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BioC 3.5: CHECK report for MultiAssayExperiment on tokay2

This page was generated on 2017-08-16 13:25:36 -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: 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

Command output

##############################################################################
##############################################################################
###
### 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.


MultiAssayExperiment.Rcheck/00install.out:


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)

MultiAssayExperiment.Rcheck/examples_i386/MultiAssayExperiment-Ex.timings:

nameusersystemelapsed
API000
ExperimentList-class0.000.020.01
ExperimentList0.160.030.19
MultiAssayExperiment-class3.450.063.51
MultiAssayExperiment-methods0.500.030.53
MultiAssayExperiment0.440.020.46
RangedRaggedAssay0.170.010.18
assay-RangedRaggedAssay-missing-method0.420.000.42
clusterOn0.720.030.75
hasAssay0.020.000.02
mapToList0.480.000.48
prepMultiAssay0.920.000.93
subsetByAssay0.860.030.89
subsetByColData1.130.001.12
subsetByColumn1.060.021.08
subsetByRow1.390.021.41
upsetSamples2.440.002.44

MultiAssayExperiment.Rcheck/examples_x64/MultiAssayExperiment-Ex.timings:

nameusersystemelapsed
API000
ExperimentList-class0.010.000.02
ExperimentList0.140.050.18
MultiAssayExperiment-class3.970.034.00
MultiAssayExperiment-methods1.030.001.03
MultiAssayExperiment0.480.000.49
RangedRaggedAssay0.160.000.16
assay-RangedRaggedAssay-missing-method0.390.010.40
clusterOn1.270.021.28
hasAssay000
mapToList0.610.040.65
prepMultiAssay1.250.001.25
subsetByAssay1.450.021.47
subsetByColData1.370.021.39
subsetByColumn1.080.001.07
subsetByRow1.110.001.11
upsetSamples2.460.042.50