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This page was generated on 2021-11-26 15:05:49 -0500 (Fri, 26 Nov 2021).

CHECK results for FlowSOM on machv2

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: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
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 20.04.3 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FlowSOM_2.2.0.tar.gz
StartedAt: 2021-11-25 16:42:37 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 16:55:44 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 786.5 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FlowSOM_2.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/FlowSOM.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
FlowSOMmary        85.463  2.450  88.031
PlotDimRed         67.442  1.312  68.894
UpdateMetaclusters 34.078  1.584  35.781
PlotMarker         29.347  1.515  30.950
GroupStats         24.055  1.400  25.490
PlotGroups         21.632  1.395  23.064
FlowSOM            20.006  1.216  21.257
AddAnnotation      14.326  0.880  15.329
QueryMultiple      14.153  0.469  14.638
query_multiple     13.339  0.505  13.874
UpdateNodeSize     13.354  0.427  13.799
PlotNode           12.076  0.902  12.991
PlotStars          11.391  0.919  12.325
QueryStarPlot      11.121  0.329  11.481
PlotFlowSOM         9.794  1.080  10.887
PlotNumbers         9.455  1.378  10.895
Plot2DScatters      9.910  0.624  10.611
PlotManualBars      9.360  1.035  10.407
PlotPies            9.003  0.908   9.932
GetFlowJoLabels     9.303  0.562   9.923
CountGroups         8.207  0.748   8.968
PlotVariable        7.136  0.988   8.137
PlotLabels          6.661  0.863   7.572
SaveClustersToFCS   6.517  0.893   7.457
NClusters           6.488  0.902   7.909
TestOutliers        6.582  0.756   7.364
MetaclusterMFIs     6.622  0.707   7.528
NMetaclusters       6.307  0.912   7.316
print.FlowSOM       5.729  0.993   6.775
MetaclusterCVs      5.898  0.747   6.658
GetFeatures         6.336  0.279   6.627
FlowSOMSubset       6.206  0.389   6.647
GetMetaclusterCVs   5.655  0.922   6.588
GetPercentages      5.602  0.753   6.370
GetMetaclusters     5.569  0.671   6.249
GetMetaclusterMFIs  5.622  0.614   6.264
GetClusterMFIs      5.684  0.531   6.227
PlotOverview2D      5.462  0.689   6.161
GetClusters         5.645  0.499   6.154
GetMFIs             5.410  0.649   6.072
GetCounts           5.162  0.388   5.564
ReadInput           4.947  0.556   5.512
MetaClustering      4.934  0.482   5.470
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.



Installation output

FlowSOM.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FlowSOM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c som.c -o som.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o FlowSOM.so som.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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
AddAnnotation14.326 0.88015.329
AggregateFlowFrames0.1610.0060.167
BuildMST1.7070.0941.803
BuildSOM2.0950.0932.190
CountGroups8.2070.7488.968
FMeasure0.0030.0010.004
FlowSOM20.006 1.21621.257
FlowSOMSubset6.2060.3896.647
FlowSOMmary85.463 2.45088.031
GetChannels0.0590.0030.063
GetClusterMFIs5.6840.5316.227
GetClusters5.6450.4996.154
GetCounts5.1620.3885.564
GetFeatures6.3360.2796.627
GetFlowJoLabels9.3030.5629.923
GetMFIs5.4100.6496.072
GetMarkers0.0560.0020.059
GetMetaclusterCVs5.6550.9226.588
GetMetaclusterMFIs5.6220.6146.264
GetMetaclusters5.5690.6716.249
GetPercentages5.6020.7536.370
GroupStats24.055 1.40025.490
Initialize_KWSP0.0110.0000.011
Initialize_PCA0.0010.0010.002
MetaClustering4.9340.4825.470
MetaclusterCVs5.8980.7476.658
MetaclusterMFIs6.6220.7077.528
NClusters6.4880.9027.909
NMetaclusters6.3070.9127.316
NewData4.5140.4554.980
Plot2DScatters 9.910 0.62410.611
PlotCenters1.5110.1371.650
PlotClusters2D1.5890.0911.684
PlotDimRed67.442 1.31268.894
PlotFileScatters1.0220.0291.051
PlotFlowSOM 9.794 1.08010.887
PlotGroups21.632 1.39523.064
PlotLabels6.6610.8637.572
PlotManualBars 9.360 1.03510.407
PlotMarker29.347 1.51530.950
PlotNode12.076 0.90212.991
PlotNumbers 9.455 1.37810.895
PlotOverview2D5.4620.6896.161
PlotPies9.0030.9089.932
PlotSD3.1170.1873.306
PlotStars11.391 0.91912.325
PlotVariable7.1360.9888.137
Purity0.0010.0000.002
QueryMultiple14.153 0.46914.638
QueryStarPlot11.121 0.32911.481
ReadInput4.9470.5565.512
SaveClustersToFCS6.5170.8937.457
TestOutliers6.5820.7567.364
UpdateMetaclusters34.078 1.58435.781
UpdateNodeSize13.354 0.42713.799
get_channels0.0590.0030.062
get_markers0.0490.0010.051
metaClustering_consensus3.7330.3744.167
plotStarLegend0.4840.0030.488
print.FlowSOM5.7290.9936.775
query_multiple13.339 0.50513.874