BioC 3.6: CHECK report for FlowSOM on malbec1

Package: FlowSOM

Version: 1.9.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings FlowSOM_1.9.0.tar.gz

StartedAt: 2017-08-15 23:11:48 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 23:13:29 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 100.8 seconds

RetCode: 0

Status:  OK

CheckDir: FlowSOM.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings FlowSOM_1.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/FlowSOM.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.9.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
CountGroups     7.572  0.072   7.650
FlowSOM         6.644  0.024   6.670
ProcessGatingML 4.996  0.016   5.015
* 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-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c som.c -o som.o
gcc -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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	0.784	0.000	0.786
BuildMST	1.488	0.024	1.513
BuildSOM	2.136	0.024	2.168
CountGroups	7.572	0.072	7.650
FMeasure	0.004	0.000	0.002
FlowSOM	6.644	0.024	6.670
FlowSOMSubset	2.988	0.012	3.005
MetaClustering	3.048	0.024	3.075
NewData	2.684	0.012	2.698
PlotCenters	1.092	0.020	1.113
PlotClusters2D	0.828	0.000	0.829
PlotGroups	0.000	0.000	0.001
PlotMarker	1.004	0.000	1.004
PlotNode	3.072	0.020	3.097
PlotNumbers	0.916	0.004	0.918
PlotPies	4.376	0.064	4.443
PlotStars	1.232	0.004	1.236
PlotVariable	0.964	0.024	0.990
ProcessGatingML	4.996	0.016	5.015
Purity	0.004	0.000	0.001
QueryStarPlot	1.796	0.024	1.822
ReadInput	2.972	0.024	2.997
UpdateNodeSize	1.340	0.012	1.354
metaClustering_consensus	2.372	0.036	2.408