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This page was generated on 2024-05-04 11:40:32 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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: 2024-05-03 14:00:19 -0400 (Fri, 03 May 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for FlowSOM on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: FlowSOM
Version: 2.12.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings FlowSOM_2.12.0.tar.gz
StartedAt: 2024-05-04 07:36:13 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 07:48:15 -0000 (Sat, 04 May 2024)
EllapsedTime: 722.4 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --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 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 (GCC) 10.3.1’
* 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
PlotDimRed                        87.433  0.140  87.750
FlowSOMmary                       79.346  0.387  79.750
PlotOutliers                      24.855  0.104  25.014
PlotMarker                        23.542  0.108  23.701
UpdateMetaclusters                21.743  0.072  21.861
PlotStars                         18.928  0.048  19.015
GroupStats                        17.942  0.036  18.017
FlowSOM                           16.856  0.108  16.999
PlotGroups                        15.933  0.040  16.008
AddAnnotation                     12.350  0.244  12.623
query_multiple                    12.043  0.060  12.129
QueryMultiple                     11.933  0.048  12.005
Plot2DScatters                    11.411  0.044  11.472
PlotManualBars                    10.808  0.032  10.863
GetFlowJoLabels                   10.362  0.060  10.448
PlotNode                           9.788  0.028   9.836
CountGroups                        9.363  0.118   9.501
QueryStarPlot                      9.424  0.032   9.476
PlotNumbers                        9.329  0.020   9.369
PlotVariable                       8.860  0.035   8.913
PlotPies                           8.868  0.008   8.896
PlotFlowSOM                        8.173  0.047   8.237
UpdateNodeSize                     7.969  0.028   8.012
SaveClustersToFCS                  7.607  0.056   7.679
GetFeatures                        7.504  0.004   7.524
PlotLabels                         7.220  0.016   7.250
NMetaclusters                      7.179  0.048   7.244
NClusters                          7.144  0.027   7.187
MetaclusterMFIs                    7.101  0.060   7.175
TestOutliers                       6.760  0.008   6.782
GetPercentages                     6.728  0.016   6.759
PlotOverview2D                     6.654  0.012   6.681
MetaclusterCVs                     6.559  0.028   6.599
GetMetaclusterCVs                  6.503  0.024   6.541
GetMetaclusters                    6.341  0.064   6.419
GetMFIs                            6.312  0.076   6.403
GetClusters                        6.344  0.035   6.394
GetMetaclusterMFIs                 6.367  0.008   6.388
FlowSOMSubset                      6.249  0.076   6.338
GetMetaclusterPercentagesPositive  6.289  0.000   6.300
GetClusterPercentagesPositive      6.228  0.040   6.281
print.FlowSOM                      6.095  0.016   6.123
GetClusterMFIs                     6.001  0.068   6.082
GetCounts                          5.985  0.012   6.014
NewData                            5.218  0.012   5.240
ReadInput                          5.191  0.032   5.233
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.19-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.


Installation output

FlowSOM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c som.c -o som.o
gcc -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/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
AddAnnotation12.350 0.24412.623
AggregateFlowFrames0.0960.0110.108
BuildMST2.2250.0252.253
BuildSOM1.8840.0111.900
CountGroups9.3630.1189.501
FMeasure0.0020.0000.002
FlowSOM16.856 0.10816.999
FlowSOMSubset6.2490.0766.338
FlowSOMmary79.346 0.38779.750
GetChannels0.0330.0040.038
GetClusterMFIs6.0010.0686.082
GetClusterPercentagesPositive6.2280.0406.281
GetClusters6.3440.0356.394
GetCounts5.9850.0126.014
GetFeatures7.5040.0047.524
GetFlowJoLabels10.362 0.06010.448
GetMFIs6.3120.0766.403
GetMarkers0.0310.0080.039
GetMetaclusterCVs6.5030.0246.541
GetMetaclusterMFIs6.3670.0086.388
GetMetaclusterPercentagesPositive6.2890.0006.300
GetMetaclusters6.3410.0646.419
GetPercentages6.7280.0166.759
GroupStats17.942 0.03618.017
Initialize_KWSP0.0060.0000.006
Initialize_PCA0.0010.0000.001
MetaClustering4.7200.0164.745
MetaclusterCVs6.5590.0286.599
MetaclusterMFIs7.1010.0607.175
NClusters7.1440.0277.187
NMetaclusters7.1790.0487.244
NewData5.2180.0125.240
Plot2DScatters11.411 0.04411.472
PlotCenters1.8950.0201.922
PlotClusters2D1.8650.0041.879
PlotDimRed87.433 0.14087.750
PlotFileScatters1.4620.0761.541
PlotFlowSOM8.1730.0478.237
PlotGroups15.933 0.04016.008
PlotLabels7.2200.0167.250
PlotManualBars10.808 0.03210.863
PlotMarker23.542 0.10823.701
PlotNode9.7880.0289.836
PlotNumbers9.3290.0209.369
PlotOutliers24.855 0.10425.014
PlotOverview2D6.6540.0126.681
PlotPies8.8680.0088.896
PlotSD3.5540.0403.602
PlotStars18.928 0.04819.015
PlotVariable8.8600.0358.913
Purity0.0010.0000.001
QueryMultiple11.933 0.04812.005
QueryStarPlot9.4240.0329.476
ReadInput5.1910.0325.233
SaveClustersToFCS7.6070.0567.679
TestOutliers6.7600.0086.782
UpdateMetaclusters21.743 0.07221.861
UpdateNodeSize7.9690.0288.012
get_channels0.0340.0000.034
get_markers0.0350.0000.035
metaClustering_consensus4.0800.0324.121
plotStarLegend0.4510.0040.457
print.FlowSOM6.0950.0166.123
query_multiple12.043 0.06012.129