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This page was generated on 2025-04-02 19:28 -0400 (Wed, 02 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4426
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 742/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.14.0  (landing page)
Sofie Van Gassen
Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025)
git_url: https://git.bioconductor.org/packages/FlowSOM
git_branch: RELEASE_3_20
git_last_commit: 85b1db5
git_last_commit_date: 2024-10-29 09:57:26 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 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 nebbiolo2

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: 2.14.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings FlowSOM_2.14.0.tar.gz
StartedAt: 2025-03-31 22:15:05 -0400 (Mon, 31 Mar 2025)
EndedAt: 2025-03-31 22:23:58 -0400 (Mon, 31 Mar 2025)
EllapsedTime: 532.7 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings FlowSOM_2.14.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.14.0’
* 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: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
FlowSOMmary        44.906  0.323  45.041
PlotDimRed         42.580  0.181  42.728
PlotOutliers       16.394  0.008  16.402
PlotMarker         15.232  0.032  15.264
UpdateMetaclusters 14.358  0.014  14.373
PlotStars          12.516  0.020  12.535
GroupStats         10.735  0.021  10.757
FlowSOM            10.202  0.076  10.279
PlotGroups          9.496  0.034   9.530
QueryMultiple       8.008  0.005   8.012
Plot2DScatters      7.824  0.029   7.842
query_multiple      7.821  0.009   7.830
AddAnnotation       7.460  0.152   7.613
PlotVariable        6.866  0.008   6.877
PlotManualBars      6.833  0.007   6.841
PlotNumbers         6.524  0.012   6.538
GetFlowJoLabels     6.294  0.146   6.441
QueryStarPlot       6.110  0.012   6.123
PlotNode            6.078  0.005   6.083
PlotFlowSOM         5.569  0.061   5.629
CountGroups         5.516  0.031   5.548
PlotPies            5.471  0.008   5.480
UpdateNodeSize      5.423  0.013   5.437
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.


Installation output

FlowSOM.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c som.c -o som.o
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/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
AddAnnotation7.4600.1527.613
AggregateFlowFrames0.0750.0050.080
BuildMST1.2480.0061.254
BuildSOM1.0190.0151.033
CountGroups5.5160.0315.548
FMeasure0.0010.0000.002
FlowSOM10.202 0.07610.279
FlowSOMSubset4.0260.0234.050
FlowSOMmary44.906 0.32345.041
GetChannels0.0270.0010.028
GetClusterMFIs3.8980.1003.997
GetClusterPercentagesPositive3.5800.0363.616
GetClusters3.5250.0143.539
GetCounts3.5680.0083.576
GetFeatures4.6790.0134.692
GetFlowJoLabels6.2940.1466.441
GetMFIs3.9070.0163.923
GetMarkers0.0260.0000.026
GetMetaclusterCVs3.9970.0624.062
GetMetaclusterMFIs4.0420.0044.047
GetMetaclusterPercentagesPositive4.7560.0244.782
GetMetaclusters3.9180.0103.929
GetPercentages4.2960.0044.300
GroupStats10.735 0.02110.757
Initialize_KWSP0.0030.0000.003
Initialize_PCA000
MetaClustering2.8010.0622.864
MetaclusterCVs4.0290.0174.047
MetaclusterMFIs4.5080.0134.521
NClusters4.8780.0774.956
NMetaclusters4.9670.0144.981
NewData4.2300.0264.256
Plot2DScatters7.8240.0297.842
PlotCenters0.9680.0000.968
PlotClusters2D0.9880.0010.989
PlotDimRed42.580 0.18142.728
PlotFileScatters0.6970.0210.718
PlotFlowSOM5.5690.0615.629
PlotGroups9.4960.0349.530
PlotLabels4.5700.0104.579
PlotManualBars6.8330.0076.841
PlotMarker15.232 0.03215.264
PlotNode6.0780.0056.083
PlotNumbers6.5240.0126.538
PlotOutliers16.394 0.00816.402
PlotOverview2D4.3020.0054.307
PlotPies5.4710.0085.480
PlotSD1.8300.0031.833
PlotStars12.516 0.02012.535
PlotVariable6.8660.0086.877
Purity0.0010.0000.001
QueryMultiple8.0080.0058.012
QueryStarPlot6.1100.0126.123
ReadInput2.8000.0342.834
SaveClustersToFCS4.7340.0144.747
TestOutliers4.3730.0074.380
UpdateMetaclusters14.358 0.01414.373
UpdateNodeSize5.4230.0135.437
get_channels0.0260.0000.027
get_markers0.0260.0000.027
metaClustering_consensus2.2190.0122.231
plotStarLegend0.3640.0020.366
print.FlowSOM4.1720.0124.184
query_multiple7.8210.0097.830