Package: FlowSOM

Version: 1.14.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings FlowSOM_1.14.1.tar.gz

StartedAt: 2019-04-15 23:58:46 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-16 00:00:36 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 110.0 seconds

RetCode: 0

Status:  OK

CheckDir: FlowSOM.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings FlowSOM_1.14.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/FlowSOM.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.14.1’
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
FlowSOM         8.520  0.036   8.572
CountGroups     8.252  0.084   8.364
ProcessGatingML 5.572  0.024   5.605
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL FlowSOM
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘FlowSOM’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c som.c -o som.o
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/FlowSOM/libs
** R
** inst
** byte-compile and prepare 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	0.012	0.215
BuildMST	1.460	0.012	1.473
BuildSOM	1.656	0.008	1.666
CountGroups	8.252	0.084	8.364
FMeasure	0.004	0.000	0.003
FlowSOM	8.520	0.036	8.572
FlowSOMSubset	3.476	0.056	3.536
MetaClustering	3.628	0.008	3.642
NewData	2.752	0.020	2.774
PlotCenters	1.012	0.008	1.021
PlotClusters2D	0.928	0.008	0.935
PlotGroups	0	0	0
PlotMarker	0.9	0.0	0.9
PlotNode	3.736	0.020	3.764
PlotNumbers	0.852	0.004	0.855
PlotPies	4.828	0.016	4.865
PlotStars	1.552	0.000	1.554
PlotVariable	1.024	0.004	1.030
ProcessGatingML	5.572	0.024	5.605
Purity	0.000	0.000	0.001
QueryStarPlot	2.184	0.004	2.196
ReadInput	3.048	0.016	3.069
UpdateNodeSize	1.848	0.004	1.854
metaClustering_consensus	3.328	0.012	3.349