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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MANOR
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'MANOR' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Rnem_arg.c -o Rnem_arg.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Rnem_exe.c -o Rnem_exe.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c exememo.c -o exememo.o
exememo.c: In function 'GenAlloc':
exememo.c:40:53: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
     sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
                                                   ~~^
                                                   %I64d
      where, what, nelem, elsize);
                   ~~~~~                              
exememo.c:40:71: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
     sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
                                                                     ~~^
                                                                     %I64d
      where, what, nelem, elsize);
                          ~~~~~~                                        
exememo.c:40:53: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
     sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
                                                   ~~^
                                                   %I64d
      where, what, nelem, elsize);
                   ~~~~~                              
exememo.c:40:71: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
     sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
                                                                     ~~^
                                                                     %I64d
      where, what, nelem, elsize);
                          ~~~~~~                                        
exememo.c:40:5: warning: 'msg' may be used uninitialized in this function [-Wmaybe-uninitialized]
     sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      where, what, nelem, elsize);
      ~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c nem_alg.c -o nem_alg.o
In function 'ClassifyByNemHeuBeta',
    inlined from 'ClassifyByNem' at nem_alg.c:578:13:
nem_alg.c:801:7: warning: 'strncpy' output may be truncated copying 100 bytes from a string of length 100 [-Wstringop-truncation]
       strncpy( namecri, NemParaP->OutBaseName, LEN_FILENAME ) ;
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c nem_hlp.c -o nem_hlp.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c nem_mod.c -o nem_mod.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c nem_nei.c -o nem_nei.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c nem_rnd.c -o nem_rnd.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c nem_ver.c -o nem_ver.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c registerDynamicSymbols.c -o registerDynamicSymbols.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o MANOR.dll tmp.def Rnem_arg.o Rnem_exe.o exememo.o nem_alg.o nem_hlp.o nem_mod.o nem_nei.o nem_rnd.o nem_ver.o registerDynamicSymbols.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-MANOR/00new/MANOR/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MANOR'
    finding HTML links ... done
    MANOR-internal                          html  
    arrayTrend                              html  
    detectSB                                html  
    flag.arrayCGH                           html  
    flag.summary                            html  
    flags                                   html  
    genome.plot                             html  
    html.report                             html  
    import                                  html  
    nem                                     html  
    norm                                    html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-MANOR/00new/MANOR/help/manor.html
    qscore                                  html  
    qscore.arrayCGH                         html  
    qscore.summary                          html  
    qscores                                 html  
    report.plot                             html  
    sort                                    html  
    spatial                                 html  
    to.flag                                 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
* DONE (MANOR)
Making 'packages.html' ... done