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BioC 3.6: CHECK report for FlowSOM on malbec1

This page was generated on 2017-08-16 13:22:45 -0400 (Wed, 16 Aug 2017).

Package 475/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 1.9.0
Sofie Van Gassen
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/FlowSOM
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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


* 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

FlowSOM.Rcheck/00install.out:

* 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)

FlowSOM.Rcheck/FlowSOM-Ex.timings:

nameusersystemelapsed
AggregateFlowFrames0.7840.0000.786
BuildMST1.4880.0241.513
BuildSOM2.1360.0242.168
CountGroups7.5720.0727.650
FMeasure0.0040.0000.002
FlowSOM6.6440.0246.670
FlowSOMSubset2.9880.0123.005
MetaClustering3.0480.0243.075
NewData2.6840.0122.698
PlotCenters1.0920.0201.113
PlotClusters2D0.8280.0000.829
PlotGroups0.0000.0000.001
PlotMarker1.0040.0001.004
PlotNode3.0720.0203.097
PlotNumbers0.9160.0040.918
PlotPies4.3760.0644.443
PlotStars1.2320.0041.236
PlotVariable0.9640.0240.990
ProcessGatingML4.9960.0165.015
Purity0.0040.0000.001
QueryStarPlot1.7960.0241.822
ReadInput2.9720.0242.997
UpdateNodeSize1.3400.0121.354
metaClustering_consensus2.3720.0362.408