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This page was generated on 2024-06-25 11:37 -0400 (Tue, 25 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4690
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4404
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
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 727/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.13.0  (landing page)
Sofie Van Gassen
Snapshot Date: 2024-06-24 14:00 -0400 (Mon, 24 Jun 2024)
git_url: https://git.bioconductor.org/packages/FlowSOM
git_branch: devel
git_last_commit: 95a62de
git_last_commit_date: 2024-04-30 10:40:56 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 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 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 2.13.0
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_2.13.0.tar.gz
StartedAt: 2024-06-24 23:01:16 -0400 (Mon, 24 Jun 2024)
EndedAt: 2024-06-24 23:10:31 -0400 (Mon, 24 Jun 2024)
EllapsedTime: 555.1 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_2.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.13.0’
* 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 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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        48.230  0.467  48.373
PlotDimRed         43.174  0.085  43.174
PlotMarker         17.065  0.076  17.141
PlotOutliers       15.934  0.040  15.975
UpdateMetaclusters 15.877  0.068  15.945
PlotStars          13.984  0.072  14.056
GroupStats         11.681  0.048  11.729
FlowSOM            10.874  0.135  11.011
PlotGroups         10.545  0.060  10.604
QueryMultiple       8.882  0.028   8.910
query_multiple      8.462  0.012   8.474
AddAnnotation       8.276  0.156   8.433
Plot2DScatters      7.266  0.016   7.254
PlotNumbers         6.997  0.076   7.074
QueryStarPlot       6.882  0.020   6.902
GetFlowJoLabels     6.648  0.100   6.749
PlotManualBars      6.702  0.012   6.714
PlotVariable        6.451  0.012   6.464
PlotNode            6.387  0.024   6.411
PlotPies            5.988  0.012   6.001
UpdateNodeSize      5.352  0.028   5.380
CountGroups         5.245  0.111   5.359
PlotFlowSOM         5.322  0.032   5.354
SaveClustersToFCS   5.058  0.040   5.097
PlotLabels          4.992  0.020   5.012
* 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 11.4.0-1ubuntu1~22.04) 11.4.0’
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
AddAnnotation8.2760.1568.433
AggregateFlowFrames0.0580.0160.074
BuildMST1.0560.0081.064
BuildSOM1.0860.0041.089
CountGroups5.2450.1115.359
FMeasure0.0010.0010.002
FlowSOM10.874 0.13511.011
FlowSOMSubset3.5780.0053.582
FlowSOMmary48.230 0.46748.373
GetChannels0.0260.0000.025
GetClusterMFIs3.6060.0563.662
GetClusterPercentagesPositive3.7740.0883.862
GetClusters4.0050.0164.021
GetCounts3.7140.0203.734
GetFeatures4.7060.0244.730
GetFlowJoLabels6.6480.1006.749
GetMFIs3.9680.0083.976
GetMarkers0.0260.0000.026
GetMetaclusterCVs3.9890.0083.997
GetMetaclusterMFIs4.1740.0124.186
GetMetaclusterPercentagesPositive4.0270.0044.030
GetMetaclusters3.9420.0323.974
GetPercentages4.2340.0324.266
GroupStats11.681 0.04811.729
Initialize_KWSP0.0030.0000.003
Initialize_PCA0.0000.0000.001
MetaClustering2.8270.0162.844
MetaclusterCVs3.9850.0204.005
MetaclusterMFIs4.7260.0084.733
NClusters4.8150.0324.847
NMetaclusters4.2950.0244.320
NewData3.5820.0083.591
Plot2DScatters7.2660.0167.254
PlotCenters0.9850.0241.010
PlotClusters2D1.3500.0321.382
PlotDimRed43.174 0.08543.174
PlotFileScatters1.0430.0401.083
PlotFlowSOM5.3220.0325.354
PlotGroups10.545 0.06010.604
PlotLabels4.9920.0205.012
PlotManualBars6.7020.0126.714
PlotMarker17.065 0.07617.141
PlotNode6.3870.0246.411
PlotNumbers6.9970.0767.074
PlotOutliers15.934 0.04015.975
PlotOverview2D4.5880.0244.612
PlotPies5.9880.0126.001
PlotSD1.8990.0121.911
PlotStars13.984 0.07214.056
PlotVariable6.4510.0126.464
Purity0.0010.0000.001
QueryMultiple8.8820.0288.910
QueryStarPlot6.8820.0206.902
ReadInput3.0350.0363.071
SaveClustersToFCS5.0580.0405.097
TestOutliers4.9090.0564.966
UpdateMetaclusters15.877 0.06815.945
UpdateNodeSize5.3520.0285.380
get_channels0.0270.0000.027
get_markers0.0260.0000.026
metaClustering_consensus2.6390.0242.664
plotStarLegend0.3550.0000.355
print.FlowSOM4.1880.0124.199
query_multiple8.4620.0128.474