Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-18 17:57 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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: 2024-06-16 14:00 -0400 (Sun, 16 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
merida1macOS 12.7.4 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


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: 2024-06-16 23:17:24 -0400 (Sun, 16 Jun 2024)
EndedAt: 2024-06-16 23:26:48 -0400 (Sun, 16 Jun 2024)
EllapsedTime: 564.2 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        50.073  0.455  50.187
PlotDimRed         41.447  0.129  41.495
PlotMarker         16.776  0.060  16.837
PlotOutliers       15.825  0.012  15.837
UpdateMetaclusters 15.479  0.044  15.522
PlotStars          13.603  0.064  13.668
GroupStats         11.807  0.064  11.879
FlowSOM            11.080  0.128  11.209
PlotGroups         10.895  0.016  10.910
query_multiple      9.240  0.012   9.252
QueryMultiple       8.883  0.048   8.932
AddAnnotation       8.388  0.160   8.549
Plot2DScatters      7.571  0.044   7.584
PlotManualBars      7.187  0.016   7.205
GetFlowJoLabels     6.980  0.103   7.086
QueryStarPlot       6.602  0.032   6.635
PlotVariable        6.577  0.012   6.588
PlotNumbers         6.196  0.060   6.256
PlotNode            6.179  0.028   6.208
PlotPies            5.818  0.024   5.842
UpdateNodeSize      5.426  0.044   5.470
CountGroups         5.340  0.088   5.428
PlotLabels          5.243  0.008   5.250
SaveClustersToFCS   5.235  0.016   5.251
PlotFlowSOM         5.120  0.048   5.169
TestOutliers        4.986  0.024   5.010
* 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

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###
### 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
AddAnnotation8.3880.1608.549
AggregateFlowFrames0.0640.0080.071
BuildMST1.0490.0121.060
BuildSOM1.0990.0121.111
CountGroups5.3400.0885.428
FMeasure0.0010.0000.002
FlowSOM11.080 0.12811.209
FlowSOMSubset3.7700.0283.798
FlowSOMmary50.073 0.45550.187
GetChannels0.0270.0000.027
GetClusterMFIs4.1420.1364.278
GetClusterPercentagesPositive3.8760.1003.976
GetClusters3.8000.0243.824
GetCounts3.8340.0203.854
GetFeatures4.7130.0924.805
GetFlowJoLabels6.9800.1037.086
GetMFIs4.6030.0204.623
GetMarkers0.0260.0040.029
GetMetaclusterCVs4.9530.0004.961
GetMetaclusterMFIs4.4980.0164.514
GetMetaclusterPercentagesPositive4.5380.0844.624
GetMetaclusters4.4940.0124.505
GetPercentages4.2940.0244.318
GroupStats11.807 0.06411.879
Initialize_KWSP0.0040.0000.004
Initialize_PCA0.0010.0000.001
MetaClustering2.8760.0002.876
MetaclusterCVs4.4620.0204.482
MetaclusterMFIs4.5640.0244.588
NClusters4.5860.0324.618
NMetaclusters4.3950.0164.411
NewData4.1280.0044.132
Plot2DScatters7.5710.0447.584
PlotCenters1.0230.0041.027
PlotClusters2D1.0030.0081.011
PlotDimRed41.447 0.12941.495
PlotFileScatters0.7500.0120.763
PlotFlowSOM5.1200.0485.169
PlotGroups10.895 0.01610.910
PlotLabels5.2430.0085.250
PlotManualBars7.1870.0167.205
PlotMarker16.776 0.06016.837
PlotNode6.1790.0286.208
PlotNumbers6.1960.0606.256
PlotOutliers15.825 0.01215.837
PlotOverview2D4.7990.0284.827
PlotPies5.8180.0245.842
PlotSD2.2920.0002.292
PlotStars13.603 0.06413.668
PlotVariable6.5770.0126.588
Purity0.0010.0000.001
QueryMultiple8.8830.0488.932
QueryStarPlot6.6020.0326.635
ReadInput2.9980.0403.037
SaveClustersToFCS5.2350.0165.251
TestOutliers4.9860.0245.010
UpdateMetaclusters15.479 0.04415.522
UpdateNodeSize5.4260.0445.470
get_channels0.0280.0000.028
get_markers0.0280.0000.028
metaClustering_consensus2.5000.0282.528
plotStarLegend0.3770.0000.378
print.FlowSOM4.3460.0404.386
query_multiple9.2400.0129.252