Package: GLAD

Version: 2.44.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GLAD.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GLAD_2.44.0.tar.gz

StartedAt: 2018-10-17 02:26:04 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 02:28:48 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 163.8 seconds

RetCode: 0

Status:  OK

CheckDir: GLAD.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GLAD.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GLAD_2.44.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/GLAD.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GLAD/DESCRIPTION' ... OK
* this is package 'GLAD' version '2.44.0'
* 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 'GLAD' 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 ... NOTE
'library' or 'require' calls in package code:
  'aws' 'tcltk'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
arrayPersp.arrayCGH: warning in matrix("green", nr = nrow(z), nc =
  ncol(z)): partial argument match of 'nr' to 'nrow'
arrayPersp.arrayCGH: warning in matrix("green", nr = nrow(z), nc =
  ncol(z)): partial argument match of 'nc' to 'ncol'
arrayPersp.default: warning in matrix("green", nr = nrow(z), nc =
  ncol(z)): partial argument match of 'nr' to 'nrow'
arrayPersp.default: warning in matrix("green", nr = nrow(z), nc =
  ncol(z)): partial argument match of 'nc' to 'ncol'
ColorBar: no visible global function definition for 'heat.colors'
ColorBar: no visible global function definition for 'image'
ColorBar: no visible global function definition for 'axis'
ColorBar: no visible global function definition for 'par'
ColorBar: no visible global function definition for 'box'
FDRThres: no visible global function definition for 'pnorm'
HaarSeg: no visible global function definition for 'median'
HaarSegGLAD: no visible global function definition for 'median'
OptimBkpFindCluster: no visible global function definition for 'qnorm'
OutliersGNL.profileCGH: no visible global function definition for
  'qnorm'
RecomputeGNL: no visible global function definition for 'qnorm'
affectationGNL.profileCGH: no visible global function definition for
  'aggregate'
affectationGNL.profileCGH: no visible binding for global variable
  'median'
affectationGNL.profileCGH: no visible binding for global variable 'var'
affectationGNL.profileCGH: no visible global function definition for
  'qnorm'
arrayPersp.arrayCGH: no visible global function definition for 'median'
arrayPersp.arrayCGH: no visible global function definition for
  'na.omit'
arrayPersp.arrayCGH: no visible global function definition for 'par'
arrayPersp.arrayCGH: no visible global function definition for 'layout'
arrayPersp.arrayCGH: no visible global function definition for
  'dev.cur'
arrayPersp.arrayCGH: no visible global function definition for 'persp'
arrayPersp.default: no visible global function definition for 'median'
arrayPersp.default: no visible global function definition for 'na.omit'
arrayPersp.default: no visible global function definition for 'par'
arrayPersp.default: no visible global function definition for 'layout'
arrayPersp.default: no visible global function definition for 'dev.cur'
arrayPersp.default: no visible global function definition for 'persp'
arrayPlot.arrayCGH: no visible global function definition for 'par'
arrayPlot.arrayCGH: no visible global function definition for 'median'
arrayPlot.arrayCGH: no visible global function definition for 'na.omit'
arrayPlot.arrayCGH: no visible global function definition for 'image'
arrayPlot.arrayCGH: no visible global function definition for 'box'
arrayPlot.arrayCGH: no visible global function definition for 'abline'
as.profileCGH.data.frame: no visible global function definition for
  'na.omit'
chrBreakpoints.profileCGH : IQRdiff: no visible global function
  definition for 'IQR'
chrBreakpoints.profileCGH: no visible global function definition for
  'median'
chrBreakpoints.profileCGH: no visible global function definition for
  'laws'
chrBreakpoints.profileCGH: no visible global function definition for
  'aws'
clusterglad.hclust: no visible global function definition for 'cutree'
daglad.profileCGH : IQRdiff: no visible global function definition for
  'IQR'
daglad.profileCGH: no visible global function definition for 'median'
detectOutliers.profileChr: no visible global function definition for
  'qnorm'
dogenomestep: no visible global function definition for 'median'
glad.profileCGH: no visible global function definition for 'median'
glad.profileCGH : IQRdiff: no visible global function definition for
  'IQR'
glad.profileCGH: no visible global function definition for 'aggregate'
glad.profileCGH: no visible binding for global variable 'median'
hclustglad: no visible global function definition for 'as.dist'
lawsglad: no visible global function definition for 'qchisq'
loopRemove.profileChr: no visible global function definition for
  'qnorm'
myPalette: no visible global function definition for 'col2rgb'
myPalette: no visible global function definition for 'rgb'
plotCytoBand.default: no visible global function definition for
  'symbols'
plotCytoBand.default: no visible global function definition for
  'arrows'
plotCytoBand.default: no visible global function definition for 'axis'
plotProfile.profileCGH: no visible global function definition for
  'na.omit'
plotProfile.profileCGH: no visible global function definition for
  'aggregate'
plotProfile.profileCGH: no visible global function definition for 'par'
plotProfile.profileCGH: no visible global function definition for
  'layout'
plotProfile.profileCGH: no visible global function definition for
  'plot'
plotProfile.profileCGH: no visible global function definition for
  'lines'
plotProfile.profileCGH: no visible global function definition for
  'abline'
removeLevel.profileChr: no visible global function definition for
  'qnorm'
tkdaglad.default: no visible global function definition for
  'tktoplevel'
tkdaglad.default: no visible global function definition for 'tkframe'
tkdaglad.default: no visible global function definition for
  'tkwm.title'
tkdaglad.default: no visible global function definition for 'tkpack'
tkdaglad.default: no visible global function definition for 'tklabel'
tkdaglad.default: no visible global function definition for 'tclVar'
tkdaglad.default: no visible global function definition for
  'tkimage.create'
tkdaglad.default: no visible global function definition for
  'tkcheckbutton'
tkdaglad.default: no visible global function definition for
  'tkradiobutton'
tkdaglad.default: no visible global function definition for 'tkentry'
tkdaglad.default : OnAnalysis: no visible global function definition
  for 'tclvalue'
tkdaglad.default : OnAnalysis: no visible global function definition
  for 'tkmessageBox'
tkdaglad.default : OnQuit: no visible global function definition for
  'tkdestroy'
tkdaglad.default : OnDefault: no visible global function definition for
  'tclvalue<-'
tkdaglad.default : OnPlot: no visible global function definition for
  'tclvalue'
tkdaglad.default : OnPlot: no visible global function definition for
  'tkget'
tkdaglad.default : OnPlot: no visible global function definition for
  'tkcurselection'
tkdaglad.default : OnPlot: no visible global function definition for
  'X11'
tkdaglad.default : OnLogo: no visible global function definition for
  'tkmessageBox'
tkdaglad.default: no visible global function definition for 'tkbutton'
tkdaglad.default: no visible global function definition for
  'tkscrollbar'
tkdaglad.default : <anonymous>: no visible global function definition
  for 'tkyview'
tkdaglad.default: no visible global function definition for 'tklistbox'
tkdaglad.default : <anonymous>: no visible global function definition
  for 'tkset'
tkdaglad.default : MakeListBox: no visible global function definition
  for 'tkdelete'
tkdaglad.default : MakeListBox: no visible global function definition
  for 'tksize'
tkdaglad.default : MakeListBox: no visible global function definition
  for 'tkinsert'
tkdaglad.default : MakeListBox: no visible global function definition
  for 'tkselection.set'
tkglad.default: no visible global function definition for 'tktoplevel'
tkglad.default: no visible global function definition for 'tkframe'
tkglad.default: no visible global function definition for 'tkwm.title'
tkglad.default: no visible global function definition for 'tkpack'
tkglad.default: no visible global function definition for 'tklabel'
tkglad.default: no visible global function definition for 'tclVar'
tkglad.default: no visible global function definition for
  'tkimage.create'
tkglad.default: no visible global function definition for
  'tkcheckbutton'
tkglad.default: no visible global function definition for
  'tkradiobutton'
tkglad.default: no visible global function definition for 'tkentry'
tkglad.default : OnAnalysis: no visible global function definition for
  'tclvalue'
tkglad.default : OnAnalysis: no visible global function definition for
  'tkmessageBox'
tkglad.default : OnQuit: no visible global function definition for
  'tkdestroy'
tkglad.default : OnDefault: no visible global function definition for
  'tclvalue<-'
tkglad.default : OnPlot: no visible global function definition for
  'tclvalue'
tkglad.default : OnPlot: no visible global function definition for
  'tkget'
tkglad.default : OnPlot: no visible global function definition for
  'tkcurselection'
tkglad.default : OnPlot: no visible global function definition for
  'X11'
tkglad.default : OnLogo: no visible global function definition for
  'tkmessageBox'
tkglad.default: no visible global function definition for 'tkbutton'
tkglad.default: no visible global function definition for 'tkscrollbar'
tkglad.default : <anonymous>: no visible global function definition for
  'tkyview'
tkglad.default: no visible global function definition for 'tklistbox'
tkglad.default : <anonymous>: no visible global function definition for
  'tkset'
tkglad.default : MakeListBox: no visible global function definition for
  'tkdelete'
tkglad.default : MakeListBox: no visible global function definition for
  'tksize'
tkglad.default : MakeListBox: no visible global function definition for
  'tkinsert'
tkglad.default : MakeListBox: no visible global function definition for
  'tkselection.set'
Undefined global functions or variables:
  IQR X11 abline aggregate arrows as.dist aws axis box col2rgb cutree
  dev.cur heat.colors image laws layout lines median na.omit par persp
  plot pnorm qchisq qnorm rgb symbols tclVar tclvalue tclvalue<-
  tkbutton tkcheckbutton tkcurselection tkdelete tkdestroy tkentry
  tkframe tkget tkimage.create tkinsert tklabel tklistbox tkmessageBox
  tkpack tkradiobutton tkscrollbar tkselection.set tkset tksize
  tktoplevel tkwm.title tkyview var
Consider adding
  importFrom("grDevices", "X11", "col2rgb", "dev.cur", "heat.colors",
             "rgb")
  importFrom("graphics", "abline", "arrows", "axis", "box", "image",
             "layout", "lines", "par", "persp", "plot", "symbols")
  importFrom("stats", "IQR", "aggregate", "as.dist", "cutree", "median",
             "na.omit", "pnorm", "qchisq", "qnorm", "var")
to your NAMESPACE file.
* 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 shell scripts ... 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-3.7-bioc/R/library/GLAD/libs/i386/GLAD.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/GLAD.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/GLAD_2.44.0.tar.gz && rm -rf GLAD.buildbin-libdir && mkdir GLAD.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GLAD.buildbin-libdir GLAD_2.44.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL GLAD_2.44.0.zip && rm GLAD_2.44.0.tar.gz GLAD_2.44.0.zip
###
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                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  385k  100  385k    0     0  6717k      0 --:--:-- --:--:-- --:--:-- 7703k

install for i386

* installing *source* package 'GLAD' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BkpInfo.cpp -o BkpInfo.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c HaarSeg.cpp -o HaarSeg.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c MoveBkp.cpp -o MoveBkp.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c OutliersGNL.cpp -o OutliersGNL.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chrBreakpoints.cpp -o chrBreakpoints.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cutree.cpp -o cutree.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c daglad.cpp -o daglad.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c distance.cpp -o distance.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c filterBkp.cpp -o filterBkp.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c findCluster.cpp -o findCluster.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c glad-utils.cpp -o glad-utils.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c hclust.cpp -o hclust.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c laws.c -o laws.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c loopRemove.cpp -o loopRemove.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o GLAD.dll tmp.def BkpInfo.o HaarSeg.o MoveBkp.o OutliersGNL.o chrBreakpoints.o cutree.o daglad.o distance.o filterBkp.o findCluster.o glad-utils.o hclust.o laws.o loopRemove.o -L/i386/lib -lgsl -lgslcblas -lm -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/GLAD.buildbin-libdir/GLAD/libs/i386
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GLAD'
    finding HTML links ... done
    ChrNumeric                              html  
    ColorBar                                html  
    GLAD-internal                           html  
    arrayCGH                                html  
    arrayPersp                              html  
    arrayPlot                               html  
    as.data.frame.profileCGH                html  
    as.profileCGH                           html  
    bladder                                 html  
    cytoband                                html  
    daglad                                  html  
    glad                                    html  
    hclust                                  html  
    kernel                                  html  
    myPalette                               html  
    plotProfile                             html  
    profileCGH                              html  
    snijders                                html  
    tkdaglad                                html  
    veltman                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GLAD' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BkpInfo.cpp -o BkpInfo.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c HaarSeg.cpp -o HaarSeg.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c MoveBkp.cpp -o MoveBkp.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c OutliersGNL.cpp -o OutliersGNL.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chrBreakpoints.cpp -o chrBreakpoints.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cutree.cpp -o cutree.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c daglad.cpp -o daglad.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c distance.cpp -o distance.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c filterBkp.cpp -o filterBkp.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c findCluster.cpp -o findCluster.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c glad-utils.cpp -o glad-utils.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c hclust.cpp -o hclust.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c laws.c -o laws.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c loopRemove.cpp -o loopRemove.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o GLAD.dll tmp.def BkpInfo.o HaarSeg.o MoveBkp.o OutliersGNL.o chrBreakpoints.o cutree.o daglad.o distance.o filterBkp.o findCluster.o glad-utils.o hclust.o laws.o loopRemove.o -L/x64/lib -lgsl -lgslcblas -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/GLAD.buildbin-libdir/GLAD/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GLAD' as GLAD_2.44.0.zip
* DONE (GLAD)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'GLAD' successfully unpacked and MD5 sums checked
In R CMD INSTALL