BioC 3.3: CHECK report for FlowSOM on zin2

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

* 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)

name	user	system	elapsed
AggregateFlowFrames	0.176	0.008	0.196
BuildMST	1.450	0.012	1.479
BuildSOM	1.568	0.032	1.602
FMeasure	0.002	0.000	0.003
FlowSOM	8.059	0.039	8.254
FlowSOMSubset	3.732	0.016	3.749
MetaClustering	4.035	0.020	4.141
NewData	3.434	0.008	3.471
PlotCenters	1.453	0.004	1.464
PlotClusters2D	1.216	0.012	1.234
PlotGroups	0.001	0.000	0.000
PlotMarker	1.117	0.008	1.134
PlotNumbers	1.404	0.000	1.413
PlotPies	5.272	0.036	5.332
PlotStars	1.239	0.004	1.245
PlotStarsSD	1.422	0.012	1.446
PlotVariable	1.145	0.004	1.148
ProcessGatingML	5.151	0.020	5.208
Purity	0.001	0.000	0.002
QueryStarPlot	2.223	0.012	2.242
ReadInput	4.09	0.02	4.16
UpdateNodeSize	1.519	0.004	1.527
metaClustering_consensus	2.980	0.000	2.984

BioC 3.3: CHECK report for FlowSOM on zin2

Summary

Command output