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CHECK report for yarn on tokay2

This page was generated on 2018-10-17 08:43:10 -0400 (Wed, 17 Oct 2018).

Package 1558/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
yarn 1.6.0
Joseph N Paulson
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/yarn
Branch: RELEASE_3_7
Last Commit: 19d1b2e
Last Changed Date: 2018-04-30 10:35:44 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: yarn
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:yarn.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings yarn_1.6.0.tar.gz
StartedAt: 2018-10-17 05:28:30 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 05:35:27 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 417.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: yarn.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:yarn.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings yarn_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/yarn.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.6.0'
* 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-3.7-bioc/tmpdir/RtmpUJRXH4/R.INSTALL275c64e330bd/yarn/man/bladder.Rd:7: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUJRXH4/R.INSTALL275c64e330bd/yarn/man/skin.Rd:7: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-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
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
normalizeTissueAware 10.27   0.85   11.11
qsmooth               8.89   0.19    9.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
qsmooth              10.78   0.06   10.84
normalizeTissueAware 10.54   0.09   10.62
* 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-3.7-bioc/meat/yarn.Rcheck/00check.log'
for details.



Installation output

yarn.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/yarn_1.6.0.tar.gz && rm -rf yarn.buildbin-libdir && mkdir yarn.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=yarn.buildbin-libdir yarn_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL yarn_1.6.0.zip && rm yarn_1.6.0.tar.gz yarn_1.6.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2706k  100 2706k    0     0  34.6M      0 --:--:-- --:--:-- --:--:-- 37.7M

install for i386

* installing *source* package 'yarn' ...
It is recommended to use 'given' instead of 'middle'.
It is recommended to use 'given' instead of 'middle'.
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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-3.7-bioc/tmpdir/RtmpUJRXH4/R.INSTALL275c64e330bd/yarn/man/bladder.Rd:7: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    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-3.7-bioc/tmpdir/RtmpUJRXH4/R.INSTALL275c64e330bd/yarn/man/skin.Rd:7: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
** 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_1.6.0.zip
* DONE (yarn)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'yarn' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

yarn.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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] '1.6.0'
> 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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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 
   9.53    0.67   10.20 

yarn.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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] '1.6.0'
> 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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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 
  11.37    0.45   11.89 

Example timings

yarn.Rcheck/examples_i386/yarn-Ex.timings

nameusersystemelapsed
annotateFromBiomart1.200.094.37
bladder000
checkMisAnnotation0.210.020.23
checkTissuesToMerge0.860.080.94
downloadGTEx000
extractMatrix0.160.010.18
filterGenes0.140.050.18
filterLowGenes0.140.020.16
filterMissingGenes0.630.010.64
filterSamples0.090.030.12
normalizeTissueAware10.27 0.8511.11
plotCMDS0.140.010.16
plotDensity0.360.000.36
plotHeatmap2.090.202.29
qsmooth8.890.199.08
skin000

yarn.Rcheck/examples_x64/yarn-Ex.timings

nameusersystemelapsed
annotateFromBiomart1.400.034.45
bladder000
checkMisAnnotation0.220.030.25
checkTissuesToMerge1.090.001.10
downloadGTEx000
extractMatrix0.170.000.17
filterGenes0.170.000.17
filterLowGenes0.110.050.16
filterMissingGenes0.080.040.12
filterSamples0.090.070.16
normalizeTissueAware10.54 0.0910.62
plotCMDS0.140.020.16
plotDensity0.320.000.33
plotHeatmap3.020.093.11
qsmooth10.78 0.0610.84
skin000