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This page was generated on 2024-06-15 12:33 -0400 (Sat, 15 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4685
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4400
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4349
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: 2024-06-14 14:00 -0400 (Fri, 14 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: 2024-06-14 23:06:27 -0400 (Fri, 14 Jun 2024)
EndedAt: 2024-06-14 23:15:31 -0400 (Fri, 14 Jun 2024)
EllapsedTime: 544.1 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        47.549  0.443  47.641
PlotDimRed         41.284  0.128  41.331
PlotMarker         15.900  0.040  15.941
PlotOutliers       15.551  0.044  15.595
UpdateMetaclusters 15.534  0.056  15.591
PlotStars          13.360  0.016  13.377
GroupStats         11.359  0.040  11.417
FlowSOM            11.108  0.140  11.248
PlotGroups          9.893  0.028   9.920
QueryMultiple       8.885  0.016   8.901
query_multiple      8.522  0.016   8.539
AddAnnotation       8.131  0.196   8.328
GetFlowJoLabels     7.027  0.116   7.145
Plot2DScatters      6.954  0.016   6.941
PlotManualBars      6.608  0.012   6.620
PlotVariable        6.319  0.020   6.340
QueryStarPlot       6.271  0.036   6.307
PlotNode            6.060  0.016   6.077
PlotPies            5.915  0.064   5.980
PlotNumbers         5.877  0.012   5.889
CountGroups         5.454  0.091   5.549
UpdateNodeSize      5.387  0.000   5.388
PlotFlowSOM         5.040  0.044   5.084
* 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

##############################################################################
##############################################################################
###
### 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
AddAnnotation8.1310.1968.328
AggregateFlowFrames0.0660.0030.069
BuildMST1.0500.0091.058
BuildSOM1.0970.0281.125
CountGroups5.4540.0915.549
FMeasure0.0020.0000.002
FlowSOM11.108 0.14011.248
FlowSOMSubset3.7270.0593.787
FlowSOMmary47.549 0.44347.641
GetChannels0.0270.0000.027
GetClusterMFIs3.9110.1164.028
GetClusterPercentagesPositive3.6020.1323.734
GetClusters3.7050.0363.741
GetCounts3.6640.0083.672
GetFeatures4.7510.0044.756
GetFlowJoLabels7.0270.1167.145
GetMFIs4.3110.0244.335
GetMarkers0.0270.0000.027
GetMetaclusterCVs4.1360.0644.200
GetMetaclusterMFIs4.0130.0044.017
GetMetaclusterPercentagesPositive3.9400.0043.944
GetMetaclusters4.0570.0844.142
GetPercentages4.3320.0044.336
GroupStats11.359 0.04011.417
Initialize_KWSP0.0030.0000.003
Initialize_PCA0.0010.0000.001
MetaClustering2.9450.0122.959
MetaclusterCVs4.0910.0204.111
MetaclusterMFIs4.6970.0084.705
NClusters4.5040.0524.556
NMetaclusters4.2860.0244.310
NewData3.6250.0083.633
Plot2DScatters6.9540.0166.941
PlotCenters0.9610.0000.961
PlotClusters2D0.9760.0241.000
PlotDimRed41.284 0.12841.331
PlotFileScatters0.6920.0150.708
PlotFlowSOM5.0400.0445.084
PlotGroups9.8930.0289.920
PlotLabels4.5210.0404.562
PlotManualBars6.6080.0126.620
PlotMarker15.900 0.04015.941
PlotNode6.0600.0166.077
PlotNumbers5.8770.0125.889
PlotOutliers15.551 0.04415.595
PlotOverview2D4.2100.0044.214
PlotPies5.9150.0645.980
PlotSD1.8780.0081.886
PlotStars13.360 0.01613.377
PlotVariable6.3190.0206.340
Purity0.0010.0000.001
QueryMultiple8.8850.0168.901
QueryStarPlot6.2710.0366.307
ReadInput2.9150.0402.955
SaveClustersToFCS4.9510.0284.979
TestOutliers4.5360.0204.557
UpdateMetaclusters15.534 0.05615.591
UpdateNodeSize5.3870.0005.388
get_channels0.0270.0000.027
get_markers0.0270.0000.026
metaClustering_consensus2.3150.0202.335
plotStarLegend0.3590.0030.363
print.FlowSOM4.1990.0204.220
query_multiple8.5220.0168.539