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This page was generated on 2025-09-23 12:07 -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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: FlowSOM
Version: 2.17.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings FlowSOM_2.17.0.tar.gz
StartedAt: 2025-09-23 07:22:07 -0000 (Tue, 23 Sep 2025)
EndedAt: 2025-09-23 07:34:07 -0000 (Tue, 23 Sep 2025)
EllapsedTime: 720.0 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings FlowSOM_2.17.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
PlotDimRed                        75.258  0.220  75.646
FlowSOMmary                       74.340  0.354  74.786
PlotOutliers                      42.957  0.096  43.179
PlotMarker                        23.876  0.119  24.069
UpdateMetaclusters                22.667  0.044  22.769
PlotStars                         19.328  0.044  19.420
GroupStats                        17.191  0.602  17.841
PlotGroups                        15.577  0.024  15.647
FlowSOM                           15.491  0.032  15.556
Plot2DScatters                    13.203  0.143  13.386
QueryMultiple                     13.022  0.048  13.097
query_multiple                    13.023  0.000  13.055
AddAnnotation                     11.620  0.132  11.779
PlotManualBars                    11.572  0.004  11.613
QueryStarPlot                      9.701  0.024   9.745
PlotNode                           9.597  0.008   9.632
PlotNumbers                        9.375  0.044   9.444
GetFlowJoLabels                    9.263  0.147   9.433
PlotPies                           8.871  0.028   8.925
UpdateNodeSize                     8.572  0.024   8.616
PlotVariable                       8.472  0.051   8.540
CountGroups                        8.221  0.052   8.290
PlotFlowSOM                        7.924  0.052   7.999
GetFeatures                        6.996  0.084   7.094
SaveClustersToFCS                  7.052  0.012   7.080
PlotLabels                         6.978  0.071   7.070
GetPercentages                     6.483  0.403   6.906
PlotOverview2D                     6.497  0.028   6.543
NClusters                          6.445  0.079   6.545
NMetaclusters                      6.432  0.068   6.519
MetaclusterMFIs                    6.396  0.036   6.450
TestOutliers                       6.223  0.007   6.244
GetMFIs                            5.766  0.100   5.881
GetMetaclusterCVs                  5.787  0.076   5.874
GetMetaclusters                    5.785  0.063   5.864
MetaclusterCVs                     5.740  0.100   5.855
GetClusterMFIs                     5.542  0.220   5.774
GetMetaclusterPercentagesPositive  5.653  0.056   5.723
GetMetaclusterMFIs                 5.617  0.076   5.702
print.FlowSOM                      5.626  0.016   5.655
GetClusterPercentagesPositive      5.470  0.131   5.614
GetCounts                          5.488  0.060   5.560
GetClusters                        5.407  0.088   5.511
FlowSOMSubset                      5.248  0.024   5.284
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.


Installation output

FlowSOM.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.17.0’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c som.c -o som.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-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
AddAnnotation11.620 0.13211.779
AggregateFlowFrames0.0810.0040.086
BuildMST2.0140.0042.021
BuildSOM1.6750.0121.691
CountGroups8.2210.0528.290
FMeasure0.0020.0000.002
FlowSOM15.491 0.03215.556
FlowSOMSubset5.2480.0245.284
FlowSOMmary74.340 0.35474.786
GetChannels0.0350.0000.035
GetClusterMFIs5.5420.2205.774
GetClusterPercentagesPositive5.4700.1315.614
GetClusters5.4070.0885.511
GetCounts5.4880.0605.560
GetFeatures6.9960.0847.094
GetFlowJoLabels9.2630.1479.433
GetMFIs5.7660.1005.881
GetMarkers0.0350.0000.035
GetMetaclusterCVs5.7870.0765.874
GetMetaclusterMFIs5.6170.0765.702
GetMetaclusterPercentagesPositive5.6530.0565.723
GetMetaclusters5.7850.0635.864
GetPercentages6.4830.4036.906
GroupStats17.191 0.60217.841
Initialize_KWSP0.0060.0000.006
Initialize_PCA0.0010.0000.001
MetaClustering4.2010.0964.309
MetaclusterCVs5.7400.1005.855
MetaclusterMFIs6.3960.0366.450
NClusters6.4450.0796.545
NMetaclusters6.4320.0686.519
NewData4.6550.0604.728
Plot2DScatters13.203 0.14313.386
PlotCenters1.7630.0241.792
PlotClusters2D1.6430.0041.651
PlotDimRed75.258 0.22075.646
PlotFileScatters1.7680.0121.786
PlotFlowSOM7.9240.0527.999
PlotGroups15.577 0.02415.647
PlotLabels6.9780.0717.070
PlotManualBars11.572 0.00411.613
PlotMarker23.876 0.11924.069
PlotNode9.5970.0089.632
PlotNumbers9.3750.0449.444
PlotOutliers42.957 0.09643.179
PlotOverview2D6.4970.0286.543
PlotPies8.8710.0288.925
PlotSD2.8800.0202.908
PlotStars19.328 0.04419.420
PlotVariable8.4720.0518.540
Purity0.0010.0000.001
QueryMultiple13.022 0.04813.097
QueryStarPlot9.7010.0249.745
ReadInput4.4530.0244.490
SaveClustersToFCS7.0520.0127.080
TestOutliers6.2230.0076.244
UpdateMetaclusters22.667 0.04422.769
UpdateNodeSize8.5720.0248.616
get_channels0.0300.0000.031
get_markers0.0310.0000.031
metaClustering_consensus3.7730.0723.853
plotStarLegend0.6320.0000.633
print.FlowSOM5.6260.0165.655
query_multiple13.023 0.00013.055