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BioC 3.3: CHECK report for FlowSOM on zin2

This page was generated on 2016-10-13 12:45:14 -0700 (Thu, 13 Oct 2016).

Package 409/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 1.4.0
Sofie Van Gassen
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/FlowSOM
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: FlowSOM
Version: 1.4.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings FlowSOM_1.4.0.tar.gz
StartedAt: 2016-10-13 02:05:44 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 02:07:29 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 104.7 seconds
RetCode: 0
Status:  OK 
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings FlowSOM_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/FlowSOM.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘1.4.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘FlowSOM’ 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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
FlowSOM         8.059  0.039   8.254
PlotPies        5.272  0.036   5.332
ProcessGatingML 5.151  0.020   5.208
* 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

FlowSOM.Rcheck/00install.out:

* installing *source* package ‘FlowSOM’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c som.c -o som.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/FlowSOM.Rcheck/FlowSOM/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (FlowSOM)

FlowSOM.Rcheck/FlowSOM-Ex.timings:

nameusersystemelapsed
AggregateFlowFrames0.1760.0080.196
BuildMST1.4500.0121.479
BuildSOM1.5680.0321.602
FMeasure0.0020.0000.003
FlowSOM8.0590.0398.254
FlowSOMSubset3.7320.0163.749
MetaClustering4.0350.0204.141
NewData3.4340.0083.471
PlotCenters1.4530.0041.464
PlotClusters2D1.2160.0121.234
PlotGroups0.0010.0000.000
PlotMarker1.1170.0081.134
PlotNumbers1.4040.0001.413
PlotPies5.2720.0365.332
PlotStars1.2390.0041.245
PlotStarsSD1.4220.0121.446
PlotVariable1.1450.0041.148
ProcessGatingML5.1510.0205.208
Purity0.0010.0000.002
QueryStarPlot2.2230.0122.242
ReadInput4.090.024.16
UpdateNodeSize1.5190.0041.527
metaClustering_consensus2.9800.0002.984