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CHECK report for FlowSOM on tokay1

This page was generated on 2019-04-13 11:24:43 -0400 (Sat, 13 Apr 2019).

Package 546/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 1.14.1
Sofie Van Gassen
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/FlowSOM
Branch: RELEASE_3_8
Last Commit: 9c69691
Last Changed Date: 2019-01-04 13:32:51 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: FlowSOM
Version: 1.14.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FlowSOM.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings FlowSOM_1.14.1.tar.gz
StartedAt: 2019-04-13 02:18:31 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:22:27 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 235.6 seconds
RetCode: 0
Status:  OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FlowSOM.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings FlowSOM_1.14.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/FlowSOM.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.14.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/FlowSOM/libs/i386/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 or elapsed time > 5s
            user system elapsed
CountGroups 7.18   0.23    7.42
FlowSOM     7.09   0.11    7.20
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
FlowSOM     7.66   0.14    7.80
CountGroups 7.17   0.09    7.26
* 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
  'C:/Users/biocbuild/bbs-3.8-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/3.8/bioc/src/contrib/FlowSOM_1.14.1.tar.gz && rm -rf FlowSOM.buildbin-libdir && mkdir FlowSOM.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FlowSOM.buildbin-libdir FlowSOM_1.14.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL FlowSOM_1.14.1.zip && rm FlowSOM_1.14.1.tar.gz FlowSOM_1.14.1.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 1138k  100 1138k    0     0  24.8M      0 --:--:-- --:--:-- --:--:-- 27.1M

install for i386

* installing *source* package 'FlowSOM' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c som.c -o som.o
C:/Rtools/mingw_32/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˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/FlowSOM.buildbin-libdir/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  
    Initialize                              html  
    MapDataToCodes                          html  
    MetaClustering                          html  
    NewData                                 html  
    PlotCenters                             html  
    PlotClusters2D                          html  
    PlotGroups                              html  
    PlotMarker                              html  
    PlotNode                                html  
    PlotNumbers                             html  
    PlotPies                                html  
    PlotStars                               html  
    PlotVariable                            html  
    ProcessGatingML                         html  
    finding level-2 HTML links ... done

    Purity                                  html  
    QueryStarPlot                           html  
    ReadInput                               html  
    SOM                                     html  
    SaveClustersToFCS                       html  
    UpdateNodeSize                          html  
    computeBackgroundColor                  html  
    metaClustering_consensus                html  
    plotStarLegend                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'FlowSOM' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c som.c -o som.o
C:/Rtools/mingw_64/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˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/FlowSOM.buildbin-libdir/FlowSOM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FlowSOM' as FlowSOM_1.14.1.zip
* DONE (FlowSOM)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'FlowSOM' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

FlowSOM.Rcheck/examples_i386/FlowSOM-Ex.timings

nameusersystemelapsed
AggregateFlowFrames0.140.000.40
BuildMST1.160.031.18
BuildSOM1.360.061.42
CountGroups7.180.237.42
FMeasure0.020.000.02
FlowSOM7.090.117.20
FlowSOMSubset3.020.033.05
MetaClustering2.950.073.01
NewData2.840.042.89
PlotCenters1.360.021.38
PlotClusters2D1.320.001.31
PlotGroups000
PlotMarker1.140.001.14
PlotNode3.110.023.13
PlotNumbers1.20.01.2
PlotPies4.000.094.19
PlotStars1.300.001.29
PlotVariable1.340.001.35
ProcessGatingML4.440.064.50
Purity000
QueryStarPlot2.190.002.19
ReadInput3.120.033.15
UpdateNodeSize1.690.001.69
metaClustering_consensus2.730.032.77

FlowSOM.Rcheck/examples_x64/FlowSOM-Ex.timings

nameusersystemelapsed
AggregateFlowFrames0.150.000.16
BuildMST1.000.011.01
BuildSOM1.370.021.39
CountGroups7.170.097.26
FMeasure000
FlowSOM7.660.147.80
FlowSOMSubset3.080.023.09
MetaClustering3.610.043.66
NewData3.260.043.30
PlotCenters1.160.011.17
PlotClusters2D0.970.031.00
PlotGroups000
PlotMarker0.970.020.98
PlotNode3.060.033.10
PlotNumbers1.000.011.01
PlotPies4.390.044.43
PlotStars1.090.001.09
PlotVariable1.290.011.30
ProcessGatingML4.620.104.71
Purity000
QueryStarPlot2.190.042.24
ReadInput3.420.103.51
UpdateNodeSize1.450.031.49
metaClustering_consensus2.660.012.67