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BioC 3.5: CHECK report for MultiAssayExperiment on malbec2

This page was generated on 2017-10-18 14:17:37 -0400 (Wed, 18 Oct 2017).

Package 866/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MultiAssayExperiment 1.2.1
Marcel Ramos
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/MultiAssayExperiment
Branch: RELEASE_3_5
Last Commit: 1f53801
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: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings MultiAssayExperiment_1.2.1.tar.gz
StartedAt: 2017-10-18 01:02:30 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 01:05:07 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 157.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: MultiAssayExperiment.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings MultiAssayExperiment_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/MultiAssayExperiment.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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
  ‘/home/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
API000
ExperimentList-class0.0120.0000.012
ExperimentList0.1600.0000.161
MultiAssayExperiment-class3.9400.0204.019
MultiAssayExperiment-methods0.4640.0080.474
MultiAssayExperiment0.4160.0000.415
RangedRaggedAssay0.1680.0000.169
assay-RangedRaggedAssay-missing-method0.3280.0000.329
clusterOn0.8920.0001.059
hasAssay0.0040.0000.005
mapToList0.4520.0000.455
prepMultiAssay0.9440.0040.947
subsetByAssay0.7760.0000.775
subsetByColData1.0080.0001.006
subsetByColumn0.8560.0040.861
subsetByRow0.8840.0040.889
upsetSamples2.1960.0042.200