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BioC 3.5: CHECK report for SummarizedExperiment on veracruz2

This page was generated on 2017-10-18 14:33:19 -0400 (Wed, 18 Oct 2017).

Package 1286/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SummarizedExperiment 1.6.5
Bioconductor Package Maintainer
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/SummarizedExperiment
Branch: RELEASE_3_5
Last Commit: ec69cd5
Last Changed Date: 2017-09-28 02:16:38 -0400 (Thu, 28 Sep 2017)
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  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SummarizedExperiment
Version: 1.6.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SummarizedExperiment_1.6.5.tar.gz
StartedAt: 2017-10-18 09:31:32 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 09:34:42 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 190.0 seconds
RetCode: 0
Status:  OK 
CheckDir: SummarizedExperiment.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SummarizedExperiment_1.6.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SummarizedExperiment.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SummarizedExperiment/DESCRIPTION’ ... OK
* this is package ‘SummarizedExperiment’ version ‘1.6.5’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SummarizedExperiment’ 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 ... NOTE
'library' or 'require' calls in package code:
  ‘HDF5Array’ ‘rhdf5’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                           user system elapsed
makeSummarizedExperimentFromExpressionSet 7.598  0.215   8.033
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.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 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/SummarizedExperiment.Rcheck/00check.log’
for details.


SummarizedExperiment.Rcheck/00install.out:

* installing *source* package ‘SummarizedExperiment’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SummarizedExperiment)

SummarizedExperiment.Rcheck/SummarizedExperiment-Ex.timings:

nameusersystemelapsed
Assays-class0.2780.0390.349
RangedSummarizedExperiment-class0.9180.0120.976
SummarizedExperiment-class0.8230.0150.863
coverage-methods0.2620.0020.272
findOverlaps-methods0.2770.0020.291
inter-range-methods0.2680.0020.275
intra-range-methods0.4350.0040.452
makeSummarizedExperimentFromDataFrame0.3310.0030.343
makeSummarizedExperimentFromExpressionSet7.5980.2158.033
nearest-methods0.7720.0350.828
readKallisto0.8400.0230.886
saveHDF5SummarizedExperiment1.2000.0161.253