BioC 3.5: CHECK report for MultiAssayExperiment on tokay2

Package: MultiAssayExperiment

Version: 1.2.1

Command: rm -rf MultiAssayExperiment.buildbin-libdir MultiAssayExperiment.Rcheck && mkdir MultiAssayExperiment.buildbin-libdir MultiAssayExperiment.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MultiAssayExperiment.buildbin-libdir MultiAssayExperiment_1.2.1.tar.gz >MultiAssayExperiment.Rcheck\00install.out 2>&1 && cp MultiAssayExperiment.Rcheck\00install.out MultiAssayExperiment-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MultiAssayExperiment.buildbin-libdir --install="check:MultiAssayExperiment-install.out" --force-multiarch --no-vignettes --timings MultiAssayExperiment_1.2.1.tar.gz

StartedAt: 2017-08-16 01:28:34 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:33:25 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 290.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MultiAssayExperiment.Rcheck

Warnings: 2

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MultiAssayExperiment.buildbin-libdir MultiAssayExperiment.Rcheck && mkdir MultiAssayExperiment.buildbin-libdir MultiAssayExperiment.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MultiAssayExperiment.buildbin-libdir MultiAssayExperiment_1.2.1.tar.gz >MultiAssayExperiment.Rcheck\00install.out 2>&1 && cp MultiAssayExperiment.Rcheck\00install.out MultiAssayExperiment-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MultiAssayExperiment.buildbin-libdir --install="check:MultiAssayExperiment-install.out" --force-multiarch --no-vignettes --timings MultiAssayExperiment_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MultiAssayExperiment.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* 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 ... 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 ...
** running examples for arch 'i386' ... 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.
** running examples for arch 'x64' ... 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 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: 2 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/MultiAssayExperiment.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'MultiAssayExperiment' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MultiAssayExperiment' as MultiAssayExperiment_1.2.1.zip
* DONE (MultiAssayExperiment)

name	user	system	elapsed
API	0	0	0
ExperimentList-class	0.00	0.02	0.01
ExperimentList	0.16	0.03	0.19
MultiAssayExperiment-class	3.45	0.06	3.51
MultiAssayExperiment-methods	0.50	0.03	0.53
MultiAssayExperiment	0.44	0.02	0.46
RangedRaggedAssay	0.17	0.01	0.18
assay-RangedRaggedAssay-missing-method	0.42	0.00	0.42
clusterOn	0.72	0.03	0.75
hasAssay	0.02	0.00	0.02
mapToList	0.48	0.00	0.48
prepMultiAssay	0.92	0.00	0.93
subsetByAssay	0.86	0.03	0.89
subsetByColData	1.13	0.00	1.12
subsetByColumn	1.06	0.02	1.08
subsetByRow	1.39	0.02	1.41
upsetSamples	2.44	0.00	2.44

name	user	system	elapsed
API	0	0	0
ExperimentList-class	0.01	0.00	0.02
ExperimentList	0.14	0.05	0.18
MultiAssayExperiment-class	3.97	0.03	4.00
MultiAssayExperiment-methods	1.03	0.00	1.03
MultiAssayExperiment	0.48	0.00	0.49
RangedRaggedAssay	0.16	0.00	0.16
assay-RangedRaggedAssay-missing-method	0.39	0.01	0.40
clusterOn	1.27	0.02	1.28
hasAssay	0	0	0
mapToList	0.61	0.04	0.65
prepMultiAssay	1.25	0.00	1.25
subsetByAssay	1.45	0.02	1.47
subsetByColData	1.37	0.02	1.39
subsetByColumn	1.08	0.00	1.07
subsetByRow	1.11	0.00	1.11
upsetSamples	2.46	0.04	2.50