############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf affyio.buildbin-libdir && mkdir affyio.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affyio.buildbin-libdir affyio_1.64.0.tar.gz ### ############################################################################## ############################################################################## install for i386 * installing *source* package 'affyio' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fread_functions.c -o fread_functions.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init_package.c -o init_package.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_abatch.c -o read_abatch.o read_abatch.c: In function 'gzbinary_get_detailed_header_info': read_abatch.c:3410:3: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_abatch.c:3410:65: note: length computed here strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_abatch.c: In function 'binary_get_detailed_header_info': read_abatch.c:2661:3: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_abatch.c:2661:65: note: length computed here strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_bpmap.c -o read_bpmap.o read_bpmap.c: In function 'ReadBPMAPFileIntoRList': read_bpmap.c:698:20: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=] sprintf(buf, "%d", j+1); ^ read_bpmap.c:698:4: note: 'sprintf' output between 2 and 11 bytes into a destination of size 10 sprintf(buf, "%d", j+1); ^~~~~~~~~~~~~~~~~~~~~~~ read_bpmap.c:655:20: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=] sprintf(buf, "%d", j+1); ^ read_bpmap.c:655:4: note: 'sprintf' output between 2 and 11 bytes into a destination of size 10 sprintf(buf, "%d", j+1); ^~~~~~~~~~~~~~~~~~~~~~~ read_bpmap.c:603:18: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=] sprintf(buf, "%d", j+1); ^ read_bpmap.c:603:2: note: 'sprintf' output between 2 and 11 bytes into a destination of size 10 sprintf(buf, "%d", j+1); ^~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_cdf_xda.c -o read_cdf_xda.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_cdffile2.c -o read_cdffile2.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_celfile_generic.c -o read_celfile_generic.o read_celfile_generic.c: In function 'generic_get_detailed_header_info': read_celfile_generic.c:272:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] strncpy(header_info->AlgorithmParameters,"Percentile:",11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:294:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"CellMargin:",11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:315:3: warning: 'strncpy' output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierHigh:",12); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:336:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierLow:",11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:357:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"AlgVersion:",11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:378:3: warning: 'strncpy' output truncated before terminating nul copying 14 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FixedCellSize:",14); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:399:3: warning: 'strncpy' output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureWidth:",17); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:420:3: warning: 'strncpy' output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureHeight:",18); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:441:3: warning: 'strncpy' output truncated before terminating nul copying 26 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"IgnoreOutliersInShiftRows:",26); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:464:3: warning: 'strncpy' output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FeatureExtraction:",18); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:488:3: warning: 'strncpy' output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolWidthExtenstion:",20); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:510:3: warning: 'strncpy' output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolHeightExtension:",20); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:532:3: warning: 'strncpy' output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"UseSubgrids:",12); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:553:3: warning: 'strncpy' output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"RandomizePixels:",16); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:575:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"ErrorBasis:",11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:597:3: warning: 'strncpy' output truncated before terminating nul copying 8 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"StdMult:",8); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c: In function 'gzgeneric_get_detailed_header_info': read_celfile_generic.c:1270:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] strncpy(header_info->AlgorithmParameters,"Percentile:",11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1292:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"CellMargin:",11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1313:3: warning: 'strncpy' output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierHigh:",12); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1334:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierLow:",11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1355:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"AlgVersion:",11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1376:3: warning: 'strncpy' output truncated before terminating nul copying 14 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FixedCellSize:",14); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1397:3: warning: 'strncpy' output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureWidth:",17); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1418:3: warning: 'strncpy' output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureHeight:",18); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1439:3: warning: 'strncpy' output truncated before terminating nul copying 26 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"IgnoreOutliersInShiftRows:",26); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1462:3: warning: 'strncpy' output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FeatureExtraction:",18); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1486:3: warning: 'strncpy' output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolWidthExtenstion:",20); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1508:3: warning: 'strncpy' output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolHeightExtension:",20); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1530:3: warning: 'strncpy' output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"UseSubgrids:",12); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1551:3: warning: 'strncpy' output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"RandomizePixels:",16); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1573:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"ErrorBasis:",11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1595:3: warning: 'strncpy' output truncated before terminating nul copying 8 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"StdMult:",8); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_clf.c -o read_clf.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_generic.c -o read_generic.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_pgf.c -o read_pgf.o read_pgf.c:363:12: warning: 'token_ends_with' defined but not used [-Wunused-function] static int token_ends_with(char *token, char *ends_in){ ^~~~~~~~~~~~~~~ C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o affyio.dll tmp.def fread_functions.o init_package.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_clf.o read_generic.o read_multichannel_celfile_generic.o read_pgf.o -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -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/affyio.buildbin-libdir/00LOCK-affyio/00new/affyio/libs/i386 ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'affyio' finding HTML links ... done affyio-internal html check.cdf.type html get.celfile.dates html read.cdffile.list html read.celfile html read.celfile.header html read.celfile.probeintensity.matrices html read_abatch html ** building package indices ** 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 'affyio' ... ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fread_functions.c -o fread_functions.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init_package.c -o init_package.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_abatch.c -o read_abatch.o read_abatch.c: In function 'gzbinary_get_detailed_header_info': read_abatch.c:3410:3: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_abatch.c:3410:65: note: length computed here strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_abatch.c: In function 'binary_get_detailed_header_info': read_abatch.c:2661:3: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_abatch.c:2661:65: note: length computed here strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_bpmap.c -o read_bpmap.o read_bpmap.c: In function 'ReadBPMAPHeader': read_bpmap.c:110:18: warning: overflow in conversion from 'long long unsigned int' to 'long int' changes value from '18446744073709551612' to '-4' [-Woverflow] fseek(infile,-sizeof(float),SEEK_CUR); ^~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_cdf_xda.c -o read_cdf_xda.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_cdffile2.c -o read_cdffile2.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_celfile_generic.c -o read_celfile_generic.o read_celfile_generic.c: In function 'generic_get_detailed_header_info': read_celfile_generic.c:272:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] strncpy(header_info->AlgorithmParameters,"Percentile:",11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:294:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"CellMargin:",11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:315:3: warning: 'strncpy' output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierHigh:",12); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:336:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierLow:",11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:357:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"AlgVersion:",11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:378:3: warning: 'strncpy' output truncated before terminating nul copying 14 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FixedCellSize:",14); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:399:3: warning: 'strncpy' output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureWidth:",17); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:420:3: warning: 'strncpy' output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureHeight:",18); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:441:3: warning: 'strncpy' output truncated before terminating nul copying 26 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"IgnoreOutliersInShiftRows:",26); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:464:3: warning: 'strncpy' output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FeatureExtraction:",18); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:488:3: warning: 'strncpy' output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolWidthExtenstion:",20); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:510:3: warning: 'strncpy' output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolHeightExtension:",20); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:532:3: warning: 'strncpy' output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"UseSubgrids:",12); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:553:3: warning: 'strncpy' output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"RandomizePixels:",16); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:575:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"ErrorBasis:",11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:597:3: warning: 'strncpy' output truncated before terminating nul copying 8 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"StdMult:",8); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c: In function 'gzgeneric_get_detailed_header_info': read_celfile_generic.c:1270:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] strncpy(header_info->AlgorithmParameters,"Percentile:",11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1292:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"CellMargin:",11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1313:3: warning: 'strncpy' output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierHigh:",12); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1334:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierLow:",11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1355:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"AlgVersion:",11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1376:3: warning: 'strncpy' output truncated before terminating nul copying 14 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FixedCellSize:",14); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1397:3: warning: 'strncpy' output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureWidth:",17); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1418:3: warning: 'strncpy' output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureHeight:",18); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1439:3: warning: 'strncpy' output truncated before terminating nul copying 26 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"IgnoreOutliersInShiftRows:",26); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1462:3: warning: 'strncpy' output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FeatureExtraction:",18); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1486:3: warning: 'strncpy' output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolWidthExtenstion:",20); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1508:3: warning: 'strncpy' output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolHeightExtension:",20); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1530:3: warning: 'strncpy' output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"UseSubgrids:",12); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1551:3: warning: 'strncpy' output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"RandomizePixels:",16); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1573:3: warning: 'strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"ErrorBasis:",11); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_celfile_generic.c:1595:3: warning: 'strncpy' output truncated before terminating nul copying 8 bytes from a string of the same length [-Wstringop-truncation] strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"StdMult:",8); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_clf.c -o read_clf.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_generic.c -o read_generic.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_pgf.c -o read_pgf.o read_pgf.c:363:12: warning: 'token_ends_with' defined but not used [-Wunused-function] static int token_ends_with(char *token, char *ends_in){ ^~~~~~~~~~~~~~~ C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o affyio.dll tmp.def fread_functions.o init_package.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_clf.o read_generic.o read_multichannel_celfile_generic.o read_pgf.o -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -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/affyio.buildbin-libdir/affyio/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'affyio' as affyio_1.64.0.zip * DONE (affyio)