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This page was generated on 2021-07-30 12:05:28 -0400 (Fri, 30 Jul 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 650/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.1.24  (landing page)
Sofie Van Gassen
Snapshot Date: 2021-07-29 14:50:07 -0400 (Thu, 29 Jul 2021)
URL: https://git.bioconductor.org/packages/FlowSOM
Branch: master
Last Commit: aa491e2
Last Changed Date: 2021-07-02 09:32:36 -0400 (Fri, 02 Jul 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  NO, package depends on 'flowWorkspace' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

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: 2021-07-30 02:31:30 -0400 (Fri, 30 Jul 2021)
EndedAt: 2021-07-30 02:43:31 -0400 (Fri, 30 Jul 2021)
EllapsedTime: 721.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: FlowSOM.Rcheck
Warnings: 1

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 4.1.0 RC (2021-05-16 r80304)
* 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 ... WARNING
Undocumented code objects:
  ‘UpdateMetaclusters’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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        82.456  1.997  84.643
PlotDimRed         62.254  1.345  63.715
PlotMarker         27.786  1.350  29.312
GroupStats         24.205  0.902  25.171
PlotGroups         20.521  1.432  21.984
FlowSOM            19.402  0.842  20.278
AddAnnotation      13.706  0.785  14.524
QueryMultiple      13.256  0.335  13.616
query_multiple     13.214  0.332  13.663
PlotStars          11.633  0.652  12.304
UpdateNodeSize     11.808  0.329  12.158
PlotNode           11.296  0.708  12.031
QueryStarPlot      11.112  0.369  11.498
Plot2DScatters      9.990  0.565  10.624
GetFlowJoLabels     9.861  0.583  10.468
PlotManualBars      9.415  0.787  10.265
PlotNumbers         9.063  0.793   9.882
PlotPies            9.095  0.690   9.804
PlotFlowSOM         8.926  0.586   9.538
CountGroups         8.269  0.663   8.954
SaveClustersToFCS   6.961  0.661   7.633
PlotVariable        6.927  0.579   7.518
PlotLabels          6.833  0.595   7.441
NClusters           6.433  0.686   7.192
NMetaclusters       6.245  0.748   7.011
MetaclusterMFIs     6.406  0.585   7.039
TestOutliers        5.864  0.716   6.616
GetFeatures         6.228  0.313   6.597
FlowSOMSubset       5.985  0.365   6.372
print.FlowSOM       5.687  0.630   6.324
GetMetaclusterCVs   5.637  0.616   6.269
MetaclusterCVs      5.657  0.534   6.214
GetClusterMFIs      5.593  0.430   6.077
GetPercentages      5.412  0.594   6.022
GetCounts           5.548  0.396   5.963
PlotOverview2D      5.302  0.566   5.877
GetMFIs             5.366  0.492   5.871
GetMetaclusterMFIs  5.250  0.561   5.856
GetClusters         5.366  0.427   5.852
GetMetaclusters     5.215  0.545   5.776
ReadInput           4.926  0.468   5.403
NewData             4.689  0.372   5.138
* 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 WARNING, 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
AddAnnotation13.706 0.78514.524
AggregateFlowFrames0.1350.0040.139
BuildMST1.4590.0811.543
BuildSOM1.7130.0641.781
CountGroups8.2690.6638.954
FMeasure0.0030.0010.003
FlowSOM19.402 0.84220.278
FlowSOMSubset5.9850.3656.372
FlowSOMmary82.456 1.99784.643
GetChannels0.0460.0010.048
GetClusterMFIs5.5930.4306.077
GetClusters5.3660.4275.852
GetCounts5.5480.3965.963
GetFeatures6.2280.3136.597
GetFlowJoLabels 9.861 0.58310.468
GetMFIs5.3660.4925.871
GetMarkers0.0530.0020.055
GetMetaclusterCVs5.6370.6166.269
GetMetaclusterMFIs5.2500.5615.856
GetMetaclusters5.2150.5455.776
GetPercentages5.4120.5946.022
GroupStats24.205 0.90225.171
Initialize_KWSP0.0100.0000.011
Initialize_PCA0.0010.0000.002
MetaClustering4.3990.4074.839
MetaclusterCVs5.6570.5346.214
MetaclusterMFIs6.4060.5857.039
NClusters6.4330.6867.192
NMetaclusters6.2450.7487.011
NewData4.6890.3725.138
Plot2DScatters 9.990 0.56510.624
PlotCenters1.5090.0741.586
PlotClusters2D1.4460.1621.610
PlotDimRed62.254 1.34563.715
PlotFileScatters0.9730.0261.001
PlotFlowSOM8.9260.5869.538
PlotGroups20.521 1.43221.984
PlotLabels6.8330.5957.441
PlotManualBars 9.415 0.78710.265
PlotMarker27.786 1.35029.312
PlotNode11.296 0.70812.031
PlotNumbers9.0630.7939.882
PlotOverview2D5.3020.5665.877
PlotPies9.0950.6909.804
PlotSD3.4820.2753.762
PlotStars11.633 0.65212.304
PlotVariable6.9270.5797.518
Purity0.0010.0000.001
QueryMultiple13.256 0.33513.616
QueryStarPlot11.112 0.36911.498
ReadInput4.9260.4685.403
SaveClustersToFCS6.9610.6617.633
TestOutliers5.8640.7166.616
UpdateNodeSize11.808 0.32912.158
get_channels0.0500.0020.052
get_markers0.0590.0030.061
metaClustering_consensus3.9430.5154.509
plotStarLegend0.4640.0050.469
print.FlowSOM5.6870.6306.324
query_multiple13.214 0.33213.663