Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:38 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
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 |
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 1166/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
metagenomeSeq 1.41.0 (landing page) Joseph N. Paulson
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
Package: metagenomeSeq |
Version: 1.41.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings metagenomeSeq_1.41.0.tar.gz |
StartedAt: 2023-04-12 07:20:07 -0400 (Wed, 12 Apr 2023) |
EndedAt: 2023-04-12 07:25:24 -0400 (Wed, 12 Apr 2023) |
EllapsedTime: 316.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: metagenomeSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings metagenomeSeq_1.41.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/metagenomeSeq.Rcheck’ * using R Under development (unstable) (2023-02-14 r83833) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 * running under: Ubuntu 20.04.6 LTS * using session charset: UTF-8 * checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK * this is package ‘metagenomeSeq’ version ‘1.41.0’ * 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 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed wrenchNorm 15.168 0.251 15.421 MRfulltable 1.342 0.040 6.363 * 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 ... ‘fitTimeSeries.Rnw’... OK ‘metagenomeSeq.Rnw’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
metagenomeSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL metagenomeSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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
R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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. > library("testthat") > packageVersion("metagenomeSeq") [1] '1.41.0' > # 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, 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: limma Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA Loading required package: glmnet Loading required package: Matrix Loaded glmnet 4.1-7 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 101.055 2.460 103.502
metagenomeSeq.Rcheck/metagenomeSeq-Ex.timings
name | user | system | elapsed | |
MRcoefs | 1.096 | 0.156 | 1.252 | |
MRcounts | 0.675 | 0.004 | 0.680 | |
MRexperiment-class | 0 | 0 | 0 | |
MRfulltable | 1.342 | 0.040 | 6.363 | |
MRtable | 1.500 | 0.032 | 1.532 | |
aggregateBySample | 0.14 | 0.02 | 0.16 | |
aggregateByTaxonomy | 0.176 | 0.012 | 0.188 | |
biom2MRexperiment | 0.246 | 0.004 | 0.250 | |
calcNormFactors | 0.469 | 0.036 | 0.505 | |
correctIndices | 0.115 | 0.008 | 0.123 | |
correlationTest | 0.224 | 0.032 | 0.256 | |
cumNorm | 0.593 | 0.012 | 0.605 | |
cumNormMat | 0.563 | 0.036 | 0.599 | |
cumNormStat | 0.746 | 0.012 | 0.758 | |
cumNormStatFast | 0.346 | 0.008 | 0.355 | |
expSummary | 0.107 | 0.012 | 0.120 | |
exportMat | 0.849 | 0.704 | 1.554 | |
exportStats | 0.764 | 0.024 | 0.789 | |
extractMR | 0.587 | 0.316 | 0.903 | |
filterData | 0.165 | 0.004 | 0.169 | |
fitDO | 0.479 | 0.014 | 4.384 | |
fitFeatureModel | 1.515 | 0.068 | 1.583 | |
fitLogNormal | 2.433 | 0.261 | 2.693 | |
fitMultipleTimeSeries | 2.439 | 0.215 | 2.655 | |
fitPA | 0.427 | 0.092 | 4.043 | |
fitSSTimeSeries | 0.492 | 0.000 | 0.492 | |
fitTimeSeries | 0.718 | 0.012 | 0.731 | |
fitZig | 2.286 | 0.024 | 2.309 | |
libSize-set | 0.413 | 0.016 | 0.429 | |
libSize | 0.339 | 0.008 | 0.347 | |
loadBiom | 0.041 | 0.000 | 0.040 | |
loadMeta | 0.015 | 0.000 | 0.018 | |
loadMetaQ | 0.000 | 0.000 | 0.001 | |
loadPhenoData | 0.007 | 0.000 | 0.007 | |
makeLabels | 0 | 0 | 0 | |
mergeMRexperiments | 1.797 | 0.380 | 2.177 | |
newMRexperiment | 0.031 | 0.000 | 0.031 | |
normFactors-set | 0.349 | 0.004 | 0.353 | |
normFactors | 0.373 | 0.016 | 0.388 | |
plotBubble | 0.656 | 0.043 | 4.199 | |
plotClassTimeSeries | 1.23 | 0.10 | 1.33 | |
plotCorr | 0.445 | 0.019 | 0.464 | |
plotFeature | 0.137 | 0.012 | 0.149 | |
plotGenus | 0.130 | 0.004 | 0.133 | |
plotMRheatmap | 1.701 | 0.031 | 1.733 | |
plotOTU | 0.122 | 0.019 | 0.142 | |
plotOrd | 0.229 | 0.029 | 0.258 | |
plotRare | 0.119 | 0.016 | 0.134 | |
plotTimeSeries | 0.928 | 0.044 | 0.972 | |
posteriorProbs | 1.730 | 0.034 | 1.764 | |
returnAppropriateObj | 0.312 | 0.004 | 0.315 | |
ssFit | 0.000 | 0.001 | 0.000 | |
ssIntervalCandidate | 0 | 0 | 0 | |
ssPerm | 0 | 0 | 0 | |
ssPermAnalysis | 0 | 0 | 0 | |
trapz | 0 | 0 | 0 | |
ts2MRexperiment | 1.698 | 0.016 | 1.714 | |
uniqueFeatures | 0.112 | 0.008 | 0.120 | |
wrenchNorm | 15.168 | 0.251 | 15.421 | |
zigControl | 0 | 0 | 0 | |