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BioC 3.4: CHECK report for FlowSOM on zin1

This page was generated on 2016-09-21 03:39:31 -0700 (Wed, 21 Sep 2016).

Package 430/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 1.5.0
Sofie Van Gassen
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/FlowSOM
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: FlowSOM
Version: 1.5.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings FlowSOM_1.5.0.tar.gz
StartedAt: 2016-09-20 06:31:43 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 06:33:18 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 94.3 seconds
RetCode: 0
Status:  OK 
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings FlowSOM_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-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 ‘1.5.0’
* 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         8.176  0.032   8.221
ProcessGatingML 5.344  0.004   5.356
PlotPies        5.044  0.020   5.065
* 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 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c som.c -o som.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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
AggregateFlowFrames0.1880.0000.187
BuildMST1.3760.0081.384
BuildSOM1.4560.0521.509
FMeasure0.0040.0000.002
FlowSOM8.1760.0328.221
FlowSOMSubset3.4400.0123.454
MetaClustering3.5960.0163.614
NewData3.2360.0043.238
PlotCenters1.3640.0041.369
PlotClusters2D1.2360.0121.250
PlotGroups0.0040.0000.000
PlotMarker1.2280.0081.236
PlotNumbers1.1520.0081.160
PlotPies5.0440.0205.065
PlotStars1.2120.0081.220
PlotStarsSD1.4080.0121.420
PlotVariable1.1480.0041.151
ProcessGatingML5.3440.0045.356
Purity0.0000.0000.001
QueryStarPlot2.1400.0282.167
ReadInput3.7280.0163.755
UpdateNodeSize1.4160.0041.419
metaClustering_consensus2.8280.0042.832