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This page was generated on 2021-10-22 12:04:25 -0400 (Fri, 22 Oct 2021).

CHECK results for FlowSOM on riesling1

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? here 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 666/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.1.24  (landing page)
Sofie Van Gassen
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/FlowSOM
git_branch: master
git_last_commit: 2da26cf
git_last_commit_date: 2021-10-20 11:08:54 -0400 (Wed, 20 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: FlowSOM
Version: 2.1.24
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FlowSOM.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings FlowSOM_2.1.24.tar.gz
StartedAt: 2021-10-22 01:05:58 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 01:19:10 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 791.7 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FlowSOM.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings FlowSOM_2.1.24.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/FlowSOM.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'FlowSOM/DESCRIPTION' ... OK
* this is package 'FlowSOM' version '2.1.24'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.14-bioc/R/library/FlowSOM/libs/i386/FlowSOM.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbuild/bbs-3.14-bioc/R/library/FlowSOM/libs/x64/FlowSOM.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
FlowSOMmary        38.45   0.51   38.97
PlotDimRed         30.55   0.34   30.89
UpdateMetaclusters 14.40   0.03   14.47
PlotMarker         14.15   0.06   14.22
GroupStats         10.29   0.08   10.38
PlotGroups          9.33   0.10    9.46
FlowSOM             9.30   0.03    9.32
AddAnnotation       7.12   0.09    7.22
QueryMultiple       6.34   0.06    6.43
query_multiple      6.24   0.01    6.25
UpdateNodeSize      5.96   0.04    5.98
PlotNode            5.49   0.06    5.54
PlotStars           5.48   0.02    5.50
PlotFlowSOM         5.03   0.04    5.07
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
FlowSOMmary        40.01   0.63   40.67
PlotDimRed         30.42   0.17   30.59
UpdateMetaclusters 15.13   0.10   15.23
PlotMarker         14.28   0.10   14.37
GroupStats         10.62   0.08   10.74
PlotGroups          9.62   0.08    9.72
FlowSOM             9.47   0.05    9.51
AddAnnotation       7.19   0.08    7.27
query_multiple      7.12   0.08    7.20
UpdateNodeSize      6.59   0.00    6.60
QueryMultiple       6.47   0.01    6.49
PlotNode            5.49   0.03    5.52
PlotStars           5.30   0.02    5.31
QueryStarPlot       5.22   0.00    5.22
* 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: 1 NOTE
See
  'D:/biocbuild/bbs-3.14-bioc/meat/FlowSOM.Rcheck/00check.log'
for details.



Installation output

FlowSOM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/FlowSOM_2.1.24.tar.gz && rm -rf FlowSOM.buildbin-libdir && mkdir FlowSOM.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FlowSOM.buildbin-libdir FlowSOM_2.1.24.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL FlowSOM_2.1.24.zip && rm FlowSOM_2.1.24.tar.gz FlowSOM_2.1.24.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 1197k    0  1137    0     0   9169      0  0:02:13 --:--:--  0:02:13  9096
100 1197k  100 1197k    0     0  2632k      0 --:--:-- --:--:-- --:--:-- 2626k

install for i386

* installing *source* package 'FlowSOM' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c som.c -o som.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o FlowSOM.dll tmp.def som.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/FlowSOM.buildbin-libdir/00LOCK-FlowSOM/00new/FlowSOM/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'FlowSOM'
    finding HTML links ... done
    AddAnnotation                           html  
    AddBackground                           html  
    AddFlowFrame                            html  
    AddLabels                               html  
    AddMST                                  html  
    AddNodes                                html  
    AddPies                                 html  
    AddScale                                html  
    AddStars                                html  
    AddStarsPies                            html  
    AggregateFlowFrames                     html  
    AutoMaxNodeSize                         html  
    BuildMST                                html  
    BuildSOM                                html  
    CountGroups                             html  
    Dist.MST                                html  
    FMeasure                                html  
    FlowSOM                                 html  
    FlowSOMSubset                           html  
    FlowSOM_colors                          html  
    FlowSOMmary                             html  
    GetCVs                                  html  
    GetChannels                             html  
    GetClusterCVs                           html  
    GetClusterMFIs                          html  
    GetClusters                             html  
    GetCounts                               html  
    GetFeatures                             html  
    GetFlowJoLabels                         html  
    finding level-2 HTML links ... done

    GetMFIs                                 html  
    GetMarkers                              html  
    GetMetaclusterCVs                       html  
    GetMetaclusterMFIs                      html  
    GetMetaclusters                         html  
    GetPercentages                          html  
    GroupStats                              html  
    Initialize_KWSP                         html  
    Initialize_PCA                          html  
    ManualVector                            html  
    MapDataToCodes                          html  
    MetaClustering                          html  
    MetaclusterCVs                          html  
    MetaclusterMFIs                         html  
    NClusters                               html  
    NMetaclusters                           html  
    NewData                                 html  
    ParseArcs                               html  
    ParseEdges                              html  
    ParseLayout                             html  
    ParseNodeSize                           html  
    ParseQuery                              html  
    ParseSD                                 html  
    Plot2DScatters                          html  
    PlotCenters                             html  
    PlotClusters2D                          html  
    PlotDimRed                              html  
    PlotFileScatters                        html  
    PlotFlowSOM                             html  
    PlotGroups                              html  
    PlotLabels                              html  
    PlotManualBars                          html  
    PlotMarker                              html  
    PlotNode                                html  
    PlotNumbers                             html  
    PlotOverview2D                          html  
    PlotPies                                html  
    PlotSD                                  html  
    PlotStars                               html  
    PlotVariable                            html  
    Purity                                  html  
    QueryMultiple                           html  
    QueryStarPlot                           html  
    ReadInput                               html  
    SOM                                     html  
    SaveClustersToFCS                       html  
    ScaleStarHeights                        html  
    TestOutliers                            html  
    UpdateFlowSOM                           html  
    UpdateMetaclusters                      html  
    UpdateNodeSize                          html  
    get_channels                            html  
    get_markers                             html  
    gg_color_hue                            html  
    metaClustering_consensus                html  
    pipe                                    html  
    plotStarLegend                          html  
    print.FlowSOM                           html  
    query_multiple                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'FlowSOM' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c som.c -o som.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o FlowSOM.dll tmp.def som.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/FlowSOM.buildbin-libdir/FlowSOM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FlowSOM' as FlowSOM_2.1.24.zip
* DONE (FlowSOM)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'FlowSOM' successfully unpacked and MD5 sums checked

Tests output


Example timings

FlowSOM.Rcheck/examples_i386/FlowSOM-Ex.timings

nameusersystemelapsed
AddAnnotation7.120.097.22
AggregateFlowFrames0.080.050.13
BuildMST0.970.010.98
BuildSOM0.800.020.81
CountGroups4.150.064.24
FMeasure000
FlowSOM9.300.039.32
FlowSOMSubset3.110.023.13
FlowSOMmary38.45 0.5138.97
GetChannels0.050.000.05
GetClusterMFIs2.840.002.84
GetClusters2.810.022.83
GetCounts3.050.043.09
GetFeatures3.000.053.05
GetFlowJoLabels4.660.064.75
GetMFIs2.730.042.76
GetMarkers0.020.010.03
GetMetaclusterCVs3.010.003.02
GetMetaclusterMFIs2.770.022.78
GetMetaclusters2.750.012.77
GetPercentages2.830.022.84
GroupStats10.29 0.0810.38
Initialize_KWSP000
Initialize_PCA000
MetaClustering2.140.002.14
MetaclusterCVs3.000.043.05
MetaclusterMFIs3.250.023.26
NClusters3.310.003.32
NMetaclusters3.050.013.06
NewData2.420.022.44
Plot2DScatters4.330.534.87
PlotCenters0.720.030.75
PlotClusters2D0.760.020.78
PlotDimRed30.55 0.3430.89
PlotFileScatters0.550.060.61
PlotFlowSOM5.030.045.07
PlotGroups9.330.109.46
PlotLabels3.590.043.63
PlotManualBars4.580.034.61
PlotMarker14.15 0.0614.22
PlotNode5.490.065.54
PlotNumbers4.370.084.46
PlotOverview2D2.740.032.76
PlotPies4.440.054.49
PlotSD1.670.011.69
PlotStars5.480.025.50
PlotVariable3.490.023.50
Purity000
QueryMultiple6.340.066.43
QueryStarPlot4.910.034.94
ReadInput2.390.012.42
SaveClustersToFCS3.470.053.52
TestOutliers3.250.033.28
UpdateMetaclusters14.40 0.0314.47
UpdateNodeSize5.960.045.98
get_channels0.030.010.05
get_markers0.030.000.03
metaClustering_consensus1.900.051.95
plotStarLegend0.240.000.24
print.FlowSOM2.760.032.79
query_multiple6.240.016.25

FlowSOM.Rcheck/examples_x64/FlowSOM-Ex.timings

nameusersystemelapsed
AddAnnotation7.190.087.27
AggregateFlowFrames0.080.000.08
BuildMST0.750.010.77
BuildSOM0.790.000.80
CountGroups3.960.033.98
FMeasure0.010.000.02
FlowSOM9.470.059.51
FlowSOMSubset3.130.033.16
FlowSOMmary40.01 0.6340.67
GetChannels0.020.010.03
GetClusterMFIs3.150.063.22
GetClusters2.910.052.98
GetCounts3.330.003.33
GetFeatures3.220.003.22
GetFlowJoLabels4.620.094.81
GetMFIs3.160.023.18
GetMarkers0.030.000.03
GetMetaclusterCVs2.870.022.89
GetMetaclusterMFIs2.910.002.90
GetMetaclusters2.840.032.88
GetPercentages2.910.012.92
GroupStats10.62 0.0810.74
Initialize_KWSP000
Initialize_PCA000
MetaClustering2.130.052.17
MetaclusterCVs2.840.012.86
MetaclusterMFIs3.250.023.27
NClusters3.220.033.25
NMetaclusters3.250.023.26
NewData2.970.012.99
Plot2DScatters4.310.614.94
PlotCenters0.720.000.72
PlotClusters2D0.70.00.7
PlotDimRed30.42 0.1730.59
PlotFileScatters0.530.020.55
PlotFlowSOM4.930.014.94
PlotGroups9.620.089.72
PlotLabels3.520.003.51
PlotManualBars4.620.034.66
PlotMarker14.28 0.1014.37
PlotNode5.490.035.52
PlotNumbers4.510.054.56
PlotOverview2D2.800.012.81
PlotPies4.800.064.86
PlotSD1.510.001.52
PlotStars5.300.025.31
PlotVariable3.560.003.56
Purity000
QueryMultiple6.470.016.49
QueryStarPlot5.220.005.22
ReadInput2.280.042.31
SaveClustersToFCS3.580.073.65
TestOutliers3.340.043.38
UpdateMetaclusters15.13 0.1015.23
UpdateNodeSize6.590.006.60
get_channels0.050.000.04
get_markers0.010.020.04
metaClustering_consensus1.990.052.03
plotStarLegend0.250.000.25
print.FlowSOM3.080.013.09
query_multiple7.120.087.20