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This page was generated on 2024-05-04 11:39:13 -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 lconway


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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FlowSOM_2.12.0.tar.gz
StartedAt: 2024-05-03 21:59:13 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 22:09:19 -0400 (Fri, 03 May 2024)
EllapsedTime: 606.5 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FlowSOM_2.12.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.0 beta (2024-04-14 r86421)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
FlowSOMmary                       53.332  2.568  56.208
PlotDimRed                        44.326  2.896  48.023
PlotOutliers                      20.360  1.070  21.754
PlotMarker                        19.649  1.405  21.332
UpdateMetaclusters                17.817  1.513  19.659
PlotStars                         15.892  1.340  17.573
GroupStats                        14.001  1.080  15.273
FlowSOM                           12.952  1.146  14.307
PlotGroups                        12.468  1.219  13.876
QueryMultiple                     10.659  0.541  11.366
AddAnnotation                     10.181  0.692  11.008
query_multiple                    10.098  0.540  10.797
Plot2DScatters                     9.629  0.849  10.639
PlotManualBars                     8.089  0.890   9.123
GetFlowJoLabels                    7.955  0.707   8.769
PlotNode                           7.733  0.827   8.719
QueryStarPlot                      7.766  0.395   8.279
PlotNumbers                        7.273  0.816   8.219
PlotVariable                       7.106  0.765   7.997
PlotPies                           7.021  0.785   7.933
UpdateNodeSize                     6.765  0.325   7.197
CountGroups                        6.350  0.671   7.116
SaveClustersToFCS                  5.941  1.073   7.185
PlotFlowSOM                        6.171  0.825   7.101
PlotLabels                         5.697  0.693   6.477
NMetaclusters                      5.401  0.959   6.449
MetaclusterMFIs                    5.438  0.891   6.426
GetFeatures                        5.620  0.458   6.158
TestOutliers                       5.250  0.738   6.106
PlotOverview2D                     5.230  0.745   6.130
NClusters                          5.171  0.764   6.018
GetMetaclusterMFIs                 5.080  0.839   6.051
GetMFIs                            4.980  0.753   5.818
GetPercentages                     4.722  0.784   5.593
GetMetaclusterCVs                  4.815  0.609   5.504
MetaclusterCVs                     4.780  0.599   5.458
GetMetaclusters                    4.621  0.711   5.410
GetMetaclusterPercentagesPositive  4.684  0.635   5.388
print.FlowSOM                      4.549  0.678   5.308
NewData                            4.644  0.547   5.277
GetCounts                          4.548  0.633   5.243
FlowSOMSubset                      4.565  0.459   5.090
GetClusterPercentagesPositive      4.361  0.602   5.023
* 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.


Installation output

FlowSOM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c som.c -o som.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o FlowSOM.so som.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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
AddAnnotation10.181 0.69211.008
AggregateFlowFrames0.1010.0070.108
BuildMST1.3600.0981.483
BuildSOM1.4050.0871.520
CountGroups6.3500.6717.116
FMeasure0.0010.0000.001
FlowSOM12.952 1.14614.307
FlowSOMSubset4.5650.4595.090
FlowSOMmary53.332 2.56856.208
GetChannels0.0430.0040.049
GetClusterMFIs4.4090.4814.960
GetClusterPercentagesPositive4.3610.6025.023
GetClusters4.2360.5854.881
GetCounts4.5480.6335.243
GetFeatures5.6200.4586.158
GetFlowJoLabels7.9550.7078.769
GetMFIs4.9800.7535.818
GetMarkers0.0410.0030.045
GetMetaclusterCVs4.8150.6095.504
GetMetaclusterMFIs5.0800.8396.051
GetMetaclusterPercentagesPositive4.6840.6355.388
GetMetaclusters4.6210.7115.410
GetPercentages4.7220.7845.593
GroupStats14.001 1.08015.273
Initialize_KWSP0.0040.0010.005
Initialize_PCA0.0010.0000.001
MetaClustering3.7150.6774.456
MetaclusterCVs4.7800.5995.458
MetaclusterMFIs5.4380.8916.426
NClusters5.1710.7646.018
NMetaclusters5.4010.9596.449
NewData4.6440.5475.277
Plot2DScatters 9.629 0.84910.639
PlotCenters1.3960.1241.542
PlotClusters2D1.3930.1291.540
PlotDimRed44.326 2.89648.023
PlotFileScatters0.9960.0511.063
PlotFlowSOM6.1710.8257.101
PlotGroups12.468 1.21913.876
PlotLabels5.6970.6936.477
PlotManualBars8.0890.8909.123
PlotMarker19.649 1.40521.332
PlotNode7.7330.8278.719
PlotNumbers7.2730.8168.219
PlotOutliers20.360 1.07021.754
PlotOverview2D5.2300.7456.130
PlotPies7.0210.7857.933
PlotSD2.2760.2322.544
PlotStars15.892 1.34017.573
PlotVariable7.1060.7657.997
Purity0.0010.0000.001
QueryMultiple10.659 0.54111.366
QueryStarPlot7.7660.3958.279
ReadInput3.8910.7404.762
SaveClustersToFCS5.9411.0737.185
TestOutliers5.2500.7386.106
UpdateMetaclusters17.817 1.51319.659
UpdateNodeSize6.7650.3257.197
get_channels0.0440.0030.047
get_markers0.0440.0050.053
metaClustering_consensus2.7880.6063.470
plotStarLegend0.4480.0090.466
print.FlowSOM4.5490.6785.308
query_multiple10.098 0.54010.797