Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-26 13:05:23 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for FlowSOM on nebbiolo2


To the developers/maintainers of the FlowSOM package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FlowSOM.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 670/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.2.0  (landing page)
Sofie Van Gassen
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/FlowSOM
git_branch: RELEASE_3_14
git_last_commit: 44e9c9b
git_last_commit_date: 2021-10-26 12:18:07 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: FlowSOM
Version: 2.2.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings FlowSOM_2.2.0.tar.gz
StartedAt: 2022-01-25 07:43:07 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 07:52:00 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 533.4 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings FlowSOM_2.2.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/FlowSOM.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘2.2.0’
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
FlowSOMmary        61.381  0.136  61.517
PlotDimRed         49.209  0.020  49.229
PlotMarker         20.466  0.044  20.513
UpdateMetaclusters 20.187  0.012  20.199
GroupStats         16.204  0.040  16.245
FlowSOM            14.649  0.040  14.688
PlotGroups         14.527  0.052  14.581
AddAnnotation      10.591  0.135  10.727
PlotFlowSOM         8.989  0.012   9.002
query_multiple      8.857  0.024   8.882
QueryMultiple       8.447  0.016   8.464
UpdateNodeSize      8.376  0.008   8.384
PlotManualBars      7.724  0.024   7.749
Plot2DScatters      7.678  0.008   7.686
PlotNode            7.497  0.016   7.515
PlotStars           7.324  0.020   7.345
PlotNumbers         6.890  0.016   6.907
PlotPies            6.789  0.028   6.818
GetFlowJoLabels     6.678  0.028   6.707
QueryStarPlot       6.599  0.000   6.600
NClusters           5.866  0.012   5.878
CountGroups         5.724  0.048   5.772
GetFeatures         5.404  0.020   5.425
PlotLabels          5.333  0.036   5.369
MetaclusterMFIs     5.184  0.011   5.196
GetMetaclusterMFIs  5.128  0.012   5.140
MetaclusterCVs      5.078  0.017   5.095
NMetaclusters       5.013  0.024   5.039
* 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-3.14-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.



Installation output

FlowSOM.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c som.c -o som.o
gcc -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-FlowSOM/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (FlowSOM)

Tests output


Example timings

FlowSOM.Rcheck/FlowSOM-Ex.timings

nameusersystemelapsed
AddAnnotation10.591 0.13510.727
AggregateFlowFrames0.0740.0040.078
BuildMST1.0370.0121.049
BuildSOM1.0580.0191.078
CountGroups5.7240.0485.772
FMeasure0.0020.0000.001
FlowSOM14.649 0.04014.688
FlowSOMSubset4.9090.0204.929
FlowSOMmary61.381 0.13661.517
GetChannels0.0250.0000.024
GetClusterMFIs4.3270.0324.358
GetClusters4.6140.0164.629
GetCounts4.5560.0204.577
GetFeatures5.4040.0205.425
GetFlowJoLabels6.6780.0286.707
GetMFIs4.1410.0164.159
GetMarkers0.0230.0000.024
GetMetaclusterCVs4.2920.0034.296
GetMetaclusterMFIs5.1280.0125.140
GetMetaclusters4.7090.0014.709
GetPercentages4.7840.0044.789
GroupStats16.204 0.04016.245
Initialize_KWSP0.0030.0000.004
Initialize_PCA0.0010.0000.001
MetaClustering3.3740.0113.386
MetaclusterCVs5.0780.0175.095
MetaclusterMFIs5.1840.0115.196
NClusters5.8660.0125.878
NMetaclusters5.0130.0245.039
NewData4.8150.0164.831
Plot2DScatters7.6780.0087.686
PlotCenters1.0850.0081.092
PlotClusters2D0.9260.0040.929
PlotDimRed49.209 0.02049.229
PlotFileScatters1.3190.0041.322
PlotFlowSOM8.9890.0129.002
PlotGroups14.527 0.05214.581
PlotLabels5.3330.0365.369
PlotManualBars7.7240.0247.749
PlotMarker20.466 0.04420.513
PlotNode7.4970.0167.515
PlotNumbers6.8900.0166.907
PlotOverview2D4.0980.0044.103
PlotPies6.7890.0286.818
PlotSD2.0920.0082.100
PlotStars7.3240.0207.345
PlotVariable4.7270.0084.735
Purity0.0000.0000.001
QueryMultiple8.4470.0168.464
QueryStarPlot6.5990.0006.600
ReadInput2.9250.0242.981
SaveClustersToFCS4.8850.0084.893
TestOutliers4.8970.0204.917
UpdateMetaclusters20.187 0.01220.199
UpdateNodeSize8.3760.0088.384
get_channels0.0210.0000.021
get_markers0.0180.0040.023
metaClustering_consensus2.1780.0122.190
plotStarLegend0.3040.0000.304
print.FlowSOM3.9090.0163.926
query_multiple8.8570.0248.882