Joseph N Paulson
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/yarn |
| Branch: RELEASE_3_6 |
| Last Commit: 36100f4 |
| Last Changed Date: 2017-10-30 12:41:23 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:29:02 -0400 (Thu, 12 Apr 2018).
| Package 1469/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| yarn 1.4.0 Joseph N Paulson
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: yarn |
| Version: 1.4.0 |
| Command: rm -rf yarn.buildbin-libdir yarn.Rcheck && mkdir yarn.buildbin-libdir yarn.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=yarn.buildbin-libdir yarn_1.4.0.tar.gz >yarn.Rcheck\00install.out 2>&1 && cp yarn.Rcheck\00install.out yarn-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=yarn.buildbin-libdir --install="check:yarn-install.out" --force-multiarch --no-vignettes --timings yarn_1.4.0.tar.gz |
| StartedAt: 2018-04-12 03:53:37 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 04:00:25 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 408.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: yarn.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf yarn.buildbin-libdir yarn.Rcheck && mkdir yarn.buildbin-libdir yarn.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=yarn.buildbin-libdir yarn_1.4.0.tar.gz >yarn.Rcheck\00install.out 2>&1 && cp yarn.Rcheck\00install.out yarn-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=yarn.buildbin-libdir --install="check:yarn-install.out" --force-multiarch --no-vignettes --timings yarn_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/yarn.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'yarn/DESCRIPTION' ... OK
* this is package 'yarn' version '1.4.0'
* package encoding: UTF-8
* 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 'yarn' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAZiF1o/R.INSTALL352c56a9216a/yarn/man/bladder.Rd:7: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAZiF1o/R.INSTALL352c56a9216a/yarn/man/skin.Rd:7: missing file link 'ExpressionSet'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/yarn.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ...It is recommended to use 'given' instead of 'middle'.
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
** checking loading without being on the library search path ... 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 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
qsmooth 12.63 0.78 13.40
normalizeTissueAware 12.21 0.09 12.31
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
normalizeTissueAware 15.67 0.14 15.81
qsmooth 12.41 0.04 12.45
* 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: 1 WARNING
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/yarn.Rcheck/00check.log'
for details.
yarn.Rcheck/00install.out
install for i386
* installing *source* package 'yarn' ...
It is recommended to use 'given' instead of 'middle'.
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'yarn'
finding HTML links ... done
annotateFromBiomart html
bladder html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAZiF1o/R.INSTALL352c56a9216a/yarn/man/bladder.Rd:7: missing file link 'ExpressionSet'
checkMisAnnotation html
checkTissuesToMerge html
downloadGTEx html
extractMatrix html
filterGenes html
filterLowGenes html
filterMissingGenes html
filterSamples html
normalizeTissueAware html
plotCMDS html
plotDensity html
plotHeatmap html
qsmooth html
qstats html
skin html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAZiF1o/R.INSTALL352c56a9216a/yarn/man/skin.Rd:7: missing file link 'ExpressionSet'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'yarn' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'yarn' as yarn_1.4.0.zip
* DONE (yarn)
In R CMD INSTALL
In R CMD INSTALL
|
yarn.Rcheck/tests_i386/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("yarn")
[1] '1.4.0'
> test_check("yarn")
Loading required package: yarn
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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, 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")'.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
== testthat results ===========================================================
OK: 2 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
8.82 0.39 9.20
|
yarn.Rcheck/tests_x64/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("yarn")
[1] '1.4.0'
> test_check("yarn")
Loading required package: yarn
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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, 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")'.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
== testthat results ===========================================================
OK: 2 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
10.50 0.31 10.81
|
|
yarn.Rcheck/examples_i386/yarn-Ex.timings
|
yarn.Rcheck/examples_x64/yarn-Ex.timings
|