Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-08-04 11:47 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 756/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.16.0  (landing page)
Sofie Van Gassen
Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 2025)
git_url: https://git.bioconductor.org/packages/FlowSOM
git_branch: RELEASE_3_21
git_last_commit: 4bdaa3d
git_last_commit_date: 2025-04-15 10:36:59 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for FlowSOM on kunpeng2

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: 2.16.0
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_2.16.0.tar.gz
StartedAt: 2025-08-01 09:24:21 -0000 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 09:36:05 -0000 (Fri, 01 Aug 2025)
EllapsedTime: 704.4 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_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.16.0’
* 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                        78.957  0.160  79.238
FlowSOMmary                       73.436  0.307  73.810
PlotOutliers                      24.814  0.096  24.974
UpdateMetaclusters                21.991  0.072  22.124
PlotMarker                        21.734  0.052  21.841
PlotStars                         18.891  0.040  18.973
GroupStats                        16.547  0.079  16.670
FlowSOM                           16.262  0.132  16.431
PlotGroups                        15.456  0.004  15.500
AddAnnotation                     11.835  0.208  12.075
QueryMultiple                     11.756  0.020  11.806
query_multiple                    11.744  0.016  11.791
Plot2DScatters                    10.782  0.020  10.830
PlotManualBars                    10.482  0.012  10.519
GetFlowJoLabels                    9.774  0.056   9.857
PlotNode                           9.575  0.020   9.621
CountGroups                        9.020  0.072   9.113
PlotVariable                       8.827  0.047   8.898
QueryStarPlot                      8.848  0.008   8.877
PlotNumbers                        8.795  0.012   8.830
PlotPies                           8.479  0.016   8.516
PlotFlowSOM                        7.776  0.048   7.841
UpdateNodeSize                     7.744  0.004   7.769
SaveClustersToFCS                  7.651  0.004   7.675
NClusters                          7.421  0.008   7.446
GetFeatures                        7.325  0.044   7.388
PlotLabels                         7.185  0.040   7.240
NMetaclusters                      7.020  0.016   7.051
TestOutliers                       6.726  0.044   6.791
MetaclusterMFIs                    6.562  0.016   6.596
GetMetaclusterPercentagesPositive  6.475  0.020   6.508
PlotOverview2D                     6.365  0.036   6.416
GetMetaclusterCVs                  6.309  0.028   6.351
MetaclusterCVs                     6.210  0.032   6.256
print.FlowSOM                      6.221  0.008   6.245
GetMFIs                            6.177  0.012   6.203
FlowSOMSubset                      6.154  0.008   6.176
GetMetaclusters                    6.122  0.032   6.169
GetPercentages                     6.119  0.004   6.137
GetMetaclusterMFIs                 6.110  0.008   6.133
GetCounts                          5.739  0.008   5.761
GetClusterMFIs                     5.668  0.064   5.747
GetClusterPercentagesPositive      5.716  0.012   5.744
GetClusters                        5.688  0.012   5.715
NewData                            5.138  0.044   5.194
ReadInput                          5.100  0.024   5.137
* 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-3.21-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.


Installation output

FlowSOM.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.16.0’
** 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/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/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/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
AddAnnotation11.835 0.20812.075
AggregateFlowFrames0.0870.0120.099
BuildMST2.0660.0152.088
BuildSOM1.8080.0201.832
CountGroups9.0200.0729.113
FMeasure0.0020.0000.002
FlowSOM16.262 0.13216.431
FlowSOMSubset6.1540.0086.176
FlowSOMmary73.436 0.30773.810
GetChannels0.0310.0000.031
GetClusterMFIs5.6680.0645.747
GetClusterPercentagesPositive5.7160.0125.744
GetClusters5.6880.0125.715
GetCounts5.7390.0085.761
GetFeatures7.3250.0447.388
GetFlowJoLabels9.7740.0569.857
GetMFIs6.1770.0126.203
GetMarkers0.0340.0000.034
GetMetaclusterCVs6.3090.0286.351
GetMetaclusterMFIs6.1100.0086.133
GetMetaclusterPercentagesPositive6.4750.0206.508
GetMetaclusters6.1220.0326.169
GetPercentages6.1190.0046.137
GroupStats16.547 0.07916.670
Initialize_KWSP0.0060.0000.007
Initialize_PCA0.0010.0000.001
MetaClustering4.5170.0244.551
MetaclusterCVs6.2100.0326.256
MetaclusterMFIs6.5620.0166.596
NClusters7.4210.0087.446
NMetaclusters7.0200.0167.051
NewData5.1380.0445.194
Plot2DScatters10.782 0.02010.830
PlotCenters1.7440.0001.748
PlotClusters2D1.7450.0001.749
PlotDimRed78.957 0.16079.238
PlotFileScatters1.0620.0391.106
PlotFlowSOM7.7760.0487.841
PlotGroups15.456 0.00415.500
PlotLabels7.1850.0407.240
PlotManualBars10.482 0.01210.519
PlotMarker21.734 0.05221.841
PlotNode9.5750.0209.621
PlotNumbers8.7950.0128.830
PlotOutliers24.814 0.09624.974
PlotOverview2D6.3650.0366.416
PlotPies8.4790.0168.516
PlotSD2.8890.0002.896
PlotStars18.891 0.04018.973
PlotVariable8.8270.0478.898
Purity0.0010.0000.001
QueryMultiple11.756 0.02011.806
QueryStarPlot8.8480.0088.877
ReadInput5.1000.0245.137
SaveClustersToFCS7.6510.0047.675
TestOutliers6.7260.0446.791
UpdateMetaclusters21.991 0.07222.124
UpdateNodeSize7.7440.0047.769
get_channels0.0480.0000.048
get_markers0.0330.0000.034
metaClustering_consensus3.7610.0123.783
plotStarLegend0.4870.0040.491
print.FlowSOM6.2210.0086.245
query_multiple11.744 0.01611.791