############################################################################## ############################################################################## ### ### Running command: ### ### 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 ### ############################################################################## ############################################################################## 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)