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BioC 3.5: CHECK report for MultiAssayExperiment on veracruz2

This page was generated on 2017-08-16 13:34:28 -0400 (Wed, 16 Aug 2017).

Package 866/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MultiAssayExperiment 1.2.1
Marcel Ramos
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/MultiAssayExperiment
Last Changed Rev: 129680 / Revision: 131943
Last Changed Date: 2017-05-18 02:03:16 -0400 (Thu, 18 May 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS 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
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: MultiAssayExperiment
Version: 1.2.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MultiAssayExperiment_1.2.1.tar.gz
StartedAt: 2017-08-16 05:44:01 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 05:47:07 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 186.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: MultiAssayExperiment.Rcheck
Warnings: 1

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MultiAssayExperiment_1.2.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MultiAssayExperiment.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MultiAssayExperiment/DESCRIPTION’ ... OK
* this is package ‘MultiAssayExperiment’ version ‘1.2.1’
* 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 ‘MultiAssayExperiment’ 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
Unexported object imported by a ':::' call: ‘BiocGenerics:::replaceSlots’
  See the note in ?`:::` about the use of this operator.
* 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 ... WARNING
Found the following significant warnings:

  Warning: 'RangedRaggedAssay' is deprecated.
  Warning: 'RangedRaggedAssay' is deprecated.
  Warning: 'RangedRaggedAssay' is deprecated.
  Warning: 'RangedRaggedAssay' is deprecated.
  Warning: 'RangedRaggedAssay' is deprecated.
  Warning: 'RangedRaggedAssay' is deprecated.
  Warning: 'RangedRaggedAssay' is deprecated.
  Warning: 'RangedRaggedAssay' is deprecated.
  Warning: 'RangedRaggedAssay' is deprecated.
  Warning: 'RangedRaggedAssay' is deprecated.
  Warning: 'RangedRaggedAssay' is deprecated.
  Warning: 'RangedRaggedAssay' is deprecated.
  Warning: 'RangedRaggedAssay' is deprecated.
  Warning: 'RangedRaggedAssay' is deprecated.
  Warning: 'RangedRaggedAssay' is deprecated.
  Warning: 'RangedRaggedAssay' is deprecated.
  Warning: 'RangedRaggedAssay' is deprecated.
  Warning: 'RangedRaggedAssay' is deprecated.
  Warning: 'RangedRaggedAssay' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/MultiAssayExperiment.Rcheck/00check.log’
for details.


MultiAssayExperiment.Rcheck/00install.out:

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

MultiAssayExperiment.Rcheck/MultiAssayExperiment-Ex.timings:

nameusersystemelapsed
API0.0000.0000.001
ExperimentList-class0.0180.0010.019
ExperimentList0.2310.0010.256
MultiAssayExperiment-class4.3440.0454.518
MultiAssayExperiment-methods0.5160.0070.535
MultiAssayExperiment0.4600.0060.481
RangedRaggedAssay0.1650.0030.179
assay-RangedRaggedAssay-missing-method0.4120.0070.433
clusterOn0.7460.0080.775
hasAssay0.0060.0000.006
mapToList0.4840.0060.505
prepMultiAssay1.0080.0171.065
subsetByAssay0.9340.0090.986
subsetByColData1.1960.0151.237
subsetByColumn1.0440.0091.075
subsetByRow1.1330.0091.177
upsetSamples2.7160.0122.830