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This page was generated on 2021-10-22 12:04:58 -0400 (Fri, 22 Oct 2021).

CHECK results for FlowSOM on merida1

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 666/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.1.24  (landing page)
Sofie Van Gassen
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 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    NA  

Summary

Package: FlowSOM
Version: 2.1.24
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_2.1.24.tar.gz
StartedAt: 2021-10-22 03:55:32 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 04:08:12 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 760.6 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_2.1.24.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/FlowSOM.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* 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 ‘2.1.24’
* 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 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        78.780  1.905  80.835
PlotDimRed         61.864  1.420  63.399
UpdateMetaclusters 33.344  1.120  34.527
PlotMarker         28.999  1.083  30.133
GroupStats         23.719  0.926  24.686
PlotGroups         21.032  0.902  21.972
FlowSOM            19.146  0.919  20.103
AddAnnotation      14.089  0.712  14.842
UpdateNodeSize     14.323  0.300  14.646
QueryMultiple      14.258  0.326  14.621
query_multiple     14.023  0.341  14.389
PlotStars          11.904  0.604  12.562
PlotNode           11.075  0.631  11.729
QueryStarPlot      11.075  0.264  11.407
Plot2DScatters     10.149  0.542  10.722
PlotManualBars      9.578  0.590  10.191
PlotFlowSOM         9.278  0.699  10.001
GetFlowJoLabels     9.099  0.367   9.489
PlotNumbers         8.843  0.609   9.482
PlotPies            8.844  0.492   9.359
CountGroups         7.779  0.638   8.433
SaveClustersToFCS   6.764  0.796   7.576
MetaclusterMFIs     6.704  0.692   7.415
TestOutliers        6.742  0.651   7.412
PlotVariable        6.929  0.455   7.415
NClusters           6.413  0.722   7.162
PlotLabels          6.602  0.498   7.120
NMetaclusters       6.451  0.557   7.024
GetFeatures         6.570  0.196   6.787
GetCounts           6.329  0.256   6.603
GetClusters         6.013  0.325   6.355
print.FlowSOM       5.755  0.569   6.340
MetaclusterCVs      5.463  0.582   6.070
GetClusterMFIs      5.692  0.303   6.012
FlowSOMSubset       5.583  0.294   5.891
GetPercentages      5.431  0.378   5.826
PlotOverview2D      5.453  0.353   5.826
GetMetaclusterCVs   5.297  0.491   5.807
ReadInput           5.244  0.517   5.780
GetMetaclusterMFIs  5.314  0.443   5.773
GetMetaclusters     5.249  0.435   5.698
GetMFIs             4.921  0.382   5.319
NewData             4.867  0.259   5.141
* 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
AddAnnotation14.089 0.71214.842
AggregateFlowFrames0.1470.0040.151
BuildMST1.6480.0881.742
BuildSOM1.8580.0631.923
CountGroups7.7790.6388.433
FMeasure0.0020.0000.002
FlowSOM19.146 0.91920.103
FlowSOMSubset5.5830.2945.891
FlowSOMmary78.780 1.90580.835
GetChannels0.0460.0010.047
GetClusterMFIs5.6920.3036.012
GetClusters6.0130.3256.355
GetCounts6.3290.2566.603
GetFeatures6.5700.1966.787
GetFlowJoLabels9.0990.3679.489
GetMFIs4.9210.3825.319
GetMarkers0.0450.0010.047
GetMetaclusterCVs5.2970.4915.807
GetMetaclusterMFIs5.3140.4435.773
GetMetaclusters5.2490.4355.698
GetPercentages5.4310.3785.826
GroupStats23.719 0.92624.686
Initialize_KWSP0.0090.0000.009
Initialize_PCA0.0010.0000.002
MetaClustering4.3930.1944.601
MetaclusterCVs5.4630.5826.070
MetaclusterMFIs6.7040.6927.415
NClusters6.4130.7227.162
NMetaclusters6.4510.5577.024
NewData4.8670.2595.141
Plot2DScatters10.149 0.54210.722
PlotCenters1.4730.0871.563
PlotClusters2D1.4540.0841.540
PlotDimRed61.864 1.42063.399
PlotFileScatters0.9400.0120.953
PlotFlowSOM 9.278 0.69910.001
PlotGroups21.032 0.90221.972
PlotLabels6.6020.4987.120
PlotManualBars 9.578 0.59010.191
PlotMarker28.999 1.08330.133
PlotNode11.075 0.63111.729
PlotNumbers8.8430.6099.482
PlotOverview2D5.4530.3535.826
PlotPies8.8440.4929.359
PlotSD3.0850.1353.231
PlotStars11.904 0.60412.562
PlotVariable6.9290.4557.415
Purity0.0010.0000.001
QueryMultiple14.258 0.32614.621
QueryStarPlot11.075 0.26411.407
ReadInput5.2440.5175.780
SaveClustersToFCS6.7640.7967.576
TestOutliers6.7420.6517.412
UpdateMetaclusters33.344 1.12034.527
UpdateNodeSize14.323 0.30014.646
get_channels0.0560.0010.058
get_markers0.0570.0020.059
metaClustering_consensus3.9010.3294.247
plotStarLegend0.5240.0040.529
print.FlowSOM5.7550.5696.340
query_multiple14.023 0.34114.389