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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 1183/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metagenomeSeq 1.47.0  (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: devel
git_last_commit: 7a5a260
git_last_commit_date: 2024-04-30 10:31:19 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 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 metagenomeSeq on palomino4

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: 1.47.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metagenomeSeq.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings metagenomeSeq_1.47.0.tar.gz
StartedAt: 2024-06-10 05:03:10 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 05:09:40 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 390.2 seconds
RetCode: 0
Status:   OK  
CheckDir: metagenomeSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metagenomeSeq.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings metagenomeSeq_1.47.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/metagenomeSeq.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 'metagenomeSeq/DESCRIPTION' ... OK
* this is package 'metagenomeSeq' version '1.47.0'
* 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 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  15.71   0.53   16.23
MRfulltable  1.07   0.12   11.92
fitDO        0.41   0.20    6.04
fitPA        0.35   0.11    6.00
plotBubble   0.23   0.09    6.05
* 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:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL metagenomeSeq
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 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.

> library("testthat")
> packageVersion("metagenomeSeq")
[1] '1.47.0'
> # 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 
  92.20   10.70  102.81 

Example timings

metagenomeSeq.Rcheck/metagenomeSeq-Ex.timings

nameusersystemelapsed
MRcoefs1.280.371.66
MRcounts0.530.130.65
MRexperiment-class000
MRfulltable 1.07 0.1211.92
MRtable0.900.141.05
aggregateBySample0.140.020.15
aggregateByTaxonomy0.140.010.16
biom2MRexperiment0.240.270.53
calcNormFactors0.800.090.89
correctIndices0.110.050.16
correlationTest0.260.050.31
cumNorm0.640.090.74
cumNormMat0.530.140.67
cumNormStat0.780.050.83
cumNormStatFast0.490.030.51
expSummary0.110.050.16
exportMat2.292.114.42
exportStats0.380.120.51
extractMR1.980.772.75
filterData0.220.030.25
fitDO0.410.206.04
fitFeatureModel1.230.271.50
fitLogNormal1.820.342.15
fitMultipleTimeSeries1.820.332.16
fitPA0.350.116.00
fitSSTimeSeries0.360.140.50
fitTimeSeries0.420.030.45
fitZig1.750.221.97
libSize-set0.310.060.38
libSize0.270.130.39
loadBiom0.030.000.03
loadMeta0.010.010.03
loadMetaQ000
loadPhenoData0.000.020.00
makeLabels000
mergeMRexperiments1.450.331.78
newMRexperiment0.020.010.03
normFactors-set0.280.100.38
normFactors0.250.090.34
plotBubble0.230.096.05
plotClassTimeSeries0.990.251.23
plotCorr0.470.100.56
plotFeature0.150.000.16
plotGenus0.140.040.19
plotMRheatmap2.540.212.73
plotOTU0.180.030.22
plotOrd0.360.030.39
plotRare0.160.030.19
plotTimeSeries1.150.271.42
posteriorProbs1.630.422.05
returnAppropriateObj0.310.080.39
ssFit000
ssIntervalCandidate000
ssPerm000
ssPermAnalysis000
trapz000
ts2MRexperiment1.640.261.91
uniqueFeatures0.100.000.09
wrenchNorm15.71 0.5316.23
zigControl000