BioC 3.5: CHECK report for MultiAssayExperiment on toluca2

Package: MultiAssayExperiment

Version: 1.1.59

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MultiAssayExperiment_1.1.59.tar.gz

StartedAt: 2017-04-23 07:08:28 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 07:12:05 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 216.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MultiAssayExperiment.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MultiAssayExperiment_1.1.59.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MultiAssayExperiment.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MultiAssayExperiment/DESCRIPTION’ ... OK
* this is package ‘MultiAssayExperiment’ version ‘1.1.59’
* 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.
Examples with CPU or elapsed time > 5s
                            user system elapsed
MultiAssayExperiment-class 5.444  0.058   5.559
* 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.

* 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)

name	user	system	elapsed
API	0.001	0.000	0.000
ExperimentList-class	0.02	0.00	0.02
ExperimentList	0.294	0.003	0.301
MultiAssayExperiment-class	5.444	0.058	5.559
MultiAssayExperiment-methods	0.687	0.008	0.701
MultiAssayExperiment	0.546	0.007	0.561
RangedRaggedAssay	0.195	0.004	0.208
assay-RangedRaggedAssay-missing-method	0.492	0.005	0.504
clusterOn	1.056	0.009	1.085
hasAssay	0.006	0.001	0.006
mapToList	0.641	0.007	0.652
prepMultiAssay	1.224	0.008	1.251
subsetByAssay	1.162	0.009	1.187
subsetByColData	1.508	0.010	1.531
subsetByColumn	1.196	0.008	1.222
subsetByRow	1.290	0.009	1.319
upsetSamples	3.246	0.015	3.286