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### Running command:
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### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MANOR_1.66.0.tar.gz && rm -rf MANOR.buildbin-libdir && mkdir MANOR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MANOR.buildbin-libdir MANOR_1.66.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MANOR_1.66.0.zip && rm MANOR_1.66.0.tar.gz MANOR_1.66.0.zip
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install for i386
* installing *source* package 'MANOR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rnem_arg.c -o Rnem_arg.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rnem_exe.c -o Rnem_exe.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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 'unsigned int'} [-Wformat=]
sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
~~^
%d
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 'unsigned int'} [-Wformat=]
sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
~~^
%d
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 'unsigned int'} [-Wformat=]
sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
~~^
%d
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 'unsigned int'} [-Wformat=]
sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
~~^
%d
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/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c nem_hlp.c -o nem_hlp.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c nem_mod.c -o nem_mod.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c nem_nei.c -o nem_nei.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c nem_rnd.c -o nem_rnd.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c nem_ver.c -o nem_ver.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c registerDynamicSymbols.c -o registerDynamicSymbols.o
C:/rtools40/mingw32/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/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/MANOR.buildbin-libdir/00LOCK-MANOR/00new/MANOR/libs/i386
** 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: C:/Users/biocbuild/bbs-3.14-bioc/meat/MANOR.buildbin-libdir/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
install for x64
* installing *source* package 'MANOR' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rnem_arg.c -o Rnem_arg.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rnem_exe.c -o Rnem_exe.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c nem_hlp.c -o nem_hlp.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c nem_mod.c -o nem_mod.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c nem_nei.c -o nem_nei.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c nem_rnd.c -o nem_rnd.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c nem_ver.c -o nem_ver.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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 -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/MANOR.buildbin-libdir/MANOR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MANOR' as MANOR_1.66.0.zip
* DONE (MANOR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MANOR' successfully unpacked and MD5 sums checked
