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This page was generated on 2024-06-11 14:42 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 1217/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metagenomeSeq 1.46.0  (landing page)
Joseph N. Paulson
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/metagenomeSeq
git_branch: RELEASE_3_19
git_last_commit: d0655e4
git_last_commit_date: 2024-04-30 10:31:19 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for metagenomeSeq on lconway

To the developers/maintainers of the metagenomeSeq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metagenomeSeq.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: metagenomeSeq
Version: 1.46.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metagenomeSeq_1.46.0.tar.gz
StartedAt: 2024-06-09 21:23:46 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 21:27:57 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 251.8 seconds
RetCode: 0
Status:   OK  
CheckDir: metagenomeSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metagenomeSeq_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/metagenomeSeq.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK
* this is package ‘metagenomeSeq’ version ‘1.46.0’
* 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 ‘metagenomeSeq’ 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
wrenchNorm  14.154  1.321  15.551
MRfulltable  1.135  0.034   5.948
* 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

metagenomeSeq.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘metagenomeSeq’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘MRihw’ with signature ‘"fitFeatureModelResults"’: no definition for class “fitFeatureModelResults”
in method for ‘MRihw’ with signature ‘"fitZigResults"’: no definition for class “fitZigResults”
** 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 (metagenomeSeq)

Tests output

metagenomeSeq.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
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.

> library("testthat")
> packageVersion("metagenomeSeq")
[1] '1.46.0'
> # As suggested for opt-out option on testing by users, 
> # recommended by CRAN: http://adv-r.had.co.nz/Testing.html
> # Previously, best practice was to put all test files in inst/tests 
> # and ensure that R CMD check ran them by putting the following code in tests/test-all.R:  
> # >library(testthat)
> # >library(yourpackage)
> # >test_package("yourpackage")
> # Now, recommended practice is to put your tests in tests/testthat, 
> # and ensure R CMD check runs them by putting the following code in tests/test-all.R:
> # >library(testthat)
> # >test_check("yourpackage")
> # The advantage of this new structure is that the user has control over whether or not tests are installed using the –install-tests parameter to 
> # R CMD install, or INSTALL_opts = c(“–install-tests”) argument to install.packages(). I’m not sure why you wouldn’t want to install the tests, 
> # but now you have the flexibility as requested by CRAN maintainers.
> test_check("metagenomeSeq")
Loading required package: metagenomeSeq
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: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: glmnet
Loading required package: Matrix
Loaded glmnet 4.1-8
Loading required package: RColorBrewer
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 15 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 15 ]
> 
> proc.time()
   user  system elapsed 
 92.629   7.388 100.582 

Example timings

metagenomeSeq.Rcheck/metagenomeSeq-Ex.timings

nameusersystemelapsed
MRcoefs1.2650.0631.337
MRcounts0.5500.0220.574
MRexperiment-class0.0000.0000.001
MRfulltable1.1350.0345.948
MRtable1.0340.0201.055
aggregateBySample0.1550.0110.166
aggregateByTaxonomy0.1870.0120.200
biom2MRexperiment0.2820.0160.298
calcNormFactors0.7100.0930.805
correctIndices0.1020.0100.112
correlationTest0.2400.0220.264
cumNorm0.4650.0940.562
cumNormMat0.4980.1000.601
cumNormStat0.6960.0550.753
cumNormStatFast0.3140.0270.341
expSummary0.0990.0090.108
exportMat1.3592.6714.051
exportStats0.4930.0250.522
extractMR1.0041.0942.106
filterData0.1370.0210.158
fitDO0.3950.0143.229
fitFeatureModel1.0390.0511.093
fitLogNormal1.6050.2211.863
fitMultipleTimeSeries1.8460.2062.058
fitPA0.4490.0323.138
fitSSTimeSeries0.4180.0310.451
fitTimeSeries0.4470.0580.507
fitZig1.7510.1991.957
libSize-set0.3440.0160.359
libSize0.3720.0150.389
loadBiom0.0470.0020.047
loadMeta0.0190.0020.021
loadMetaQ000
loadPhenoData0.0100.0010.012
makeLabels0.0000.0000.001
mergeMRexperiments1.5140.1671.695
newMRexperiment0.0360.0000.037
normFactors-set0.3730.0270.401
normFactors0.3000.0030.304
plotBubble0.2480.0202.965
plotClassTimeSeries1.0530.1911.254
plotCorr0.4810.0350.519
plotFeature0.1580.0120.170
plotGenus0.1340.0060.141
plotMRheatmap1.9500.0972.054
plotOTU0.1200.0040.123
plotOrd0.2530.0070.262
plotRare0.1530.0070.162
plotTimeSeries0.9490.1841.135
posteriorProbs1.7880.2422.033
returnAppropriateObj0.3520.1200.475
ssFit000
ssIntervalCandidate000
ssPerm000
ssPermAnalysis000
trapz0.0010.0010.000
ts2MRexperiment1.7400.1481.894
uniqueFeatures0.1260.0110.137
wrenchNorm14.154 1.32115.551
zigControl0.0000.0000.001