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BioC 3.4: CHECK report for clusterExperiment on tokay1

This page was generated on 2017-04-15 16:21:17 -0400 (Sat, 15 Apr 2017).

Package 220/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clusterExperiment 1.0.0
Elizabeth Purdom
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/clusterExperiment
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: clusterExperiment
Version: 1.0.0
Command: rm -rf clusterExperiment.buildbin-libdir clusterExperiment.Rcheck && mkdir clusterExperiment.buildbin-libdir clusterExperiment.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clusterExperiment.buildbin-libdir clusterExperiment_1.0.0.tar.gz >clusterExperiment.Rcheck\00install.out 2>&1 && cp clusterExperiment.Rcheck\00install.out clusterExperiment-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=clusterExperiment.buildbin-libdir --install="check:clusterExperiment-install.out" --force-multiarch --no-vignettes --timings clusterExperiment_1.0.0.tar.gz
StartedAt: 2017-04-14 21:33:46 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:44:59 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 673.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: clusterExperiment.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf clusterExperiment.buildbin-libdir clusterExperiment.Rcheck && mkdir clusterExperiment.buildbin-libdir clusterExperiment.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clusterExperiment.buildbin-libdir clusterExperiment_1.0.0.tar.gz >clusterExperiment.Rcheck\00install.out 2>&1 && cp clusterExperiment.Rcheck\00install.out clusterExperiment-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=clusterExperiment.buildbin-libdir --install="check:clusterExperiment-install.out" --force-multiarch --no-vignettes --timings clusterExperiment_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/clusterExperiment.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.0.0'
* 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 ... WARNING
Missing link or links in documentation object 'seqCluster.Rd':
  'tightClust'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 32.64   0.05   32.68
plotHeatmap         12.97   0.09   13.90
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
subsampleClustering 31.84   0.04   31.89
plotHeatmap         17.03   0.10   17.13
* 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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/clusterExperiment.Rcheck/00check.log'
for details.


clusterExperiment.Rcheck/00install.out:


install for i386

* installing *source* package 'clusterExperiment' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
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_1.0.0.zip
* DONE (clusterExperiment)

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

nameusersystemelapsed
ClusterExperiment-class0.10.00.1
addClusters0.530.020.56
clusterContrasts1.120.041.17
clusterD2.350.082.47
clusterMany2.690.052.73
clusterSingle0.170.000.17
combineMany1.980.062.05
getBestFeatures1.290.001.28
makeDendrogram0.500.030.53
mergeClusters1.230.101.33
plotClusters3.450.083.53
plotHeatmap12.97 0.0913.90
plottingFunctions0.200.000.21
seqCluster000
simData0.030.000.03
subsampleClustering32.64 0.0532.68
transform0.020.000.02
workflowClusters2.200.032.23

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

nameusersystemelapsed
ClusterExperiment-class0.110.000.11
addClusters1.020.021.03
clusterContrasts1.450.001.45
clusterD2.220.022.24
clusterMany3.760.073.84
clusterSingle0.530.020.55
combineMany1.930.001.92
getBestFeatures1.000.021.02
makeDendrogram0.530.010.54
mergeClusters1.920.051.97
plotClusters4.160.094.25
plotHeatmap17.03 0.1017.13
plottingFunctions0.170.030.20
seqCluster000
simData0.030.000.03
subsampleClustering31.84 0.0431.89
transform0.040.000.03
workflowClusters1.930.001.94