Joseph N. Paulson
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/metagenomeSeq |
| Branch: RELEASE_3_9 |
| Last Commit: 8de127d |
| Last Changed Date: 2019-08-04 12:53:02 -0400 (Sun, 04 Aug 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:02:36 -0400 (Wed, 16 Oct 2019).
| Package 964/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| metagenomeSeq 1.26.3 Joseph N. Paulson
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: metagenomeSeq |
| Version: 1.26.3 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings metagenomeSeq_1.26.3.tar.gz |
| StartedAt: 2019-10-16 03:01:13 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:05:56 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 283.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: metagenomeSeq.Rcheck |
| Warnings: 2 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings metagenomeSeq_1.26.3.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK
* this is package ‘metagenomeSeq’ version ‘1.26.3’
* 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 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 ... WARNING
Missing link or links in documentation object 'MRihw-fitFeatureModelResults.Rd':
‘fitFeatureModelResults’ ‘fitZigResults’
Missing link or links in documentation object 'MRihw-fitZigResults.Rd':
‘fitFeatureModelResults’ ‘fitZigResults’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'MRcoefs':
‘IHWcov’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 or elapsed time > 5s
user system elapsed
wrenchNorm 20.278 0.135 20.414
MRfulltable 1.573 0.099 7.155
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/metagenomeSeq.Rcheck/00check.log’
for details.
metagenomeSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL metagenomeSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-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
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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] '1.26.3'
> # 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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, 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, 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
Loading required package: foreach
Loaded glmnet 2.0-18
Loading required package: RColorBrewer
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 15 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
>
> proc.time()
user system elapsed
118.318 1.358 119.695
metagenomeSeq.Rcheck/metagenomeSeq-Ex.timings
| name | user | system | elapsed | |
| MRcoefs | 1.631 | 0.100 | 1.732 | |
| MRcounts | 0.719 | 0.028 | 0.747 | |
| MRexperiment-class | 0 | 0 | 0 | |
| MRfulltable | 1.573 | 0.099 | 7.155 | |
| MRtable | 1.298 | 0.052 | 1.350 | |
| aggregateBySample | 0.148 | 0.008 | 0.156 | |
| aggregateByTaxonomy | 0.170 | 0.004 | 0.175 | |
| biom2MRexperiment | 0.333 | 0.000 | 0.444 | |
| calcNormFactors | 1.006 | 0.004 | 1.009 | |
| correctIndices | 0.191 | 0.007 | 0.198 | |
| correlationTest | 0.377 | 0.032 | 0.409 | |
| cumNorm | 0.715 | 0.004 | 0.720 | |
| cumNormMat | 0.937 | 0.016 | 0.952 | |
| cumNormStat | 0.810 | 0.008 | 0.818 | |
| cumNormStatFast | 0.539 | 0.012 | 0.551 | |
| expSummary | 0.180 | 0.004 | 0.185 | |
| exportMat | 1.587 | 1.080 | 2.720 | |
| exportStats | 0.823 | 0.020 | 0.843 | |
| extractMR | 1.485 | 0.464 | 1.949 | |
| filterData | 0.163 | 0.008 | 0.170 | |
| fitDO | 0.546 | 0.052 | 4.284 | |
| fitFeatureModel | 1.700 | 0.080 | 1.781 | |
| fitLogNormal | 2.450 | 0.052 | 2.503 | |
| fitMultipleTimeSeries | 2.114 | 0.028 | 2.142 | |
| fitPA | 0.477 | 0.032 | 3.379 | |
| fitSSTimeSeries | 0.627 | 0.040 | 0.666 | |
| fitTimeSeries | 0.596 | 0.016 | 0.612 | |
| fitZig | 2.736 | 0.112 | 2.848 | |
| libSize-set | 0.378 | 0.020 | 0.397 | |
| libSize | 0.404 | 0.028 | 0.432 | |
| loadBiom | 0.038 | 0.000 | 0.037 | |
| loadMeta | 0.035 | 0.000 | 0.079 | |
| loadMetaQ | 0 | 0 | 0 | |
| loadPhenoData | 0.032 | 0.000 | 0.040 | |
| makeLabels | 0 | 0 | 0 | |
| mergeMRexperiments | 2.197 | 0.188 | 2.386 | |
| newMRexperiment | 0.047 | 0.000 | 0.047 | |
| normFactors-set | 0.367 | 0.024 | 0.391 | |
| normFactors | 0.341 | 0.024 | 0.364 | |
| plotBubble | 0.389 | 0.047 | 3.885 | |
| plotClassTimeSeries | 1.442 | 0.076 | 1.520 | |
| plotCorr | 0.777 | 0.024 | 0.800 | |
| plotFeature | 0.243 | 0.015 | 0.259 | |
| plotGenus | 0.222 | 0.028 | 0.250 | |
| plotMRheatmap | 2.147 | 0.040 | 2.187 | |
| plotOTU | 0.191 | 0.004 | 0.196 | |
| plotOrd | 0.316 | 0.024 | 0.340 | |
| plotRare | 0.154 | 0.004 | 0.157 | |
| plotTimeSeries | 1.174 | 0.020 | 1.193 | |
| posteriorProbs | 2.497 | 0.024 | 2.524 | |
| returnAppropriateObj | 0.408 | 0.027 | 0.434 | |
| ssFit | 0.000 | 0.000 | 0.001 | |
| ssIntervalCandidate | 0.000 | 0.001 | 0.001 | |
| ssPerm | 0.000 | 0.001 | 0.001 | |
| ssPermAnalysis | 0.000 | 0.001 | 0.001 | |
| trapz | 0.001 | 0.000 | 0.001 | |
| ts2MRexperiment | 2.055 | 0.051 | 2.107 | |
| uniqueFeatures | 0.113 | 0.005 | 0.116 | |
| wrenchNorm | 20.278 | 0.135 | 20.414 | |
| zigControl | 0.001 | 0.000 | 0.000 | |