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This page was generated on 2024-12-23 12:07 -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 502/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DaMiRseq 2.18.0  (landing page)
Mattia Chiesa
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/DaMiRseq
git_branch: RELEASE_3_20
git_last_commit: 753fc77
git_last_commit_date: 2024-10-29 10:18:00 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 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
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for DaMiRseq on kjohnson1

To the developers/maintainers of the DaMiRseq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DaMiRseq.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: DaMiRseq
Version: 2.18.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DaMiRseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DaMiRseq_2.18.0.tar.gz
StartedAt: 2024-12-20 16:54:16 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 17:01:38 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 441.6 seconds
RetCode: 0
Status:   OK  
CheckDir: DaMiRseq.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DaMiRseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DaMiRseq_2.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/DaMiRseq.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DaMiRseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DaMiRseq’ version ‘2.18.0’
* 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 ‘DaMiRseq’ 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 ... NOTE
DaMiR.Clustplot: warning in pheatmap(count_data,
  clustering_distance_rows = d_r, clustering_distance_cols = d_c, scale
  = "row", col = colors, annotation_col = df): partial argument match
  of 'col' to 'color'
DaMiR.Allplot: no visible binding for global variable ‘X1’
DaMiR.Allplot: no visible binding for global variable ‘X2’
DaMiR.Allplot: no visible binding for global variable ‘PC1’
DaMiR.Allplot: no visible binding for global variable ‘PC2’
DaMiR.Allplot: no visible binding for global variable ‘value’
DaMiR.Allplot: no visible binding for global variable ‘variable’
DaMiR.EnsembleLearning2cl: no visible binding for global variable
  ‘Classifiers’
DaMiR.EnsembleLearning2cl: no visible binding for global variable
  ‘Accuracy’
DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘MCC’
DaMiR.EnsembleLearning2cl: no visible binding for global variable
  ‘Specificity’
DaMiR.EnsembleLearning2cl: no visible binding for global variable
  ‘Sensitivity’
DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘PPV’
DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘NPV’
DaMiR.EnsembleLearning2cl: no visible global function definition for
  ‘colSds’
DaMiR.EnsembleLearningNcl: no visible binding for global variable
  ‘Classifiers’
DaMiR.EnsembleLearningNcl: no visible binding for global variable
  ‘Accuracy’
DaMiR.EnsembleLearningNcl: no visible global function definition for
  ‘colSds’
DaMiR.MDSplot: no visible binding for global variable ‘X1’
DaMiR.MDSplot: no visible binding for global variable ‘X2’
DaMiR.ModelSelect: no visible binding for global variable ‘Metrics’
DaMiR.ModelSelect: no visible binding for global variable
  ‘N.predictors’
DaMiR.ModelSelect: no visible binding for global variable ‘Counts’
DaMiR.iTSadjust: no visible binding for global variable ‘value’
DaMiR.iTSadjust: no visible binding for global variable ‘variable’
DaMiR.iTSnorm: no visible binding for global variable ‘value’
DaMiR.iTSnorm: no visible binding for global variable ‘variable’
Undefined global functions or variables:
  Accuracy Classifiers Counts MCC Metrics N.predictors NPV PC1 PC2 PPV
  Sensitivity Specificity X1 X2 colSds value variable
* 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 LazyData ... 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
DaMiR.Allplot 5.084  0.148   5.231
* 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/DaMiRseq.Rcheck/00check.log’
for details.


Installation output

DaMiRseq.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘DaMiRseq’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (DaMiRseq)

Tests output

DaMiRseq.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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.

> library(testthat)
> library(DaMiRseq)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

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


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: ggplot2
> 
> test_check("DaMiRseq")
10 Predictors have been selected for classification 
3 Predictors have been selected for classification 
100 Highly correlated features have been discarded for classification. 
 0 Features remained. 
100 Highly correlated features have been discarded for classification. 
 0 Features remained. 
Your dataset has: 
100 Features; 
11 Samples, divided in:  
3 variables: a b class ; 
 'class' included. 
Your dataset has: 
100 Features; 
11 Samples, divided in:  
3 variables: a b class ; 
 'class' included. 
0 Features have been filtered out by espression. 100 Features remained. 
0 'Hypervariant' Features have been filtered out. 100 Features remained. 
Performing Normalization by 'vst' with dispersion parameter:  parametric 
0 Samples have been excluded by averaged Sample-per-Sample correlation. 
 40 Samples remained. 
The number of SVs identified, which explain 95 % of Variance, is: 4 
All the sv have been used to adjust the dataAll the sv have been used to adjust the data[ FAIL 0 | WARN 0 | SKIP 0 | PASS 106 ]
> 
> proc.time()
   user  system elapsed 
 27.694   1.166  28.486 

Example timings

DaMiRseq.Rcheck/DaMiRseq-Ex.timings

nameusersystemelapsed
DaMiR.Allplot5.0840.1485.231
DaMiR.Clustplot0.2380.0140.253
DaMiR.EnsL_Predict0.0020.0050.006
DaMiR.EnsL_Test0.0020.0040.006
DaMiR.EnsL_Train0.0020.0040.006
DaMiR.EnsembleLearning0.0010.0040.006
DaMiR.EnsembleLearning2cl0.0020.0050.006
DaMiR.EnsembleLearningNcl0.0020.0050.007
DaMiR.FBest0.0100.0050.015
DaMiR.FReduct0.0230.0040.027
DaMiR.FSelect0.4110.0300.443
DaMiR.FSort0.3560.0100.365
DaMiR.MDSplot0.1600.0060.167
DaMiR.ModelSelect0.0000.0000.001
DaMiR.SV0.6240.0270.652
DaMiR.SVadjust0.1080.0110.118
DaMiR.corrplot0.0030.0040.007
DaMiR.goldenDice0.0020.0000.002
DaMiR.iTSadjust0.0010.0020.003
DaMiR.iTSnorm0.0010.0030.004
DaMiR.makeSE0.0230.0020.025
DaMiR.normalization1.4860.0181.505
DaMiR.sampleFilt0.1640.0070.170
DaMiR.transpose0.0510.0080.059