Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-13 12:45:18 -0400 (Fri, 13 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4344
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4151
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4183
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

CHECK results for FlowSOM on nebbiolo1


To the developers/maintainers of the FlowSOM package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 691/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.4.0  (landing page)
Sofie Van Gassen
Snapshot Date: 2022-05-12 13:55:13 -0400 (Thu, 12 May 2022)
git_url: https://git.bioconductor.org/packages/FlowSOM
git_branch: RELEASE_3_15
git_last_commit: bf61833
git_last_commit_date: 2022-04-26 11:23:11 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: FlowSOM
Version: 2.4.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings FlowSOM_2.4.0.tar.gz
StartedAt: 2022-05-12 19:35:51 -0400 (Thu, 12 May 2022)
EndedAt: 2022-05-12 19:44:19 -0400 (Thu, 12 May 2022)
EllapsedTime: 507.7 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings FlowSOM_2.4.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/FlowSOM.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.4.0’
* 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
* 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 R 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 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 ... NOTE
Plot2DScatters: no visible binding for global variable ‘Population’
Undefined global functions or variables:
  Population
* checking Rd files ... OK
* 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        53.827  0.348  54.176
PlotDimRed         42.413  0.072  42.487
PlotMarker         19.430  0.094  19.527
UpdateMetaclusters 19.350  0.023  19.375
GroupStats         15.801  0.076  15.878
PlotGroups         13.854  0.048  13.903
FlowSOM            13.670  0.136  13.807
AddAnnotation       9.271  0.211   9.486
QueryMultiple       9.148  0.016   9.165
query_multiple      8.395  0.016   8.411
UpdateNodeSize      7.791  0.072   7.864
PlotNode            7.767  0.012   7.780
PlotStars           7.339  0.048   7.386
PlotPies            7.163  0.008   7.171
GetFlowJoLabels     7.011  0.036   7.048
Plot2DScatters      6.948  0.040   6.989
PlotManualBars      6.880  0.060   6.941
CountGroups         6.690  0.116   6.806
QueryStarPlot       6.733  0.064   6.797
PlotNumbers         6.736  0.011   6.748
PlotFlowSOM         6.605  0.052   6.658
MetaclusterMFIs     5.564  0.088   5.652
GetFeatures         5.448  0.044   5.493
SaveClustersToFCS   5.280  0.024   5.304
PlotLabels          5.185  0.048   5.233
PlotVariable        5.124  0.044   5.168
NClusters           5.075  0.020   5.095
NMetaclusters       5.037  0.012   5.050
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.



Installation output

FlowSOM.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c som.c -o som.o
gcc -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/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
AddAnnotation9.2710.2119.486
AggregateFlowFrames0.0970.0070.104
BuildMST1.3510.0201.372
BuildSOM1.5110.0161.526
CountGroups6.6900.1166.806
FMeasure0.0020.0000.002
FlowSOM13.670 0.13613.807
FlowSOMSubset4.5590.0244.583
FlowSOMmary53.827 0.34854.176
GetChannels0.0260.0000.027
GetClusterMFIs4.3390.0484.387
GetClusterPercentagesPositive4.3840.0164.400
GetClusters4.2350.0044.239
GetCounts4.6940.0074.702
GetFeatures5.4480.0445.493
GetFlowJoLabels7.0110.0367.048
GetMFIs4.1750.0124.187
GetMarkers0.0270.0000.026
GetMetaclusterCVs4.7760.0564.833
GetMetaclusterMFIs4.4750.0124.487
GetMetaclusterPercentagesPositive4.3920.0004.391
GetMetaclusters4.3170.0084.326
GetPercentages4.4360.0204.456
GroupStats15.801 0.07615.878
Initialize_KWSP0.0030.0000.004
Initialize_PCA0.0010.0000.001
MetaClustering2.8490.0162.866
MetaclusterCVs4.8710.0114.882
MetaclusterMFIs5.5640.0885.652
NClusters5.0750.0205.095
NMetaclusters5.0370.0125.050
NewData4.2360.0164.252
Plot2DScatters6.9480.0406.989
PlotCenters1.0870.0041.092
PlotClusters2D1.0540.0161.070
PlotDimRed42.413 0.07242.487
PlotFileScatters0.5930.0120.605
PlotFlowSOM6.6050.0526.658
PlotGroups13.854 0.04813.903
PlotLabels5.1850.0485.233
PlotManualBars6.8800.0606.941
PlotMarker19.430 0.09419.527
PlotNode7.7670.0127.780
PlotNumbers6.7360.0116.748
PlotOverview2D4.5530.0034.556
PlotPies7.1630.0087.171
PlotSD2.0770.0122.088
PlotStars7.3390.0487.386
PlotVariable5.1240.0445.168
Purity0.0010.0000.001
QueryMultiple9.1480.0169.165
QueryStarPlot6.7330.0646.797
ReadInput3.0770.0323.108
SaveClustersToFCS5.2800.0245.304
TestOutliers4.7830.0204.803
UpdateMetaclusters19.350 0.02319.375
UpdateNodeSize7.7910.0727.864
get_channels0.0330.0030.037
get_markers0.0230.0040.027
metaClustering_consensus2.3570.0282.385
plotStarLegend0.2950.0000.295
print.FlowSOM4.3890.0084.397
query_multiple8.3950.0168.411