| Back to Mac ARM64 build report for BioC 3.18 |
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This page was generated on 2024-04-18 11:32:14 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 1366/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MultiRNAflow 1.0.0 (landing page) Rodolphe Loubaton
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the MultiRNAflow package: - 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: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2024-04-17 20:55:51 -0400 (Wed, 17 Apr 2024) |
| EndedAt: 2024-04-17 21:02:51 -0400 (Wed, 17 Apr 2024) |
| EllapsedTime: 419.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MultiRNAflow.Rcheck |
| Warnings: 0 |
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###
### 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_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/MultiRNAflow.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MultiRNAflow/DESCRIPTION’ ... OK
* this is package ‘MultiRNAflow’ version ‘1.0.0’
* 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 R 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
DEanalysisTimeAndGroup 8.639 0.409 9.086
DEplotHeatmaps 7.161 0.443 7.614
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MultiRNAflow ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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)
MultiRNAflow.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
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, sort, 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")
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
[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 : Biological conditions only"
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."
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
converting counts to integer mode
0 genes excluded.
1 genes excluded.
0 genes excluded.
1 genes excluded.
0 genes excluded.
3 genes excluded.
0 genes excluded.
4 genes excluded.
0 genes excluded.
3 genes excluded.
0 genes excluded.
4 genes excluded.
0 genes excluded.
3 genes excluded.
0 genes excluded.
4 genes excluded.
0 genes excluded.
3 genes excluded.
0 genes excluded.
4 genes excluded.
converting counts to integer mode
converting counts to integer mode
converting counts to integer mode
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 197 ]
>
> proc.time()
user system elapsed
97.900 5.260 103.538
MultiRNAflow.Rcheck/MultiRNAflow-Ex.timings
| name | user | system | elapsed | |
| CharacterNumbers | 0.001 | 0.001 | 0.002 | |
| ColnamesToFactors | 0.018 | 0.002 | 0.019 | |
| DATAnormalization | 1.242 | 0.076 | 1.319 | |
| DATAplotBoxplotSamples | 0.708 | 0.039 | 0.747 | |
| DATAplotExpression1Gene | 0.831 | 0.055 | 0.888 | |
| DATAplotExpressionGenes | 1.958 | 0.076 | 2.040 | |
| DATAprepSE | 0.195 | 0.014 | 0.208 | |
| DEanalysisGlobal | 2.780 | 0.166 | 2.946 | |
| DEanalysisGroup | 2.335 | 0.150 | 2.493 | |
| DEanalysisSubData | 0.557 | 0.037 | 0.596 | |
| DEanalysisTime | 4.151 | 0.211 | 4.373 | |
| DEanalysisTimeAndGroup | 8.639 | 0.409 | 9.086 | |
| DEplotAlluvial | 0.567 | 0.016 | 0.584 | |
| DEplotBarplot | 0.295 | 0.009 | 0.308 | |
| DEplotBarplotFacetGrid | 0.760 | 0.021 | 0.782 | |
| DEplotBarplotTime | 0.274 | 0.007 | 0.282 | |
| DEplotHeatmaps | 7.161 | 0.443 | 7.614 | |
| DEplotVennBarplotGroup | 0.932 | 0.024 | 0.956 | |
| DEplotVennBarplotTime | 1.109 | 0.025 | 1.136 | |
| DEplotVolcanoMA | 3.745 | 0.181 | 3.931 | |
| DEresultGroup | 2.048 | 0.139 | 2.194 | |
| DEresultGroupPerTime | 3.153 | 0.202 | 3.360 | |
| GSEAQuickAnalysis | 0.220 | 0.016 | 0.235 | |
| GSEApreprocessing | 2.739 | 0.167 | 2.911 | |
| HCPCanalysis | 2.023 | 0.101 | 2.162 | |
| MFUZZanalysis | 0.867 | 0.056 | 0.924 | |
| MFUZZclustersNumber | 0.641 | 0.042 | 0.684 | |
| PCAanalysis | 1.755 | 0.076 | 1.838 | |
| PCAgraphics | 1.037 | 0.049 | 1.088 | |
| PCApreprocessing | 0.535 | 0.036 | 0.571 | |
| PCArealization | 0.561 | 0.038 | 0.598 | |
| RawCountsSimulation | 0.044 | 0.028 | 0.072 | |
| RawCounts_Antoszewski2022_MOUSEsub500 | 0.005 | 0.003 | 0.008 | |
| RawCounts_Leong2014_FISSIONsub500wt | 0.007 | 0.003 | 0.010 | |
| RawCounts_Schleiss2021_CLLsub500 | 0.014 | 0.003 | 0.018 | |
| RawCounts_Weger2021_MOUSEsub500 | 0.025 | 0.003 | 0.028 | |
| Results_DEanalysis_sub500 | 0.133 | 0.006 | 0.139 | |