Rodolphe Loubaton
| Snapshot Date: 2024-05-20 14:05:07 -0400 (Mon, 20 May 2024) |
| git_url: https://git.bioconductor.org/packages/MultiRNAflow |
| git_branch: devel |
| git_last_commit: 850819a |
| git_last_commit_date: 2024-04-30 11:51:10 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-22 11:37:04 -0400 (Wed, 22 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4665 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4400 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4427 |
| 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 1340/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MultiRNAflow 1.3.0 (landing page) Rodolphe Loubaton
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: MultiRNAflow |
| Version: 1.3.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MultiRNAflow.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MultiRNAflow_1.3.0.tar.gz |
| StartedAt: 2024-05-21 02:58:39 -0400 (Tue, 21 May 2024) |
| EndedAt: 2024-05-21 03:07:18 -0400 (Tue, 21 May 2024) |
| EllapsedTime: 519.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MultiRNAflow.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MultiRNAflow.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MultiRNAflow_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/MultiRNAflow.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MultiRNAflow/DESCRIPTION' ... OK
* this is package 'MultiRNAflow' version '1.3.0'
* 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 '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
PCAanalysis 11.38 0.11 11.50
DEplotHeatmaps 8.87 1.10 8.76
DEanalysisTimeAndGroup 8.28 0.18 8.49
PCAgraphics 5.33 0.06 5.39
* 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
MultiRNAflow.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL MultiRNAflow ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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)
MultiRNAflow.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
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(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, 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
194.18 5.64 199.12
MultiRNAflow.Rcheck/MultiRNAflow-Ex.timings
| name | user | system | elapsed | |
| CharacterNumbers | 0 | 0 | 0 | |
| ColnamesToFactors | 0.01 | 0.00 | 0.02 | |
| DATAnormalization | 1.28 | 0.06 | 1.34 | |
| DATAplotBoxplotSamples | 1.49 | 0.02 | 1.50 | |
| DATAplotExpression1Gene | 0.58 | 0.01 | 0.60 | |
| DATAplotExpressionGenes | 1.23 | 0.05 | 1.28 | |
| DATAprepSE | 0.22 | 0.00 | 0.22 | |
| DEanalysisGlobal | 2.52 | 0.09 | 2.60 | |
| DEanalysisGroup | 2.06 | 0.11 | 2.19 | |
| DEanalysisSubData | 0.51 | 0.04 | 0.55 | |
| DEanalysisTime | 3.96 | 0.14 | 4.09 | |
| DEanalysisTimeAndGroup | 8.28 | 0.18 | 8.49 | |
| DEplotAlluvial | 0.55 | 0.00 | 0.54 | |
| DEplotBarplot | 0.29 | 0.02 | 0.32 | |
| DEplotBarplotFacetGrid | 1.06 | 0.00 | 1.06 | |
| DEplotBarplotTime | 0.41 | 0.01 | 0.43 | |
| DEplotHeatmaps | 8.87 | 1.10 | 8.76 | |
| DEplotVennBarplotGroup | 1.08 | 0.12 | 1.21 | |
| DEplotVennBarplotTime | 1.37 | 0.03 | 1.41 | |
| DEplotVolcanoMA | 2.67 | 0.08 | 2.77 | |
| DEresultGroup | 2.44 | 0.05 | 2.48 | |
| DEresultGroupPerTime | 3.39 | 0.06 | 3.46 | |
| GSEAQuickAnalysis | 0.19 | 0.00 | 0.19 | |
| GSEApreprocessing | 2.83 | 0.10 | 2.92 | |
| HCPCanalysis | 2.70 | 0.08 | 2.78 | |
| MFUZZanalysis | 1.76 | 0.07 | 1.85 | |
| MFUZZclustersNumber | 0.97 | 0.02 | 0.98 | |
| PCAanalysis | 11.38 | 0.11 | 11.50 | |
| PCAgraphics | 5.33 | 0.06 | 5.39 | |
| PCApreprocessing | 0.64 | 0.03 | 0.67 | |
| PCArealization | 0.61 | 0.00 | 0.61 | |
| RawCountsSimulation | 0.04 | 0.05 | 0.10 | |
| RawCounts_Antoszewski2022_MOUSEsub500 | 0.02 | 0.00 | 0.01 | |
| RawCounts_Leong2014_FISSIONsub500wt | 0.01 | 0.01 | 0.03 | |
| RawCounts_Schleiss2021_CLLsub500 | 0.04 | 0.00 | 0.03 | |
| RawCounts_Weger2021_MOUSEsub500 | 0.03 | 0.00 | 0.04 | |
| Results_DEanalysis_sub500 | 0.11 | 0.02 | 0.12 | |
| Transcript_HomoSapiens_Database | 0.07 | 0.00 | 0.08 | |