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 12:27:45 -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: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagenomeSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings metagenomeSeq_1.26.3.tar.gz |
| StartedAt: 2019-10-16 05:04:49 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:13:43 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 534.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: metagenomeSeq.Rcheck |
| Warnings: 3 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagenomeSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings metagenomeSeq_1.26.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/metagenomeSeq.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'metagenomeSeq' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6BNxsQ/R.INSTALLc8833803c53/metagenomeSeq/man/MRihw-fitFeatureModelResults.Rd:16: missing link 'fitFeatureModelResults'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6BNxsQ/R.INSTALLc8833803c53/metagenomeSeq/man/MRihw-fitFeatureModelResults.Rd:17: missing link 'fitZigResults'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6BNxsQ/R.INSTALLc8833803c53/metagenomeSeq/man/MRihw-fitZigResults.Rd:16: missing link 'fitFeatureModelResults'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6BNxsQ/R.INSTALLc8833803c53/metagenomeSeq/man/MRihw-fitZigResults.Rd:17: missing link 'fitZigResults'
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/metagenomeSeq.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
wrenchNorm 19.00 1.02 20.02
MRfulltable 1.36 0.10 6.37
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
wrenchNorm 22.36 0.34 22.71
MRfulltable 1.69 0.16 6.95
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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: 3 WARNINGs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/metagenomeSeq.Rcheck/00check.log'
for details.
metagenomeSeq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/metagenomeSeq_1.26.3.tar.gz && rm -rf metagenomeSeq.buildbin-libdir && mkdir metagenomeSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metagenomeSeq.buildbin-libdir metagenomeSeq_1.26.3.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL metagenomeSeq_1.26.3.zip && rm metagenomeSeq_1.26.3.tar.gz metagenomeSeq_1.26.3.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 949k 100 949k 0 0 12.0M 0 --:--:-- --:--:-- --:--:-- 13.2M
install for i386
* 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
converting help for package 'metagenomeSeq'
finding HTML links ... done
MRcoefs html
MRcounts html
MRexperiment-class html
MRexperiment2biom html
MRfulltable html
MRihw-fitFeatureModelResults html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6BNxsQ/R.INSTALLc8833803c53/metagenomeSeq/man/MRihw-fitFeatureModelResults.Rd:16: missing link 'fitFeatureModelResults'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6BNxsQ/R.INSTALLc8833803c53/metagenomeSeq/man/MRihw-fitFeatureModelResults.Rd:17: missing link 'fitZigResults'
MRihw-fitZigResults html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6BNxsQ/R.INSTALLc8833803c53/metagenomeSeq/man/MRihw-fitZigResults.Rd:16: missing link 'fitFeatureModelResults'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6BNxsQ/R.INSTALLc8833803c53/metagenomeSeq/man/MRihw-fitZigResults.Rd:17: missing link 'fitZigResults'
MRihw html
MRtable html
aggregateBySample html
aggregateByTaxonomy html
biom2MRexperiment html
calcNormFactors html
calcPosComponent html
calcShrinkParameters html
calcStandardError html
calcZeroAdjustment html
calcZeroComponent html
calculateEffectiveSamples html
correctIndices html
correlationTest html
cumNorm html
cumNormMat html
cumNormStat html
cumNormStatFast html
doCountMStep html
doEStep html
doZeroMStep html
expSummary html
exportMat html
exportStats html
extractMR html
filterData html
fitDO html
fitFeatureModel html
fitFeatureModelResults-class html
fitLogNormal html
fitMultipleTimeSeries html
fitPA html
fitSSTimeSeries html
fitTimeSeries html
fitZeroLogNormal html
fitZig html
fitZigResults-class html
getCountDensity html
getEpsilon html
getNegativeLogLikelihoods html
getPi html
getZ html
isItStillActive html
libSize-set html
libSize html
loadBiom html
loadMeta html
loadMetaQ html
loadPhenoData html
lungData html
makeLabels html
mergeMRexperiments html
mergeTable html
metagenomeSeq-deprecated html
metagenomeSeq-package html
mouseData html
newMRexperiment html
normFactors-set html
normFactors html
plotBubble html
plotClassTimeSeries html
plotCorr html
plotFeature html
plotGenus html
plotMRheatmap html
plotOTU html
plotOrd html
plotRare html
plotTimeSeries html
posteriorProbs html
returnAppropriateObj html
ssFit html
ssIntervalCandidate html
ssPerm html
ssPermAnalysis html
trapz html
ts2MRexperiment html
uniqueFeatures html
wrenchNorm html
zigControl html
** 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
install for x64
* installing *source* package 'metagenomeSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'metagenomeSeq' as metagenomeSeq_1.26.3.zip
* DONE (metagenomeSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'metagenomeSeq' successfully unpacked and MD5 sums checked
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metagenomeSeq.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
124.10 5.93 130.15
|
metagenomeSeq.Rcheck/tests_x64/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-w64-mingw32/x64 (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
131.90 2.48 134.36
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metagenomeSeq.Rcheck/examples_i386/metagenomeSeq-Ex.timings
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metagenomeSeq.Rcheck/examples_x64/metagenomeSeq-Ex.timings
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