.2341.118
PCAanalysis8.7710.7159.461
PCAgraphics4.7250.4465.169
PCApreprocessing0.6230.1940.804
PCArealization0.6890.2080.885
RawCountsSimulation0.0370.0270.064
RawCounts_Antoszewski2022_MOUSEsub5000.0030.0020.005
RawCounts_Leong2014_FISSIONsub500wt0.0050.0010.006
RawCounts_Schleiss2021_CLLsub5000.0080.0020.011
RawCounts_Weger2021_MOUSEsub5000.0130.0020.014
Results_DEanalysis_sub5000.0810.0050.086
Transcript_HomoSapiens_Database0.1050.0040.111