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This page was generated on 2021-10-23 14:05:59 -0400 (Sat, 23 Oct 2021).

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 2.1.24  (landing page)
Sofie Van Gassen
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/FlowSOM
git_branch: master
git_last_commit: 2da26cf
git_last_commit_date: 2021-10-20 11:08:54 -0400 (Wed, 20 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: FlowSOM
Version: 2.1.24
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_2.1.24.tar.gz
StartedAt: 2021-10-22 20:08:31 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 20:16:46 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 494.8 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_2.1.24.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/FlowSOM.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘2.1.24’
* 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        57.713  0.632  58.351
PlotDimRed         43.858  0.040  43.899
PlotMarker         20.269  0.028  20.299
UpdateMetaclusters 18.924  0.056  18.981
GroupStats         15.230  0.036  15.267
PlotGroups         14.177  0.087  14.265
FlowSOM            12.484  0.080  12.566
AddAnnotation       9.840  0.139   9.981
QueryMultiple       9.041  0.012   9.055
PlotStars           7.896  0.012   7.909
query_multiple      7.812  0.032   7.844
PlotNode            7.678  0.016   7.694
UpdateNodeSize      7.489  0.012   7.502
PlotManualBars      7.428  0.012   7.441
PlotFlowSOM         7.293  0.024   7.318
GetFlowJoLabels     7.166  0.024   7.191
QueryStarPlot       7.121  0.016   7.137
Plot2DScatters      7.111  0.008   7.120
PlotNumbers         6.628  0.020   6.649
PlotPies            6.439  0.016   6.455
PlotVariable        5.728  0.008   5.737
MetaclusterMFIs     5.439  0.004   5.443
PlotLabels          5.314  0.016   5.330
CountGroups         5.088  0.079   5.171
NMetaclusters       5.056  0.032   5.087
SaveClustersToFCS   5.061  0.012   5.073
* 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
###
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* 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
AddAnnotation9.8400.1399.981
AggregateFlowFrames0.0700.0010.071
BuildMST0.9950.0161.012
BuildSOM1.0090.0041.014
CountGroups5.0880.0795.171
FMeasure0.0010.0000.001
FlowSOM12.484 0.08012.566
FlowSOMSubset4.7280.1964.924
FlowSOMmary57.713 0.63258.351
GetChannels0.0230.0000.023
GetClusterMFIs4.8770.0244.917
GetClusters4.3980.0204.418
GetCounts4.9650.0044.969
GetFeatures4.6650.0084.674
GetFlowJoLabels7.1660.0247.191
GetMFIs4.3220.0244.346
GetMarkers0.0230.0000.023
GetMetaclusterCVs4.5870.0284.616
GetMetaclusterMFIs4.3640.0124.378
GetMetaclusters4.7100.0044.714
GetPercentages4.8110.0204.831
GroupStats15.230 0.03615.267
Initialize_KWSP0.0040.0000.005
Initialize_PCA0.0010.0000.001
MetaClustering2.8480.0322.881
MetaclusterCVs4.2620.0004.263
MetaclusterMFIs5.4390.0045.443
NClusters4.8370.0124.849
NMetaclusters5.0560.0325.087
NewData3.9990.0044.004
Plot2DScatters7.1110.0087.120
PlotCenters0.9470.0040.951
PlotClusters2D0.9040.0000.904
PlotDimRed43.858 0.04043.899
PlotFileScatters0.5990.0000.599
PlotFlowSOM7.2930.0247.318
PlotGroups14.177 0.08714.265
PlotLabels5.3140.0165.330
PlotManualBars7.4280.0127.441
PlotMarker20.269 0.02820.299
PlotNode7.6780.0167.694
PlotNumbers6.6280.0206.649
PlotOverview2D4.2080.0004.209
PlotPies6.4390.0166.455
PlotSD2.4680.0202.488
PlotStars7.8960.0127.909
PlotVariable5.7280.0085.737
Purity0.0000.0000.001
QueryMultiple9.0410.0129.055
QueryStarPlot7.1210.0167.137
ReadInput2.9270.0162.943
SaveClustersToFCS5.0610.0125.073
TestOutliers4.7990.0244.824
UpdateMetaclusters18.924 0.05618.981
UpdateNodeSize7.4890.0127.502
get_channels0.0180.0040.022
get_markers0.0210.0000.021
metaClustering_consensus2.2190.0322.251
plotStarLegend0.3060.0000.306
print.FlowSOM3.5510.0203.571
query_multiple7.8120.0327.844