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This page was generated on 2024-06-11 14:39 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 750/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.12.0  (landing page)
Sofie Van Gassen
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/FlowSOM
git_branch: RELEASE_3_19
git_last_commit: 128641a
git_last_commit_date: 2024-04-30 10:40:56 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    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 nebbiolo1

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: 2.12.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings FlowSOM_2.12.0.tar.gz
StartedAt: 2024-06-09 23:06:26 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 23:15:48 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 561.3 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings FlowSOM_2.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 ‘2.12.0’
* 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        47.440  0.468  47.574
PlotDimRed         42.642  0.148  42.702
PlotMarker         16.933  0.092  17.026
PlotOutliers       16.174  0.008  16.181
UpdateMetaclusters 15.873  0.060  15.933
PlotStars          14.071  0.052  14.123
GroupStats         12.231  0.064  12.296
FlowSOM            11.325  0.125  11.448
PlotGroups         10.395  0.028  10.424
query_multiple      8.799  0.016   8.815
QueryMultiple       8.609  0.036   8.645
AddAnnotation       8.375  0.203   8.580
Plot2DScatters      7.428  0.012   7.409
PlotManualBars      7.335  0.000   7.336
GetFlowJoLabels     7.166  0.128   7.297
PlotPies            6.725  0.016   6.741
QueryStarPlot       6.543  0.040   6.583
PlotNode            6.352  0.016   6.368
PlotNumbers         6.177  0.064   6.241
PlotVariable        6.215  0.020   6.235
UpdateNodeSize      5.633  0.048   5.680
CountGroups         5.549  0.071   5.620
PlotFlowSOM         5.154  0.028   5.182
MetaclusterMFIs     5.080  0.024   5.106
* 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-3.19-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.


Installation output

FlowSOM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c som.c -o som.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-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
AddAnnotation8.3750.2038.580
AggregateFlowFrames0.0650.0080.073
BuildMST1.0720.0121.084
BuildSOM1.0740.0251.098
CountGroups5.5490.0715.620
FMeasure0.0020.0000.002
FlowSOM11.325 0.12511.448
FlowSOMSubset4.0260.0234.051
FlowSOMmary47.440 0.46847.574
GetChannels0.0270.0000.026
GetClusterMFIs3.7780.0963.873
GetClusterPercentagesPositive3.9100.0563.966
GetClusters4.0370.0164.053
GetCounts3.5880.0123.600
GetFeatures4.7320.0364.768
GetFlowJoLabels7.1660.1287.297
GetMFIs4.1960.0244.220
GetMarkers0.0280.0000.028
GetMetaclusterCVs4.1840.0124.197
GetMetaclusterMFIs4.1260.0114.138
GetMetaclusterPercentagesPositive4.4980.0124.510
GetMetaclusters4.2190.0614.280
GetPercentages4.3030.0004.306
GroupStats12.231 0.06412.296
Initialize_KWSP0.0040.0000.004
Initialize_PCA0.0010.0000.001
MetaClustering3.4030.0273.431
MetaclusterCVs4.3900.0094.399
MetaclusterMFIs5.0800.0245.106
NClusters4.9620.0204.983
NMetaclusters4.8030.0044.807
NewData3.8920.0203.912
Plot2DScatters7.4280.0127.409
PlotCenters1.4690.0361.504
PlotClusters2D0.9790.0000.978
PlotDimRed42.642 0.14842.702
PlotFileScatters0.7050.0040.710
PlotFlowSOM5.1540.0285.182
PlotGroups10.395 0.02810.424
PlotLabels4.9010.0124.912
PlotManualBars7.3350.0007.336
PlotMarker16.933 0.09217.026
PlotNode6.3520.0166.368
PlotNumbers6.1770.0646.241
PlotOutliers16.174 0.00816.181
PlotOverview2D4.4860.0324.518
PlotPies6.7250.0166.741
PlotSD1.9270.0041.932
PlotStars14.071 0.05214.123
PlotVariable6.2150.0206.235
Purity0.0010.0000.001
QueryMultiple8.6090.0368.645
QueryStarPlot6.5430.0406.583
ReadInput2.9260.0202.946
SaveClustersToFCS4.7920.0364.829
TestOutliers4.6360.0084.644
UpdateMetaclusters15.873 0.06015.933
UpdateNodeSize5.6330.0485.680
get_channels0.0290.0000.029
get_markers0.0230.0030.027
metaClustering_consensus2.5830.0202.603
plotStarLegend0.3770.0040.381
print.FlowSOM4.2860.0324.317
query_multiple8.7990.0168.815