BioC 3.4: CHECK report for FlowSOM on zin1

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

##############################################################################
##############################################################################
###
### 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

* 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)

name	user	system	elapsed
AggregateFlowFrames	0.188	0.000	0.187
BuildMST	1.376	0.008	1.384
BuildSOM	1.456	0.052	1.509
FMeasure	0.004	0.000	0.002
FlowSOM	8.176	0.032	8.221
FlowSOMSubset	3.440	0.012	3.454
MetaClustering	3.596	0.016	3.614
NewData	3.236	0.004	3.238
PlotCenters	1.364	0.004	1.369
PlotClusters2D	1.236	0.012	1.250
PlotGroups	0.004	0.000	0.000
PlotMarker	1.228	0.008	1.236
PlotNumbers	1.152	0.008	1.160
PlotPies	5.044	0.020	5.065
PlotStars	1.212	0.008	1.220
PlotStarsSD	1.408	0.012	1.420
PlotVariable	1.148	0.004	1.151
ProcessGatingML	5.344	0.004	5.356
Purity	0.000	0.000	0.001
QueryStarPlot	2.140	0.028	2.167
ReadInput	3.728	0.016	3.755
UpdateNodeSize	1.416	0.004	1.419
metaClustering_consensus	2.828	0.004	2.832