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This page was generated on 2025-09-23 12:04 -0400 (Tue, 23 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4816
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4605
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4549
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4560
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

Package 756/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.17.0  (landing page)
Sofie Van Gassen
Snapshot Date: 2025-09-22 13:45 -0400 (Mon, 22 Sep 2025)
git_url: https://git.bioconductor.org/packages/FlowSOM
git_branch: devel
git_last_commit: d549275
git_last_commit_date: 2025-04-15 10:36:59 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for FlowSOM on lconway

To the developers/maintainers of the FlowSOM package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: FlowSOM
Version: 2.17.0
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_2.17.0.tar.gz
StartedAt: 2025-09-22 21:06:29 -0400 (Mon, 22 Sep 2025)
EndedAt: 2025-09-22 21:16:57 -0400 (Mon, 22 Sep 2025)
EllapsedTime: 628.2 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_2.17.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.17.0’
* package encoding: UTF-8
* 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
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 code 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 whether startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) PlotDimRed.Rd:55: Lost braces
    55 | of the dimred default = function(dimred){dimred$Y}.}
       |                                         ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'pipe.Rd':
  ‘[magrittr:pipe]{%>%}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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                       53.278  2.117  55.515
PlotDimRed                        43.425  2.243  46.154
PlotOutliers                      35.041  1.029  36.489
PlotMarker                        21.242  1.272  22.965
UpdateMetaclusters                17.489  1.251  18.925
PlotStars                         16.426  1.003  17.630
PlotGroups                        14.334  1.232  15.880
GroupStats                        13.605  0.867  14.588
FlowSOM                           12.839  0.980  13.940
Plot2DScatters                    11.975  0.740  12.843
QueryMultiple                     10.987  0.458  11.706
query_multiple                    10.781  0.428  11.334
AddAnnotation                      9.892  0.644  10.625
PlotManualBars                     9.560  0.814  10.537
PlotNode                           8.576  0.837   9.600
QueryStarPlot                      8.741  0.328   9.160
PlotNumbers                        8.160  0.700   9.012
PlotVariable                       7.597  0.740   8.442
PlotPies                           7.446  0.833   8.382
GetFlowJoLabels                    7.547  0.602   8.214
PlotFlowSOM                        6.754  0.828   7.734
UpdateNodeSize                     6.895  0.355   7.329
NClusters                          5.896  0.744   6.727
SaveClustersToFCS                  5.607  0.984   6.819
CountGroups                        5.891  0.602   6.546
NMetaclusters                      5.746  0.729   6.559
PlotLabels                         5.645  0.684   6.439
PlotOverview2D                     5.459  0.704   6.242
MetaclusterMFIs                    5.343  0.742   6.167
GetFeatures                        5.716  0.360   6.144
GetPercentages                     5.166  0.675   5.911
TestOutliers                       4.991  0.680   5.744
print.FlowSOM                      4.674  0.796   5.543
MetaclusterCVs                     4.741  0.721   5.528
GetMetaclusterPercentagesPositive  4.743  0.680   5.472
GetMFIs                            4.643  0.612   5.293
GetMetaclusterMFIs                 4.600  0.640   5.290
GetMetaclusters                    4.665  0.573   5.281
GetMetaclusterCVs                  4.566  0.595   5.194
NewData                            4.567  0.506   5.136
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.


Installation output

FlowSOM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.17.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c som.c -o som.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o FlowSOM.so som.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/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
AddAnnotation 9.892 0.64410.625
AggregateFlowFrames0.1030.0050.110
BuildMST1.5640.0871.664
BuildSOM1.5970.0911.711
CountGroups5.8910.6026.546
FMeasure0.0010.0000.002
FlowSOM12.839 0.98013.940
FlowSOMSubset4.2310.4164.679
FlowSOMmary53.278 2.11755.515
GetChannels0.0450.0030.048
GetClusterMFIs4.2990.3984.741
GetClusterPercentagesPositive4.4160.4304.895
GetClusters4.2610.4504.757
GetCounts4.2450.4474.743
GetFeatures5.7160.3606.144
GetFlowJoLabels7.5470.6028.214
GetMFIs4.6430.6125.293
GetMarkers0.0390.0020.042
GetMetaclusterCVs4.5660.5955.194
GetMetaclusterMFIs4.600.645.29
GetMetaclusterPercentagesPositive4.7430.6805.472
GetMetaclusters4.6650.5735.281
GetPercentages5.1660.6755.911
GroupStats13.605 0.86714.588
Initialize_KWSP0.0060.0000.007
Initialize_PCA0.0010.0010.001
MetaClustering3.3760.6764.097
MetaclusterCVs4.7410.7215.528
MetaclusterMFIs5.3430.7426.167
NClusters5.8960.7446.727
NMetaclusters5.7460.7296.559
NewData4.5670.5065.136
Plot2DScatters11.975 0.74012.843
PlotCenters1.3750.0991.484
PlotClusters2D1.2870.1231.423
PlotDimRed43.425 2.24346.154
PlotFileScatters1.5650.0381.617
PlotFlowSOM6.7540.8287.734
PlotGroups14.334 1.23215.880
PlotLabels5.6450.6846.439
PlotManualBars 9.560 0.81410.537
PlotMarker21.242 1.27222.965
PlotNode8.5760.8379.600
PlotNumbers8.1600.7009.012
PlotOutliers35.041 1.02936.489
PlotOverview2D5.4590.7046.242
PlotPies7.4460.8338.382
PlotSD2.7900.2143.032
PlotStars16.426 1.00317.630
PlotVariable7.5970.7408.442
Purity0.0010.0010.001
QueryMultiple10.987 0.45811.706
QueryStarPlot8.7410.3289.160
ReadInput3.2630.6073.955
SaveClustersToFCS5.6070.9846.819
TestOutliers4.9910.6805.744
UpdateMetaclusters17.489 1.25118.925
UpdateNodeSize6.8950.3557.329
get_channels0.0430.0030.046
get_markers0.0420.0020.045
metaClustering_consensus2.4910.4933.026
plotStarLegend0.4940.0060.503
print.FlowSOM4.6740.7965.543
query_multiple10.781 0.42811.334