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CHECK report for FlowSOM on tokay1

This page was generated on 2021-01-19 11:55:17 -0500 (Tue, 19 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE FlowSOM PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 631/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 1.22.0
Sofie Van Gassen
Snapshot Date: 2021-01-18 14:42:24 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/FlowSOM
Branch: RELEASE_3_12
Last Commit: 89cd5ba
Last Changed Date: 2020-10-27 11:01:34 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: FlowSOM
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FlowSOM.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings FlowSOM_1.22.0.tar.gz
StartedAt: 2021-01-19 03:04:33 -0500 (Tue, 19 Jan 2021)
EndedAt: 2021-01-19 03:11:21 -0500 (Tue, 19 Jan 2021)
EllapsedTime: 407.9 seconds
RetCode: 0
Status:  OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FlowSOM.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings FlowSOM_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/FlowSOM.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.22.0'
* 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 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 ... NOTE
AddFlowFrame: no visible global function definition for 'is'
ReadInput: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/FlowSOM/libs/i386/FlowSOM.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-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
CountGroups    10.80   0.27   11.11
PlotOverview2D  5.28   3.82    9.11
FlowSOM         8.11   0.03    8.83
TestOutliers    5.58   0.08    5.66
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
CountGroups     13.66   0.27   13.96
PlotOverview2D   7.09   5.08   12.17
FlowSOM         10.78   0.11   10.91
PlotNode         6.19   0.01    6.20
GetMetaclusters  5.96   0.07    6.03
GetFlowJoLabels  5.89   0.10    6.16
GetMFIs          5.79   0.04    5.89
MetaclusterMFIs  5.16   0.05    5.38
TestOutliers     4.59   0.03   30.34
* 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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/FlowSOM.Rcheck/00check.log'
for details.



Installation output

FlowSOM.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/FlowSOM_1.22.0.tar.gz && rm -rf FlowSOM.buildbin-libdir && mkdir FlowSOM.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FlowSOM.buildbin-libdir FlowSOM_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL FlowSOM_1.22.0.zip && rm FlowSOM_1.22.0.tar.gz FlowSOM_1.22.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1157k  100 1157k    0     0  11.3M      0 --:--:-- --:--:-- --:--:-- 11.7M

install for i386

* installing *source* package 'FlowSOM' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/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 -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-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
    AddFlowFrame                            html  
    AggregateFlowFrames                     html  
    BuildMST                                html  
    BuildSOM                                html  
    CountGroups                             html  
    Dist.MST                                html  
    FMeasure                                html  
    FlowSOM                                 html  
    FlowSOMSubset                           html  
    GetCVs                                  html  
    GetClusters                             html  
    GetFlowJoLabels                         html  
    finding level-2 HTML links ... done

    GetMFIs                                 html  
    GetMetaclusters                         html  
    Initialize_KWSP                         html  
    Initialize_PCA                          html  
    MapDataToCodes                          html  
    MetaClustering                          html  
    MetaclusterCVs                          html  
    MetaclusterMFIs                         html  
    NewData                                 html  
    PlotCenters                             html  
    PlotClusters2D                          html  
    PlotGroups                              html  
    PlotLabels                              html  
    PlotMarker                              html  
    PlotNode                                html  
    PlotNumbers                             html  
    PlotOverview2D                          html  
    PlotPies                                html  
    PlotSD                                  html  
    PlotStars                               html  
    PlotVariable                            html  
    Purity                                  html  
    QueryStarPlot                           html  
    ReadInput                               html  
    SOM                                     html  
    SaveClustersToFCS                       html  
    TestOutliers                            html  
    UpdateNodeSize                          html  
    computeBackgroundColor                  html  
    get_channels                            html  
    get_markers                             html  
    metaClustering_consensus                html  
    plotStarLegend                          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"C:/Users/BIOCBU~1/BBS-3~1.12-/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 -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/FlowSOM.buildbin-libdir/FlowSOM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FlowSOM' as FlowSOM_1.22.0.zip
* DONE (FlowSOM)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'FlowSOM' successfully unpacked and MD5 sums checked

Tests output


Example timings

FlowSOM.Rcheck/examples_i386/FlowSOM-Ex.timings

nameusersystemelapsed
AggregateFlowFrames0.210.000.96
BuildMST1.370.051.43
BuildSOM1.280.031.31
CountGroups10.80 0.2711.11
FMeasure000
FlowSOM8.110.038.83
FlowSOMSubset4.060.044.11
GetClusters3.440.053.48
GetFlowJoLabels4.430.094.53
GetMFIs3.680.023.68
GetMetaclusters3.810.023.83
Initialize_KWSP000
Initialize_PCA000
MetaClustering4.320.074.40
MetaclusterCVs4.140.054.19
MetaclusterMFIs4.790.054.85
NewData3.220.033.25
PlotCenters1.330.001.33
PlotClusters2D1.230.011.25
PlotGroups000
PlotLabels3.940.074.00
PlotMarker1.350.041.40
PlotNode3.730.033.76
PlotNumbers1.130.041.16
PlotOverview2D5.283.829.11
PlotPies3.810.043.84
PlotSD1.310.041.36
PlotStars1.390.051.44
PlotVariable1.380.011.39
Purity0.010.000.01
QueryStarPlot2.570.022.58
ReadInput4.510.084.60
TestOutliers5.580.085.66
UpdateNodeSize2.200.032.33
get_channels0.080.010.09
get_markers0.060.000.06
metaClustering_consensus3.660.073.85

FlowSOM.Rcheck/examples_x64/FlowSOM-Ex.timings

nameusersystemelapsed
AggregateFlowFrames0.240.050.28
BuildMST1.780.061.84
BuildSOM1.680.061.75
CountGroups13.66 0.2713.96
FMeasure000
FlowSOM10.78 0.1110.91
FlowSOMSubset4.200.084.28
GetClusters4.850.014.86
GetFlowJoLabels5.890.106.16
GetMFIs5.790.045.89
GetMetaclusters5.960.076.03
Initialize_KWSP000
Initialize_PCA000
MetaClustering4.760.044.81
MetaclusterCVs3.830.033.86
MetaclusterMFIs5.160.055.38
NewData4.540.004.58
PlotCenters1.610.011.63
PlotClusters2D1.520.031.54
PlotGroups000
PlotLabels4.940.034.97
PlotMarker1.370.041.41
PlotNode6.190.016.20
PlotNumbers1.300.031.33
PlotOverview2D 7.09 5.0812.17
PlotPies4.410.084.48
PlotSD1.430.011.46
PlotStars1.110.001.11
PlotVariable1.390.021.40
Purity000
QueryStarPlot2.740.022.75
ReadInput4.160.064.22
TestOutliers 4.59 0.0330.34
UpdateNodeSize1.580.001.60
get_channels0.060.000.06
get_markers0.050.000.04
metaClustering_consensus3.160.003.60