Multiple platform build/check report for BioC 3.8 - CHECK report for flowCore on tokay1

Package: flowCore

Version: 1.48.1

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowCore.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings flowCore_1.48.1.tar.gz

StartedAt: 2019-04-13 02:16:13 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 02:20:03 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 229.5 seconds

RetCode: 0

Status: WARNINGS

CheckDir: flowCore.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowCore.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings flowCore_1.48.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/flowCore.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 'flowCore/DESCRIPTION' ... OK
* this is package 'flowCore' version '1.48.1'
* 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 'flowCore' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpE90dmD/R.INSTALL17c5f824abe/flowCore/man/FCSTransTransform.Rd:44: file link 'estimateLogicle' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpE90dmD/R.INSTALL17c5f824abe/flowCore/man/filters-class.Rd:13: file link 'filterList' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpE90dmD/R.INSTALL17c5f824abe/flowCore/man/logicleTransform.Rd:50: file link 'estimateLogicle' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpE90dmD/R.INSTALL17c5f824abe/flowCore/man/normalization-class.Rd:82: file link 'normalize-methods' in package 'flowStats' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/flowCore.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    data      5.0Mb
    extdata   1.1Mb
    libs      1.7Mb
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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/flowCore/libs/i386/flowCore.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
biexponentialTransform  5.6   0.05    5.64
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
biexponentialTransform 5.39    0.1    5.48
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* 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 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/flowCore.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/flowCore_1.48.1.tar.gz && rm -rf flowCore.buildbin-libdir && mkdir flowCore.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowCore.buildbin-libdir flowCore_1.48.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL flowCore_1.48.1.zip && rm flowCore_1.48.1.tar.gz flowCore_1.48.1.zip
###
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100 7867k  100 7867k    0     0  59.9M      0 --:--:-- --:--:-- --:--:-- 61.4M

install for i386

* installing *source* package 'flowCore' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c FastLogicle.cpp -o FastLogicle.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Hyperlog.cpp -o Hyperlog.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Logicle.cpp -o Logicle.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c biexponential.cpp -o biexponential.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c convertRawBytes.cpp -o convertRawBytes.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c fcsTextParse.cpp -o fcsTextParse.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c hyperlogTransform.cpp -o hyperlogTransform.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c inPolygon.cpp -o inPolygon.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c inPolytope.cpp -o inPolytope.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c logicleTransform.cpp -o logicleTransform.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c sortBytes.cpp -o sortBytes.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c uint2double.cpp -o uint2double.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c zeroin.cpp -o zeroin.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o flowCore.dll tmp.def FastLogicle.o Hyperlog.o Logicle.o RcppExports.o biexponential.o convertRawBytes.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o logicleTransform.o pairVectorRcppWrap.o sortBytes.o uint2double.o zeroin.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowCore.dll; fi
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/flowCore.buildbin-libdir/flowCore/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowCore'
    finding HTML links ... done
    EHtrans-class                           html  
    FCSTransTransform                       html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpE90dmD/R.INSTALL17c5f824abe/flowCore/man/FCSTransTransform.Rd:44: file link 'estimateLogicle' in package 'flowCore' does not exist and so has been treated as a topic
    GvHD                                    html  
    Subset-methods                          html  
    actionItem-class                        html  
    arcsinhTransform                        html  
    asinht-class                            html  
    asinhtGml2-class                        html  
    biexponentialTransform                  html  
    boundaryFilter-class                    html  
    characterOrTransformation-class         html  
    checkOffset                             html  
    coerce                                  html  
    compensateActionItem-class              html  
    compensateView-class                    html  
    compensatedParameter-class              html  
    compensation-class                      html  
    concreteFilter-class                    html  
    decompensate                            html  
    dg1polynomial-class                     html  
    each_col-methods                        html  
    ellipsoidGate                           html  
    estimateMedianLogicle                   html  
    exponential-class                       html  
    expressionFilter-class                  html  
    fcReference-class                       html  
    filter-and-methods                      html  
    filter-class                            html  
    filter-in-methods                       html  
    filter-methods                          html  
    filter-on-methods                       html  
    filterDetails-methods                   html  
    filterList-class                        html  
    filterReference-class                   html  
    filterResult-class                      html  
    filterResultList-class                  html  
    filterSet-class                         html  
    filterSummary-class                     html  
    filterSummaryList-class                 html  
    filters-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpE90dmD/R.INSTALL17c5f824abe/flowCore/man/filters-class.Rd:13: file link 'filterList' in package 'flowCore' does not exist and so has been treated as a topic
    flowCore-package                        html  
    flowFrame-class                         html  
    flowSet-class                           html  
    fr_append_cols                          html  
    fsApply                                 html  
    gateActionItem-class                    html  
    gateView-class                          html  
    getChannelMarker                        html  
    getIndexSort-methods                    html  
    hyperlog-class                          html  
    hyperlogtGml2-class                     html  
    identifier-methods                      html  
    inverseLogicleTransform                 html  
    invsplitscale-class                     html  
    keyword-methods                         html  
    kmeansFilter                            html  
    linearTransform                         html  
    lintGml2-class                          html  
    lnTransform                             html  
    logTransform                            html  
    logarithm-class                         html  
    logicalFilterResult-class               html  
    logicleTransform                        html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpE90dmD/R.INSTALL17c5f824abe/flowCore/man/logicleTransform.Rd:50: file link 'estimateLogicle' in package 'flowCore' does not exist and so has been treated as a topic
    logicletGml2-class                      html  
    logtGml2-class                          html  
    manyFilterResult-class                  html  
    markernames                             html  
    multipleFilterResult-class              html  
    norm2Filter-class                       html  
    normalization-class                     html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpE90dmD/R.INSTALL17c5f824abe/flowCore/man/normalization-class.Rd:82: file link 'normalize-methods' in package 'flowStats' does not exist and so has been treated as a topic
    normalizeActionItem-class               html  
    normalizeView-class                     html  
    parameterFilter-class                   html  
    parameterTransform-class                html  
    parameters-class                        html  
    parameters-methods                      html  
    polygonGate                             html  
    polytopeGate                            html  
    quadGate                                html  
    quadratic-class                         html  
    quadraticTransform                      html  
    randomFilterResult-class                html  
    ratio-class                             html  
    ratiotGml2-class                        html  
    read.FCS                                html  
    read.FCSheader                          html  
    read.flowSet                            html  
    rectangleGate                           html  
    sampleFilter-class                      html  
    scaleTransform                          html  
    setOperationFilter-class                html  
    singleParameterTransform-class          html  
    sinht-class                             html  
    spillover-flowSet                       html  
    spillover_ng-flowSet                    html  
    split-methods                           html  
    splitScaleTransform                     html  
    splitscale-class                        html  
    squareroot-class                        html  
    subsetting-class                        html  
    subsettingActionItem-class              html  
    subsettingView-class                    html  
    summarizeFilter-methods                 html  
    timeFilter-class                        html  
    transform-class                         html  
    transformActionItem-class               html  
    transformFilter-class                   html  
    transformList-class                     html  
    transformMap-class                      html  
    transformReference-class                html  
    transformView-class                     html  
    transformation-class                    html  
    truncateTransform                       html  
    unitytransform-class                    html  
    updateTransformKeywords                 html  
    validFilters                            html  
    view-class                              html  
    workFlow-class                          html  
    write.FCS                               html  
    write.flowSet                           html  
** building package indices
** installing vignettes
   'HowTo-flowCore.Rnw' 
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'flowCore' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c FastLogicle.cpp -o FastLogicle.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Hyperlog.cpp -o Hyperlog.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Logicle.cpp -o Logicle.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c biexponential.cpp -o biexponential.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c convertRawBytes.cpp -o convertRawBytes.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c fcsTextParse.cpp -o fcsTextParse.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c hyperlogTransform.cpp -o hyperlogTransform.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c inPolygon.cpp -o inPolygon.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c inPolytope.cpp -o inPolytope.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c logicleTransform.cpp -o logicleTransform.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c sortBytes.cpp -o sortBytes.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c uint2double.cpp -o uint2double.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c zeroin.cpp -o zeroin.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o flowCore.dll tmp.def FastLogicle.o Hyperlog.o Logicle.o RcppExports.o biexponential.o convertRawBytes.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o logicleTransform.o pairVectorRcppWrap.o sortBytes.o uint2double.o zeroin.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowCore.dll; fi
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/flowCore.buildbin-libdir/flowCore/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowCore' as flowCore_1.48.1.zip
* DONE (flowCore)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'flowCore' successfully unpacked and MD5 sums checked
In R CMD INSTALL


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(flowCore)
> 
> 
> test_check("flowCore")
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:flowCore':

    normalize

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

     orig_channel_name new_channel_name
$P5N            B710-A              FL1
$P9N            V545-A              FL1
== testthat results  ===========================================================
OK: 224 SKIPPED: 0 FAILED: 0
> 
> #devtools::test("˜/rglab/workspace/flowCore")
> #the FCS files are not included in package due to the size , thus only for internal testing
> #test_file("/home/wjiang2/rglab/workspace/flowCore/tests/testthat/IO-testSuite.R")
> 
> proc.time()
   user  system elapsed 
  13.23    1.39   14.87


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(flowCore)
> 
> 
> test_check("flowCore")
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:flowCore':

    normalize

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

     orig_channel_name new_channel_name
$P5N            B710-A              FL1
$P9N            V545-A              FL1
== testthat results  ===========================================================
OK: 224 SKIPPED: 0 FAILED: 0
> 
> #devtools::test("˜/rglab/workspace/flowCore")
> #the FCS files are not included in package due to the size , thus only for internal testing
> #test_file("/home/wjiang2/rglab/workspace/flowCore/tests/testthat/IO-testSuite.R")
> 
> proc.time()
   user  system elapsed 
  12.53    1.25   13.89

name	user	system	elapsed
EHtrans-class	0.05	0.02	0.06
FCSTransTransform	0.76	0.04	0.81
Subset-methods	0.18	0.02	0.25
actionItem-class	0	0	0
arcsinhTransform	0.04	0.00	0.05
asinht-class	0.03	0.00	0.03
asinhtGml2-class	0.03	0.00	0.03
biexponentialTransform	5.60	0.05	5.64
boundaryFilter-class	0.17	0.01	0.19
characterOrTransformation-class	0	0	0
coerce	0.06	0.00	0.06
compensateActionItem-class	0	0	0
compensateView-class	0	0	0
compensatedParameter-class	0.16	0.00	0.27
compensation-class	0.31	0.00	0.31
decompensate	0.05	0.02	0.06
dg1polynomial-class	0.03	0.00	0.03
each_col-methods	0.03	0.00	0.03
ellipsoidGate	0.03	0.01	0.05
exponential-class	0.04	0.00	0.04
expressionFilter-class	0.07	0.00	0.07
fcReference-class	0	0	0
filter-methods	0.84	0.02	0.86
filter-on-methods	0.06	0.00	0.06
filterList-class	0.02	0.00	0.01
filterResult-class	0	0	0
filterResultList-class	0	0	0
filterSummary-class	0	0	0
filterSummaryList-class	0	0	0
flowFrame-class	2.76	0.04	2.82
flowSet-class	2.11	0.10	2.20
fr_append_cols	0.72	0.04	0.75
fsApply	0.25	0.00	0.25
gateActionItem-class	0	0	0
gateView-class	0	0	0
getIndexSort-methods	0.03	0.00	0.04
hyperlog-class	0.79	0.00	0.78
hyperlogtGml2-class	0.03	0.00	0.03
identifier-methods	0.01	0.00	0.01
inverseLogicleTransform	0.88	0.04	0.93
invsplitscale-class	0.03	0.00	0.03
keyword-methods	0.76	0.05	0.81
kmeansFilter	0.13	0.01	0.14
linearTransform	0.03	0.00	0.03
lintGml2-class	0.03	0.00	0.03
lnTransform	1.31	0.07	1.38
logTransform	0.04	0.00	0.03
logarithm-class	0.03	0.00	0.03
logicalFilterResult-class	0	0	0
logicleTransform	0.82	0.01	0.84
logicletGml2-class	0.07	0.00	0.07
logtGml2-class	0.04	0.00	0.06
manyFilterResult-class	0	0	0
markernames	0.91	0.08	0.98
multipleFilterResult-class	0	0	0
norm2Filter-class	0.14	0.00	0.14
normalizeActionItem-class	0	0	0
normalizeView-class	0	0	0
parameters-methods	0.03	0.00	0.04
polygonGate	0.06	0.00	0.06
quadGate	0.18	0.00	0.17
quadratic-class	0.04	0.00	0.05
quadraticTransform	0.03	0.00	0.03
ratio-class	0.04	0.00	0.03
ratiotGml2-class	0.02	0.00	0.02
read.FCS	0.08	0.00	0.07
read.FCSheader	0	0	0
read.flowSet	0.09	0.00	0.10
rectangleGate	0.08	0.00	0.08
sampleFilter-class	0.04	0.00	0.04
scaleTransform	0.05	0.00	0.05
singleParameterTransform-class	0.02	0.00	0.02
sinht-class	0.03	0.00	0.03
split-methods	1.11	0.03	1.14
splitScaleTransform	1.06	0.06	1.12
splitscale-class	0.02	0.00	0.02
squareroot-class	0.02	0.00	0.02
subsettingActionItem-class	0	0	0
subsettingView-class	0	0	0
timeFilter-class	1.43	0.03	1.47
transform-class	0	0	0
transformActionItem-class	0	0	0
transformFilter-class	0.11	0.00	0.11
transformList-class	0.69	0.02	0.70
transformMap-class	0	0	0
transformView-class	0	0	0
truncateTransform	0.05	0.00	0.05
unitytransform-class	0.01	0.00	0.01
view-class	0	0	0
workFlow-class	0	0	0
write.FCS	0.05	0.00	0.05
write.flowSet	0.79	0.06	0.85

name	user	system	elapsed
EHtrans-class	0.05	0.01	0.07
FCSTransTransform	0.56	0.08	0.64
Subset-methods	0.23	0.02	0.25
actionItem-class	0	0	0
arcsinhTransform	0.08	0.01	0.10
asinht-class	0.03	0.00	0.03
asinhtGml2-class	0.03	0.00	0.03
biexponentialTransform	5.39	0.10	5.48
boundaryFilter-class	0.07	0.00	0.07
characterOrTransformation-class	0	0	0
coerce	0.06	0.00	0.06
compensateActionItem-class	0	0	0
compensateView-class	0	0	0
compensatedParameter-class	0.12	0.01	0.14
compensation-class	0.42	0.05	0.47
decompensate	0.04	0.01	0.05
dg1polynomial-class	0.03	0.00	0.03
each_col-methods	0.03	0.00	0.03
ellipsoidGate	0.06	0.00	0.06
exponential-class	0.02	0.00	0.02
expressionFilter-class	0.08	0.00	0.08
fcReference-class	0	0	0
filter-methods	0.66	0.04	0.69
filter-on-methods	0.09	0.00	0.09
filterList-class	0	0	0
filterResult-class	0	0	0
filterResultList-class	0	0	0
filterSummary-class	0	0	0
filterSummaryList-class	0	0	0
flowFrame-class	2.66	0.09	2.75
flowSet-class	1.84	0.05	1.89
fr_append_cols	0.52	0.02	0.53
fsApply	0.12	0.00	0.12
gateActionItem-class	0	0	0
gateView-class	0.02	0.00	0.02
getIndexSort-methods	0.01	0.00	0.01
hyperlog-class	0.89	0.00	0.90
hyperlogtGml2-class	0.03	0.00	0.03
identifier-methods	0.02	0.00	0.01
inverseLogicleTransform	0.53	0.03	0.56
invsplitscale-class	0.03	0.00	0.04
keyword-methods	0.53	0.03	0.56
kmeansFilter	0.16	0.00	0.15
linearTransform	0.03	0.00	0.04
lintGml2-class	0.03	0.00	0.03
lnTransform	1.10	0.02	1.11
logTransform	0.03	0.00	0.03
logarithm-class	0.01	0.00	0.01
logicalFilterResult-class	0	0	0
logicleTransform	0.57	0.03	0.60
logicletGml2-class	0.25	0.01	0.26
logtGml2-class	0.03	0.00	0.03
manyFilterResult-class	0	0	0
markernames	0.51	0.02	0.54
multipleFilterResult-class	0	0	0
norm2Filter-class	0.13	0.00	0.12
normalizeActionItem-class	0	0	0
normalizeView-class	0	0	0
parameters-methods	0.03	0.00	0.03
polygonGate	0.05	0.00	0.05
quadGate	0.12	0.00	0.12
quadratic-class	0.02	0.00	0.02
quadraticTransform	0.02	0.00	0.02
ratio-class	0.03	0.00	0.03
ratiotGml2-class	0.03	0.00	0.03
read.FCS	0.06	0.01	0.08
read.FCSheader	0	0	0
read.flowSet	0.08	0.00	0.08
rectangleGate	0.06	0.00	0.07
sampleFilter-class	0.03	0.00	0.03
scaleTransform	0.03	0.00	0.03
singleParameterTransform-class	0	0	0
sinht-class	0.03	0.00	0.03
split-methods	0.75	0.04	0.78
splitScaleTransform	0.80	0.01	0.81
splitscale-class	0.03	0.00	0.04
squareroot-class	0.03	0.00	0.03
subsettingActionItem-class	0	0	0
subsettingView-class	0	0	0
timeFilter-class	1.17	0.03	1.20
transform-class	0	0	0
transformActionItem-class	0	0	0
transformFilter-class	0.27	0.00	0.27
transformList-class	0.51	0.02	0.53
transformMap-class	0	0	0
transformView-class	0	0	0
truncateTransform	0.04	0.00	0.03
unitytransform-class	0.03	0.00	0.03
view-class	0	0	0
workFlow-class	0	0	0
write.FCS	0.03	0.00	0.03
write.flowSet	0.65	0.03	0.69

CHECK report for flowCore on tokay1

Summary

Command output

Installation output

Tests output

Example timings