| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (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 1207/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| metagenomeSeq 1.48.0 (landing page) Joseph N. Paulson
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
|
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. |
| Package: metagenomeSeq |
| Version: 1.48.0 |
| 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_1.48.0.tar.gz |
| StartedAt: 2024-12-20 03:15:31 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 03:20:22 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 290.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: metagenomeSeq.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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_1.48.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/metagenomeSeq.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* 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 '1.48.0'
* 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 17.66 0.86 18.55
MRfulltable 1.03 0.24 5.81
plotBubble 0.33 0.06 9.12
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
── Failure ('test-fitZig.R:67:3'): `fitZig` function treats a matrix the same ──
`fit` not equal to `fit2`.
Component "eb": Component "df.prior": Mean relative difference: 0.01522971
Component "eb": Component "s2.prior": Mean relative difference: 0.0208853
Component "eb": Component "var.prior": Mean relative difference: 0.01489299
Component "eb": Component "s2.post": Mean relative difference: 0.002818974
Component "eb": Component "t": Mean relative difference: 0.001476944
Component "eb": Component "df.total": Mean relative difference: 0.002226407
Component "eb": Component "p.value": Mean relative difference: 0.001045802
Component "eb": Component "lods": Mean relative difference: 0.002124969
Component "eb": Component "F": Mean relative difference: 0.002818882
[ FAIL 2 | WARN 6 | SKIP 0 | PASS 13 ]
Error: Test failures
Execution halted
* 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 ERROR
See
'F:/biocbuild/bbs-3.20-bioc/meat/metagenomeSeq.Rcheck/00check.log'
for details.
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)
metagenomeSeq.Rcheck/tests/testthat.Rout.fail
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
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] '1.48.0'
> # 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, saveRDS, 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 2 | WARN 6 | SKIP 0 | PASS 13 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-fitZig.R:35:3'): `fitZig` function provides expected values prior to split ──
`fit` not equal to `fit2`.
Component "eb": Component "df.prior": Mean relative difference: 0.01522971
Component "eb": Component "s2.prior": Mean relative difference: 0.0208853
Component "eb": Component "var.prior": Mean relative difference: 0.01489299
Component "eb": Component "s2.post": Mean relative difference: 0.002818974
Component "eb": Component "t": Mean relative difference: 0.001476944
Component "eb": Component "df.total": Mean relative difference: 0.002226407
Component "eb": Component "p.value": Mean relative difference: 0.001045802
Component "eb": Component "lods": Mean relative difference: 0.002124969
Component "eb": Component "F": Mean relative difference: 0.002818882
── Failure ('test-fitZig.R:67:3'): `fitZig` function treats a matrix the same ──
`fit` not equal to `fit2`.
Component "eb": Component "df.prior": Mean relative difference: 0.01522971
Component "eb": Component "s2.prior": Mean relative difference: 0.0208853
Component "eb": Component "var.prior": Mean relative difference: 0.01489299
Component "eb": Component "s2.post": Mean relative difference: 0.002818974
Component "eb": Component "t": Mean relative difference: 0.001476944
Component "eb": Component "df.total": Mean relative difference: 0.002226407
Component "eb": Component "p.value": Mean relative difference: 0.001045802
Component "eb": Component "lods": Mean relative difference: 0.002124969
Component "eb": Component "F": Mean relative difference: 0.002818882
[ FAIL 2 | WARN 6 | SKIP 0 | PASS 13 ]
Error: Test failures
Execution halted
metagenomeSeq.Rcheck/metagenomeSeq-Ex.timings
| name | user | system | elapsed | |
| MRcoefs | 1.39 | 0.11 | 1.50 | |
| MRcounts | 0.48 | 0.07 | 0.57 | |
| MRexperiment-class | 0 | 0 | 0 | |
| MRfulltable | 1.03 | 0.24 | 5.81 | |
| MRtable | 0.95 | 0.09 | 1.05 | |
| aggregateBySample | 0.11 | 0.02 | 0.13 | |
| aggregateByTaxonomy | 0.14 | 0.03 | 0.17 | |
| biom2MRexperiment | 0.27 | 0.03 | 0.31 | |
| calcNormFactors | 0.64 | 0.11 | 0.75 | |
| correctIndices | 0.09 | 0.00 | 0.09 | |
| correlationTest | 0.16 | 0.05 | 0.21 | |
| cumNorm | 0.67 | 0.09 | 0.76 | |
| cumNormMat | 0.72 | 0.08 | 0.80 | |
| cumNormStat | 0.80 | 0.12 | 0.92 | |
| cumNormStatFast | 0.23 | 0.06 | 0.29 | |
| expSummary | 0.08 | 0.00 | 0.08 | |
| exportMat | 2.03 | 2.02 | 4.06 | |
| exportStats | 0.50 | 0.15 | 0.68 | |
| extractMR | 1.98 | 0.75 | 2.73 | |
| filterData | 0.22 | 0.03 | 0.25 | |
| fitDO | 0.54 | 0.07 | 3.12 | |
| fitFeatureModel | 0.97 | 0.18 | 1.16 | |
| fitLogNormal | 2.11 | 0.33 | 2.44 | |
| fitMultipleTimeSeries | 2.08 | 0.32 | 2.39 | |
| fitPA | 0.42 | 0.15 | 2.95 | |
| fitSSTimeSeries | 0.47 | 0.08 | 0.55 | |
| fitTimeSeries | 0.52 | 0.11 | 0.62 | |
| fitZig | 2.15 | 0.28 | 2.44 | |
| libSize-set | 0.28 | 0.11 | 0.39 | |
| libSize | 0.33 | 0.14 | 0.48 | |
| loadBiom | 0.03 | 0.00 | 0.03 | |
| loadMeta | 0.04 | 0.00 | 0.04 | |
| loadMetaQ | 0 | 0 | 0 | |
| loadPhenoData | 0.01 | 0.00 | 0.01 | |
| makeLabels | 0 | 0 | 0 | |
| mergeMRexperiments | 1.75 | 0.44 | 2.20 | |
| newMRexperiment | 0.05 | 0.00 | 0.05 | |
| normFactors-set | 0.40 | 0.09 | 0.50 | |
| normFactors | 0.36 | 0.08 | 0.44 | |
| plotBubble | 0.33 | 0.06 | 9.12 | |
| plotClassTimeSeries | 1.24 | 0.25 | 1.49 | |
| plotCorr | 0.67 | 0.06 | 0.77 | |
| plotFeature | 0.18 | 0.03 | 0.20 | |
| plotGenus | 0.26 | 0.00 | 0.26 | |
| plotMRheatmap | 2.24 | 0.22 | 2.46 | |
| plotOTU | 0.23 | 0.02 | 0.25 | |
| plotOrd | 0.45 | 0.01 | 0.47 | |
| plotRare | 0.11 | 0.03 | 0.14 | |
| plotTimeSeries | 1.28 | 0.25 | 1.53 | |
| posteriorProbs | 2.33 | 0.36 | 2.72 | |
| returnAppropriateObj | 0.41 | 0.14 | 0.54 | |
| ssFit | 0 | 0 | 0 | |
| ssIntervalCandidate | 0 | 0 | 0 | |
| ssPerm | 0 | 0 | 0 | |
| ssPermAnalysis | 0 | 0 | 0 | |
| trapz | 0 | 0 | 0 | |
| ts2MRexperiment | 1.64 | 0.37 | 2.01 | |
| uniqueFeatures | 0.09 | 0.02 | 0.11 | |
| wrenchNorm | 17.66 | 0.86 | 18.55 | |
| zigControl | 0 | 0 | 0 | |