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BioC 3.5: CHECK report for clusterExperiment on tokay2

This page was generated on 2017-10-18 14:26:13 -0400 (Wed, 18 Oct 2017).

Package 235/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clusterExperiment 1.2.0
Elizabeth Purdom
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/clusterExperiment
Branch: RELEASE_3_5
Last Commit: 7bb7915
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: clusterExperiment
Version: 1.2.0
Command: rm -rf clusterExperiment.buildbin-libdir clusterExperiment.Rcheck && mkdir clusterExperiment.buildbin-libdir clusterExperiment.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clusterExperiment.buildbin-libdir clusterExperiment_1.2.0.tar.gz >clusterExperiment.Rcheck\00install.out 2>&1 && cp clusterExperiment.Rcheck\00install.out clusterExperiment-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=clusterExperiment.buildbin-libdir --install="check:clusterExperiment-install.out" --force-multiarch --no-vignettes --timings clusterExperiment_1.2.0.tar.gz
StartedAt: 2017-10-17 22:48:41 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 23:01:59 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 798.4 seconds
RetCode: 0
Status:  OK  
CheckDir: clusterExperiment.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf clusterExperiment.buildbin-libdir clusterExperiment.Rcheck && mkdir clusterExperiment.buildbin-libdir clusterExperiment.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clusterExperiment.buildbin-libdir clusterExperiment_1.2.0.tar.gz >clusterExperiment.Rcheck\00install.out 2>&1 && cp clusterExperiment.Rcheck\00install.out clusterExperiment-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=clusterExperiment.buildbin-libdir --install="check:clusterExperiment-install.out" --force-multiarch --no-vignettes --timings clusterExperiment_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/clusterExperiment.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clusterExperiment/DESCRIPTION' ... OK
* this is package 'clusterExperiment' version '1.2.0'
* 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 'clusterExperiment' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
subsampleClustering 36.22   0.07   36.29
plotHeatmap         14.11   0.04   14.19
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
subsampleClustering 41.77   0.01   41.78
plotHeatmap         20.34   0.04   20.39
plotClusters         5.52   0.07    5.57
* 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: OK

clusterExperiment.Rcheck/00install.out:


install for i386

* installing *source* package 'clusterExperiment' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Creating a new generic function for 'transform' in package 'clusterExperiment'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'clusterExperiment' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clusterExperiment' as clusterExperiment_1.2.0.zip
* DONE (clusterExperiment)

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

nameusersystemelapsed
ClusterExperiment-class0.250.000.25
addClusters1.110.041.24
clusterContrasts1.090.101.18
clusterD1.690.041.79
clusterMany2.750.022.76
clusterSingle0.110.000.11
combineMany1.970.112.08
getBestFeatures1.530.031.56
makeDendrogram0.740.000.73
mergeClusters2.040.032.08
plotClusters4.220.104.31
plotHeatmap14.11 0.0414.19
plottingFunctions0.200.010.22
seqCluster000
simData0.000.030.03
subsampleClustering36.22 0.0736.29
transform0.030.000.03
workflowClusters2.050.012.07

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

nameusersystemelapsed
ClusterExperiment-class0.360.000.36
addClusters0.680.030.70
clusterContrasts1.020.031.04
clusterD2.250.002.25
clusterMany3.010.033.05
clusterSingle0.110.020.13
combineMany2.640.012.65
getBestFeatures2.910.022.92
makeDendrogram1.030.011.05
mergeClusters2.340.002.35
plotClusters5.520.075.57
plotHeatmap20.34 0.0420.39
plottingFunctions0.210.020.22
seqCluster000
simData0.010.000.02
subsampleClustering41.77 0.0141.78
transform0.040.000.05
workflowClusters3.660.033.68