Mock Version: 1.4.9 Mock Version: 1.4.9 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/R-affyio.spec'], chrootPath='/var/lib/mock/f29-build-1125-467/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=timeout=345600uid=998gid=135user='mockbuild'nspawn_args=[]unshare_net=FalseprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/R-affyio.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False Building target platforms: riscv64 Building for target riscv64 Wrote: /builddir/build/SRPMS/R-affyio-1.46.0-3.fc29.src.rpm Child return code was: 0 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/R-affyio.spec'], chrootPath='/var/lib/mock/f29-build-1125-467/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=timeout=345600uid=998gid=135user='mockbuild'nspawn_args=[]unshare_net=FalseprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/R-affyio.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False Building target platforms: riscv64 Building for target riscv64 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.3v3Ln2 + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf affyio + /usr/bin/mkdir -p affyio + cd affyio + /usr/bin/gzip -dc /builddir/build/SOURCES/affyio_1.46.0.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + sed -i '/Imports: zlibbioc/d' affyio/DESCRIPTION + sed -i '/import(zlibbioc)/d' affyio/NAMESPACE + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.i0hzBE + umask 022 + cd /builddir/build/BUILD + cd affyio + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.9Vc8Vq + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-affyio-1.46.0-3.fc29.riscv64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-affyio-1.46.0-3.fc29.riscv64 BUILDSTDERR: ++ dirname /builddir/build/BUILDROOT/R-affyio-1.46.0-3.fc29.riscv64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-affyio-1.46.0-3.fc29.riscv64 + cd affyio + rm -rf /builddir/build/BUILDROOT/R-affyio-1.46.0-3.fc29.riscv64 + mkdir -p /builddir/build/BUILDROOT/R-affyio-1.46.0-3.fc29.riscv64/usr/lib64/R/library + R CMD INSTALL affyio -l /builddir/build/BUILDROOT/R-affyio-1.46.0-3.fc29.riscv64/usr/lib64/R/library BUILDSTDERR: * installing *source* package 'affyio' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for main in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking if zlib version >= 1.1.3... yes checking for pthread_create in -lpthread... yes checking if we can use pthreads... yes checking if PTHREAD_STACK_MIN is defined... yes configure: creating ./config.status config.status: creating src/Makevars BUILDSTDERR: ** libs gcc -I/usr/include/R -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c fread_functions.c -o fread_functions.o BUILDSTDERR: fread_functions.c: In function 'gzread_int32': BUILDSTDERR: fread_functions.c:414:19: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: result = gzread(instream,destination,sizeof(int)*n); BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from fread_functions.c:10: BUILDSTDERR: /usr/include/zlib.h:1390:28: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len)); BUILDSTDERR: ^~ BUILDSTDERR: fread_functions.c: In function 'gzread_uint32': BUILDSTDERR: fread_functions.c:439:19: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: result = gzread(instream,destination,sizeof(unsigned int)*n); BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from fread_functions.c:10: BUILDSTDERR: /usr/include/zlib.h:1390:28: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len)); BUILDSTDERR: ^~ BUILDSTDERR: fread_functions.c: In function 'gzread_int16': BUILDSTDERR: fread_functions.c:458:20: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: result = gzread(instream,destination,sizeof(short)*n); BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from fread_functions.c:10: BUILDSTDERR: /usr/include/zlib.h:1390:28: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len)); BUILDSTDERR: ^~ BUILDSTDERR: fread_functions.c: In function 'gzread_uint16': BUILDSTDERR: fread_functions.c:476:20: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: result = gzread(instream,destination,sizeof(unsigned short)*n); BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from fread_functions.c:10: BUILDSTDERR: /usr/include/zlib.h:1390:28: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len)); BUILDSTDERR: ^~ BUILDSTDERR: fread_functions.c: In function 'gzread_float32': BUILDSTDERR: fread_functions.c:497:20: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: result = gzread(instream,destination,sizeof(float)*n); BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from fread_functions.c:10: BUILDSTDERR: /usr/include/zlib.h:1390:28: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len)); BUILDSTDERR: ^~ BUILDSTDERR: fread_functions.c: In function 'gzread_char': BUILDSTDERR: fread_functions.c:513:19: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: result = gzread(instream,destination,sizeof(char)*n); BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from fread_functions.c:10: BUILDSTDERR: /usr/include/zlib.h:1390:28: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len)); BUILDSTDERR: ^~ BUILDSTDERR: fread_functions.c: In function 'gzread_uchar': BUILDSTDERR: fread_functions.c:529:19: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: result = gzread(instream,destination,sizeof(unsigned char)*n); BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from fread_functions.c:10: BUILDSTDERR: /usr/include/zlib.h:1390:28: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len)); BUILDSTDERR: ^~ BUILDSTDERR: fread_functions.c: In function 'gzread_double64': BUILDSTDERR: fread_functions.c:547:19: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: result = gzread(instream, destination,sizeof(double)*n); BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from fread_functions.c:10: BUILDSTDERR: /usr/include/zlib.h:1390:28: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len)); BUILDSTDERR: ^~ BUILDSTDERR: fread_functions.c: In function 'gzread_be_int32': BUILDSTDERR: fread_functions.c:575:19: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: result = gzread(instream,destination,sizeof(int)*n); BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from fread_functions.c:10: BUILDSTDERR: /usr/include/zlib.h:1390:28: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len)); BUILDSTDERR: ^~ BUILDSTDERR: fread_functions.c: In function 'gzread_be_uint32': BUILDSTDERR: fread_functions.c:600:19: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: result = gzread(instream,destination,sizeof(unsigned int)*n); BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from fread_functions.c:10: BUILDSTDERR: /usr/include/zlib.h:1390:28: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len)); BUILDSTDERR: ^~ BUILDSTDERR: fread_functions.c: In function 'gzread_be_int16': BUILDSTDERR: fread_functions.c:620:20: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: result = gzread(instream,destination,sizeof(short)*n); BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from fread_functions.c:10: BUILDSTDERR: /usr/include/zlib.h:1390:28: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len)); BUILDSTDERR: ^~ BUILDSTDERR: fread_functions.c: In function 'gzread_be_uint16': BUILDSTDERR: fread_functions.c:636:20: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: result = gzread(instream,destination,sizeof(unsigned short)*n); BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from fread_functions.c:10: BUILDSTDERR: /usr/include/zlib.h:1390:28: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len)); BUILDSTDERR: ^~ BUILDSTDERR: fread_functions.c: In function 'gzread_be_float32': BUILDSTDERR: fread_functions.c:656:20: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: result = gzread(instream,destination,sizeof(float)*n); BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from fread_functions.c:10: BUILDSTDERR: /usr/include/zlib.h:1390:28: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len)); BUILDSTDERR: ^~ BUILDSTDERR: fread_functions.c: In function 'gzread_be_char': BUILDSTDERR: fread_functions.c:673:19: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: result = gzread(instream,destination,sizeof(char)*n); BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from fread_functions.c:10: BUILDSTDERR: /usr/include/zlib.h:1390:28: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len)); BUILDSTDERR: ^~ BUILDSTDERR: fread_functions.c: In function 'gzread_be_uchar': BUILDSTDERR: fread_functions.c:690:19: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: result = gzread(instream,destination,sizeof(unsigned char)*n); BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from fread_functions.c:10: BUILDSTDERR: /usr/include/zlib.h:1390:28: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len)); BUILDSTDERR: ^~ BUILDSTDERR: fread_functions.c: In function 'gzread_be_double64': BUILDSTDERR: fread_functions.c:706:19: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: result = gzread(instream, destination,sizeof(double)*n); BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from fread_functions.c:10: BUILDSTDERR: /usr/include/zlib.h:1390:28: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len)); BUILDSTDERR: ^~ BUILDSTDERR: At top level: BUILDSTDERR: fread_functions.c:300:13: warning: 'swap_uint_32' defined but not used [-Wunused-function] BUILDSTDERR: static void swap_uint_32(unsigned int *tni4) /* 4 byte integer numbers */ BUILDSTDERR: ^~~~~~~~~~~~ gcc -I/usr/include/R -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c init_package.c -o init_package.o gcc -I/usr/include/R -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c read_abatch.c -o read_abatch.o BUILDSTDERR: read_abatch.c: In function 'read_cel_file_stddev': BUILDSTDERR: read_abatch.c:735:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable] BUILDSTDERR: double cur_mean, cur_stddev; BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: read_abatch.c: In function 'read_cel_file_npixels': BUILDSTDERR: read_abatch.c:841:20: warning: variable 'cur_stddev' set but not used [-Wunused-but-set-variable] BUILDSTDERR: double cur_mean, cur_stddev; BUILDSTDERR: ^~~~~~~~~~ BUILDSTDERR: read_abatch.c:841:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable] BUILDSTDERR: double cur_mean, cur_stddev; BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: read_abatch.c: In function 'read_gzcel_file_stddev': BUILDSTDERR: read_abatch.c:1630:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable] BUILDSTDERR: double cur_mean, cur_stddev; BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: read_abatch.c: In function 'read_gzcel_file_npixels': BUILDSTDERR: read_abatch.c:1735:20: warning: variable 'cur_stddev' set but not used [-Wunused-but-set-variable] BUILDSTDERR: double cur_mean, cur_stddev; BUILDSTDERR: ^~~~~~~~~~ BUILDSTDERR: read_abatch.c:1735:10: warning: variable 'cur_mean' set but not used [-Wunused-but-set-variable] BUILDSTDERR: double cur_mean, cur_stddev; BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: read_abatch.c: In function 'gz_get_detailed_header_info': BUILDSTDERR: read_abatch.c:1989:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] BUILDSTDERR: currentFile = open_gz_cel_file(filename); BUILDSTDERR: ^ BUILDSTDERR: read_abatch.c:1991:22: warning: passing argument 1 of 'gzAdvanceToSection' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzAdvanceToSection(currentFile,"[HEADER]",buffer); BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: read_abatch.c:1439:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: static void gzAdvanceToSection(gzFile my_file,char *sectiontitle, char *buffer){ BUILDSTDERR: ~~~~~~~^~~~~~~ BUILDSTDERR: read_abatch.c:1993:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzfindStartsWith(currentFile,"Cols",buffer); BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: read_abatch.c:1416:38: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){ BUILDSTDERR: ~~~~~~~^~~~~~~ BUILDSTDERR: read_abatch.c:1998:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzfindStartsWith(currentFile,"Rows",buffer); BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: read_abatch.c:1416:38: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){ BUILDSTDERR: ~~~~~~~^~~~~~~ BUILDSTDERR: read_abatch.c:2003:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzfindStartsWith(currentFile,"GridCornerUL",buffer); BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: read_abatch.c:1416:38: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){ BUILDSTDERR: ~~~~~~~^~~~~~~ BUILDSTDERR: read_abatch.c:2009:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzfindStartsWith(currentFile,"GridCornerUR",buffer); BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: read_abatch.c:1416:38: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){ BUILDSTDERR: ~~~~~~~^~~~~~~ BUILDSTDERR: read_abatch.c:2015:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzfindStartsWith(currentFile,"GridCornerLR",buffer); BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: read_abatch.c:1416:38: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){ BUILDSTDERR: ~~~~~~~^~~~~~~ BUILDSTDERR: read_abatch.c:2021:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzfindStartsWith(currentFile,"GridCornerLL",buffer); BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: read_abatch.c:1416:38: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){ BUILDSTDERR: ~~~~~~~^~~~~~~ BUILDSTDERR: read_abatch.c:2027:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzfindStartsWith(currentFile,"DatHeader",buffer); BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: read_abatch.c:1416:38: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){ BUILDSTDERR: ~~~~~~~^~~~~~~ BUILDSTDERR: read_abatch.c:2059:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzfindStartsWith(currentFile,"Algorithm",buffer); BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: read_abatch.c:1416:38: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){ BUILDSTDERR: ~~~~~~~^~~~~~~ BUILDSTDERR: read_abatch.c:2067:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzfindStartsWith(currentFile,"AlgorithmParameters",buffer); BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: read_abatch.c:1416:38: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){ BUILDSTDERR: ~~~~~~~^~~~~~~ BUILDSTDERR: read_abatch.c:2072:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(currentFile); BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_abatch.c:164: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_abatch.c: In function 'gz_get_masks_outliers': BUILDSTDERR: read_abatch.c:2100:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] BUILDSTDERR: currentFile = open_gz_cel_file(filename); BUILDSTDERR: ^ BUILDSTDERR: read_abatch.c:2104:22: warning: passing argument 1 of 'gzAdvanceToSection' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzAdvanceToSection(currentFile,"[MASKS]",buffer); BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: read_abatch.c:1439:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: static void gzAdvanceToSection(gzFile my_file,char *sectiontitle, char *buffer){ BUILDSTDERR: ~~~~~~~^~~~~~~ BUILDSTDERR: read_abatch.c:2105:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzfindStartsWith(currentFile,"NumberCells=",buffer); BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: read_abatch.c:1416:38: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){ BUILDSTDERR: ~~~~~~~^~~~~~~ BUILDSTDERR: read_abatch.c:2109:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzfindStartsWith(currentFile,"CellHeader=",buffer); BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: read_abatch.c:1416:38: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){ BUILDSTDERR: ~~~~~~~^~~~~~~ BUILDSTDERR: read_abatch.c:2118:38: warning: passing argument 3 of 'ReadgzFileLine' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: ReadgzFileLine(buffer, BUF_SIZE, currentFile); BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: read_abatch.c:1354:65: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: static void ReadgzFileLine(char *buffer, int buffersize, gzFile currentFile){ BUILDSTDERR: ~~~~~~~^~~~~~~~~~~ BUILDSTDERR: read_abatch.c:2133:22: warning: passing argument 1 of 'gzAdvanceToSection' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzAdvanceToSection(currentFile,"[OUTLIERS]",buffer); BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: read_abatch.c:1439:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: static void gzAdvanceToSection(gzFile my_file,char *sectiontitle, char *buffer){ BUILDSTDERR: ~~~~~~~^~~~~~~ BUILDSTDERR: read_abatch.c:2134:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzfindStartsWith(currentFile,"NumberCells=",buffer); BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: read_abatch.c:1416:38: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){ BUILDSTDERR: ~~~~~~~^~~~~~~ BUILDSTDERR: read_abatch.c:2138:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzfindStartsWith(currentFile,"CellHeader=",buffer); BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: read_abatch.c:1416:38: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){ BUILDSTDERR: ~~~~~~~^~~~~~~ BUILDSTDERR: read_abatch.c:2146:38: warning: passing argument 3 of 'ReadgzFileLine' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: ReadgzFileLine(buffer, BUF_SIZE, currentFile); BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: read_abatch.c:1354:65: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: static void ReadgzFileLine(char *buffer, int buffersize, gzFile currentFile){ BUILDSTDERR: ~~~~~~~^~~~~~~~~~~ BUILDSTDERR: read_abatch.c:2158:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(currentFile); BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_abatch.c:164: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_abatch.c: In function 'isgzBinaryCelFile': BUILDSTDERR: read_abatch.c:3141:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] BUILDSTDERR: if ((infile = gzopen(filename, "rb")) == NULL) BUILDSTDERR: ^ BUILDSTDERR: read_abatch.c:3148:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_abatch.c:164: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_abatch.c:3153:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_abatch.c:164: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_abatch.c:3159:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_abatch.c:164: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_abatch.c:3164:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_abatch.c:164: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_abatch.c:3169:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_abatch.c:164: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_abatch.c: In function 'gzread_binary_header': BUILDSTDERR: read_abatch.c:3192:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] BUILDSTDERR: if ((infile = gzopen(filename, "rb")) == NULL) BUILDSTDERR: ^ BUILDSTDERR: read_abatch.c:3247:15: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: if (!gzread(infile,this_header->header,sizeof(char)*this_header->header_len)){ BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_abatch.c:164: BUILDSTDERR: /usr/include/zlib.h:1390:28: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len)); BUILDSTDERR: ^~ BUILDSTDERR: read_abatch.c:3289:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_abatch.c:164: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_abatch.c: In function 'gzread_binarycel_file_intensities': BUILDSTDERR: read_abatch.c:3591:19: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(my_header->gzinfile); BUILDSTDERR: ~~~~~~~~~^~~~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_abatch.c:164: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_abatch.c:3597:19: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(my_header->infile); BUILDSTDERR: ~~~~~~~~~^~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_abatch.c:164: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'FILE *' {aka 'struct _IO_FILE *'} BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_abatch.c:3607:20: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(my_header->gzinfile); BUILDSTDERR: ~~~~~~~~~^~~~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_abatch.c:164: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_abatch.c: In function 'gzread_binarycel_file_stddev': BUILDSTDERR: read_abatch.c:3644:19: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(my_header->gzinfile); BUILDSTDERR: ~~~~~~~~~^~~~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_abatch.c:164: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_abatch.c:3654:20: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(my_header->gzinfile); BUILDSTDERR: ~~~~~~~~~^~~~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_abatch.c:164: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_abatch.c: In function 'gzread_binarycel_file_npixels': BUILDSTDERR: read_abatch.c:3692:19: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(my_header->infile); BUILDSTDERR: ~~~~~~~~~^~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_abatch.c:164: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'FILE *' {aka 'struct _IO_FILE *'} BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_abatch.c:3702:20: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(my_header->gzinfile); BUILDSTDERR: ~~~~~~~~~^~~~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_abatch.c:164: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_abatch.c: In function 'gz_binary_apply_masks': BUILDSTDERR: read_abatch.c:3735:19: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(my_header->infile,my_header->n_cells*sizeofrecords,SEEK_CUR); BUILDSTDERR: ~~~~~~~~~^~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_abatch.c:164: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'FILE *' {aka 'struct _IO_FILE *'} BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_abatch.c:3748:21: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(my_header->gzinfile,my_header->n_masks*sizeof(cur_loc),SEEK_CUR); BUILDSTDERR: ~~~~~~~~~^~~~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_abatch.c:164: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_abatch.c:3761:21: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(my_header->gzinfile,my_header->n_outliers*sizeof(cur_loc),SEEK_CUR); BUILDSTDERR: ~~~~~~~~~^~~~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_abatch.c:164: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_abatch.c:3764:20: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(my_header->gzinfile); BUILDSTDERR: ~~~~~~~~~^~~~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_abatch.c:164: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_abatch.c: In function 'gzbinary_get_masks_outliers': BUILDSTDERR: read_abatch.c:3797:19: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(my_header->gzinfile,my_header->n_cells*sizeofrecords,SEEK_CUR); BUILDSTDERR: ~~~~~~~~~^~~~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_abatch.c:164: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_abatch.c:3827:20: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(my_header->gzinfile); BUILDSTDERR: ~~~~~~~~~^~~~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_abatch.c:164: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_abatch.c: In function 'readfile_group': BUILDSTDERR: read_abatch.c:4369:9: warning: unused variable 'Current_intensity' [-Wunused-variable] BUILDSTDERR: SEXP Current_intensity; BUILDSTDERR: ^~~~~~~~~~~~~~~~~ BUILDSTDERR: read_abatch.c: In function 'read_probeintensities': BUILDSTDERR: read_abatch.c:4438:11: warning: variable 'CurintensityMatrix' set but not used [-Wunused-but-set-variable] BUILDSTDERR: double *CurintensityMatrix, *pmMatrix=0, *mmMatrix=0; BUILDSTDERR: ^~~~~~~~~~~~~~~~~~ gcc -I/usr/include/R -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c read_bpmap.c -o read_bpmap.o BUILDSTDERR: read_bpmap.c: In function 'ReadBPMAPHeader': BUILDSTDERR: read_bpmap.c:78:7: warning: unused variable 'version_number_int' [-Wunused-variable] BUILDSTDERR: int version_number_int; BUILDSTDERR: ^~~~~~~~~~~~~~~~~~ gcc -I/usr/include/R -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c read_cdf_xda.c -o read_cdf_xda.o gcc -I/usr/include/R -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c read_cdffile2.c -o read_cdffile2.o BUILDSTDERR: read_cdffile2.c:364:12: warning: 'token_ends_with' defined but not used [-Wunused-function] BUILDSTDERR: static int token_ends_with(char *token, char *ends_in){ BUILDSTDERR: ^~~~~~~~~~~~~~~ gcc -I/usr/include/R -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c read_celfile_generic.c -o read_celfile_generic.o BUILDSTDERR: read_celfile_generic.c: In function 'read_genericcel_file_intensities': BUILDSTDERR: read_celfile_generic.c:711:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_celfile_generic.c:709:10: warning: unused variable 'cur_index' [-Wunused-variable] BUILDSTDERR: size_t cur_index; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_celfile_generic.c:708:15: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: size_t i=0, j=0; BUILDSTDERR: ^ BUILDSTDERR: read_celfile_generic.c: In function 'read_genericcel_file_stddev': BUILDSTDERR: read_celfile_generic.c:761:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_celfile_generic.c:759:10: warning: unused variable 'cur_index' [-Wunused-variable] BUILDSTDERR: size_t cur_index; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_celfile_generic.c:758:15: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: size_t i=0, j=0; BUILDSTDERR: ^ BUILDSTDERR: read_celfile_generic.c: In function 'read_genericcel_file_npixels': BUILDSTDERR: read_celfile_generic.c:815:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_celfile_generic.c:813:10: warning: unused variable 'cur_index' [-Wunused-variable] BUILDSTDERR: size_t cur_index; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_celfile_generic.c:812:15: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: size_t i=0, j=0; BUILDSTDERR: ^ BUILDSTDERR: read_celfile_generic.c: In function 'generic_get_masks_outliers': BUILDSTDERR: read_celfile_generic.c:877:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_celfile_generic.c:875:7: warning: unused variable 'cur_index' [-Wunused-variable] BUILDSTDERR: int cur_index; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_celfile_generic.c:874:12: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: int i=0, j=0; BUILDSTDERR: ^ BUILDSTDERR: read_celfile_generic.c: In function 'generic_apply_masks': BUILDSTDERR: read_celfile_generic.c:969:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_celfile_generic.c:963:15: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: size_t i=0, j=0; BUILDSTDERR: ^ BUILDSTDERR: read_celfile_generic.c: In function 'isgzGenericCelFile': BUILDSTDERR: read_celfile_generic.c:1067:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] BUILDSTDERR: if ((infile = gzopen(filename, "rb")) == NULL) BUILDSTDERR: ^ BUILDSTDERR: read_celfile_generic.c:1074:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c:1080:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c:1089:12: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c:1094:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c: In function 'gzgeneric_get_header_info': BUILDSTDERR: read_celfile_generic.c:1115:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] BUILDSTDERR: if ((infile = gzopen(filename, "rb")) == NULL) BUILDSTDERR: ^ BUILDSTDERR: read_celfile_generic.c:1151:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c: In function 'gzgeneric_get_detailed_header_info': BUILDSTDERR: read_celfile_generic.c:1175:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] BUILDSTDERR: if ((infile = gzopen(filename, "rb")) == NULL) BUILDSTDERR: ^ BUILDSTDERR: read_celfile_generic.c:1633:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c: In function 'check_gzgeneric_cel_file': BUILDSTDERR: read_celfile_generic.c:1661:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] BUILDSTDERR: if ((infile = gzopen(filename, "rb")) == NULL) BUILDSTDERR: ^ BUILDSTDERR: read_celfile_generic.c:1701:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c: In function 'gzread_genericcel_file_intensities': BUILDSTDERR: read_celfile_generic.c:1726:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] BUILDSTDERR: if ((infile = gzopen(filename, "rb")) == NULL) BUILDSTDERR: ^ BUILDSTDERR: read_celfile_generic.c:1745:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c:1715:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_celfile_generic.c:1713:10: warning: unused variable 'cur_index' [-Wunused-variable] BUILDSTDERR: size_t cur_index; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_celfile_generic.c:1712:15: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: size_t i=0, j=0; BUILDSTDERR: ^ BUILDSTDERR: read_celfile_generic.c: In function 'gzread_genericcel_file_stddev': BUILDSTDERR: read_celfile_generic.c:1777:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] BUILDSTDERR: if ((infile = gzopen(filename, "rb")) == NULL) BUILDSTDERR: ^ BUILDSTDERR: read_celfile_generic.c:1790:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c:1802:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c:1766:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_celfile_generic.c:1764:10: warning: unused variable 'cur_index' [-Wunused-variable] BUILDSTDERR: size_t cur_index; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_celfile_generic.c:1763:15: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: size_t i=0, j=0; BUILDSTDERR: ^ BUILDSTDERR: read_celfile_generic.c: In function 'gzread_genericcel_file_npixels': BUILDSTDERR: read_celfile_generic.c:1831:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] BUILDSTDERR: if ((infile = gzopen(filename, "rb")) == NULL) BUILDSTDERR: ^ BUILDSTDERR: read_celfile_generic.c:1844:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c:1848:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c:1861:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c:1820:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_celfile_generic.c:1818:10: warning: unused variable 'cur_index' [-Wunused-variable] BUILDSTDERR: size_t cur_index; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_celfile_generic.c:1817:15: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: size_t i=0, j=0; BUILDSTDERR: ^ BUILDSTDERR: read_celfile_generic.c: In function 'gzgeneric_get_masks_outliers': BUILDSTDERR: read_celfile_generic.c:1896:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] BUILDSTDERR: if ((infile = gzopen(filename, "rb")) == NULL) BUILDSTDERR: ^ BUILDSTDERR: read_celfile_generic.c:1910:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c:1915:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c:1920:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c:1939:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c:1960:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c:1885:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_celfile_generic.c:1883:7: warning: unused variable 'cur_index' [-Wunused-variable] BUILDSTDERR: int cur_index; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_celfile_generic.c:1882:12: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: int i=0, j=0; BUILDSTDERR: ^ BUILDSTDERR: read_celfile_generic.c: In function 'gzgeneric_apply_masks': BUILDSTDERR: read_celfile_generic.c:1991:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] BUILDSTDERR: if ((infile = gzopen(filename, "rb")) == NULL) BUILDSTDERR: ^ BUILDSTDERR: read_celfile_generic.c:2012:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c:2017:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c:2022:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c:2038:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c:2056:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_celfile_generic.c:1977:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_celfile_generic.c:1971:15: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: size_t i=0, j=0; BUILDSTDERR: ^ gcc -I/usr/include/R -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c read_clf.c -o read_clf.o BUILDSTDERR: read_clf.c: In function 'read_clf_header': BUILDSTDERR: read_clf.c:557:7: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: int i; BUILDSTDERR: ^ BUILDSTDERR: At top level: BUILDSTDERR: read_clf.c:389:12: warning: 'IsCommentLine' defined but not used [-Wunused-function] BUILDSTDERR: static int IsCommentLine(char *buffer){ BUILDSTDERR: ^~~~~~~~~~~~~ BUILDSTDERR: read_clf.c:292:12: warning: 'token_ends_with' defined but not used [-Wunused-function] BUILDSTDERR: static int token_ends_with(char *token, char *ends_in){ BUILDSTDERR: ^~~~~~~~~~~~~~~ gcc -I/usr/include/R -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c read_generic.c -o read_generic.o BUILDSTDERR: read_generic.c: In function 'gzread_ASTRING_fw': BUILDSTDERR: read_generic.c:927:9: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(instream, length-destination->len, SEEK_CUR); BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_generic.c:50: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_generic.c: In function 'gzread_AWSTRING_fw': BUILDSTDERR: read_generic.c:973:9: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(instream, length-2*destination->len, SEEK_CUR); BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_generic.c:50: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_generic.c: In function 'gzRead_Generic': BUILDSTDERR: read_generic.c:1508:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] BUILDSTDERR: if ((infile = gzopen(cur_file_name, "rb")) == NULL) BUILDSTDERR: ^ BUILDSTDERR: read_generic.c:1540:14: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from fread_functions.h:12, BUILDSTDERR: from read_generic.c:50: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_generic.c: In function 'decode_nvt_triplet': BUILDSTDERR: read_generic.c:1683:9: warning: 'return_value' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: return(return_value); BUILDSTDERR: ^ BUILDSTDERR: read_generic.c: In function 'Read_Generic_R_List': BUILDSTDERR: read_generic.c:2029:2: warning: 'return_value' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: SET_VECTOR_ELT(VECTOR_ELT(temp_sxp2,2),i,generic_data_set_rows_R_List(&my_data_set, i)); BUILDSTDERR: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: read_generic.c:1794:3: warning: 'tmp_sexp' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: SET_VECTOR_ELT(return_value,0,tmp_sexp); BUILDSTDERR: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: read_generic.c:1783:8: note: 'tmp_sexp' was declared here BUILDSTDERR: SEXP tmp_sexp, return_names; BUILDSTDERR: ^~~~~~~~ gcc -I/usr/include/R -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o BUILDSTDERR: read_multichannel_celfile_generic.c: In function 'multichannel_determine_number_channels': BUILDSTDERR: read_multichannel_celfile_generic.c:109:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:106:7: warning: unused variable 'cur_index' [-Wunused-variable] BUILDSTDERR: int cur_index; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:105:17: warning: unused variable 'k' [-Wunused-variable] BUILDSTDERR: int i=0, j=0, k=0; BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c:105:7: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: int i=0, j=0, k=0; BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c: In function 'multichannel_determine_channel_name': BUILDSTDERR: read_multichannel_celfile_generic.c:173:20: warning: unused variable 'my_data_set' [-Wunused-variable] BUILDSTDERR: generic_data_set my_data_set; BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:165:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:162:7: warning: unused variable 'cur_index' [-Wunused-variable] BUILDSTDERR: int cur_index; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:161:12: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: int i=0, j=0, k=0; BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c:161:7: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: int i=0, j=0, k=0; BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c: In function 'read_genericcel_file_intensities_multichannel': BUILDSTDERR: read_multichannel_celfile_generic.c:223:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:221:7: warning: unused variable 'cur_index' [-Wunused-variable] BUILDSTDERR: int cur_index; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:220:12: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: int i=0, j=0, k=0; BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c: In function 'read_genericcel_file_stddev_multichannel': BUILDSTDERR: read_multichannel_celfile_generic.c:280:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:278:7: warning: unused variable 'cur_index' [-Wunused-variable] BUILDSTDERR: int cur_index; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:277:12: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: int i=0, j=0, k=0; BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c: In function 'read_genericcel_file_npixels_multichannel': BUILDSTDERR: read_multichannel_celfile_generic.c:344:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:342:7: warning: unused variable 'cur_index' [-Wunused-variable] BUILDSTDERR: int cur_index; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:341:12: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: int i=0, j=0, k=0; BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c: In function 'generic_get_masks_outliers_multichannel': BUILDSTDERR: read_multichannel_celfile_generic.c:418:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:416:7: warning: unused variable 'cur_index' [-Wunused-variable] BUILDSTDERR: int cur_index; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:415:12: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: int i=0, j=0, k=0; BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c: In function 'generic_apply_masks_multichannel': BUILDSTDERR: read_multichannel_celfile_generic.c:522:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:516:12: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: int i=0, j=0; BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c: In function 'isgzGenericMultiChannelCelFile': BUILDSTDERR: read_multichannel_celfile_generic.c:620:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] BUILDSTDERR: if ((infile = gzopen(filename, "rb")) == NULL) BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c:627:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:633:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:642:12: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:647:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c: In function 'gzmultichannel_determine_number_channels': BUILDSTDERR: read_multichannel_celfile_generic.c:677:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] BUILDSTDERR: if ((infile = gzopen(filename, "rb")) == NULL) BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c:701:12: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile,next_group,SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:704:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:664:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:661:7: warning: unused variable 'cur_index' [-Wunused-variable] BUILDSTDERR: int cur_index; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:660:17: warning: unused variable 'k' [-Wunused-variable] BUILDSTDERR: int i=0, j=0, k=0; BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c:660:7: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: int i=0, j=0, k=0; BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c: In function 'gzmultichannel_determine_channel_name': BUILDSTDERR: read_multichannel_celfile_generic.c:729:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] BUILDSTDERR: if ((infile = gzopen(filename, "rb")) == NULL) BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c:741:12: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile,next_group,SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:751:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:725:20: warning: unused variable 'my_data_set' [-Wunused-variable] BUILDSTDERR: generic_data_set my_data_set; BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:717:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:714:7: warning: unused variable 'cur_index' [-Wunused-variable] BUILDSTDERR: int cur_index; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:713:12: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: int i=0, j=0, k=0; BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c:713:7: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: int i=0, j=0, k=0; BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c: In function 'gzread_genericcel_file_intensities_multichannel': BUILDSTDERR: read_multichannel_celfile_generic.c:778:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] BUILDSTDERR: if ((infile = gzopen(filename, "rb")) == NULL) BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c:793:12: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile,next_group,SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:807:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:766:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:764:7: warning: unused variable 'cur_index' [-Wunused-variable] BUILDSTDERR: int cur_index; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:763:12: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: int i=0, j=0, k=0; BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c: In function 'gzread_genericcel_file_stddev_multichannel': BUILDSTDERR: read_multichannel_celfile_generic.c:834:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] BUILDSTDERR: if ((infile = gzopen(filename, "rb")) == NULL) BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c:849:12: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile,next_group,SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:856:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:867:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:822:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:820:7: warning: unused variable 'cur_index' [-Wunused-variable] BUILDSTDERR: int cur_index; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:819:12: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: int i=0, j=0, k=0; BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c: In function 'gzread_genericcel_file_npixels_multichannel': BUILDSTDERR: read_multichannel_celfile_generic.c:896:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] BUILDSTDERR: if ((infile = gzopen(filename, "rb")) == NULL) BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c:912:12: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile,next_group,SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:919:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:923:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:936:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:884:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:882:7: warning: unused variable 'cur_index' [-Wunused-variable] BUILDSTDERR: int cur_index; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:881:12: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: int i=0, j=0, k=0; BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c: In function 'gzgeneric_get_masks_outliers_multichannel': BUILDSTDERR: read_multichannel_celfile_generic.c:965:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] BUILDSTDERR: if ((infile = gzopen(filename, "rb")) == NULL) BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c:981:12: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile,next_group,SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:989:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:994:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:999:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:1018:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:1039:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:953:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:951:7: warning: unused variable 'cur_index' [-Wunused-variable] BUILDSTDERR: int cur_index; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:950:12: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: int i=0, j=0, k=0; BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c: In function 'gzgeneric_apply_masks_multichannel': BUILDSTDERR: read_multichannel_celfile_generic.c:1069:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] BUILDSTDERR: if ((infile = gzopen(filename, "rb")) == NULL) BUILDSTDERR: ^ BUILDSTDERR: read_multichannel_celfile_generic.c:1090:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:1095:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:1100:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:1116:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzseek(infile, my_data_set.file_pos_last, SEEK_SET); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1873:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:1134:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: gzclose(infile); BUILDSTDERR: ^~~~~~ BUILDSTDERR: In file included from /usr/include/zlib.h:34, BUILDSTDERR: from read_multichannel_celfile_generic.c:43: BUILDSTDERR: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' BUILDSTDERR: ZEXTERN int ZEXPORT gzclose OF((gzFile file)); BUILDSTDERR: ^~ BUILDSTDERR: read_multichannel_celfile_generic.c:1055:7: warning: unused variable 'fread_err' [-Wunused-variable] BUILDSTDERR: int fread_err=0; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: read_multichannel_celfile_generic.c:1049:12: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: int i=0, j=0; BUILDSTDERR: ^ gcc -I/usr/include/R -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c read_pgf.c -o read_pgf.o BUILDSTDERR: read_pgf.c: In function 'read_pgf_header': BUILDSTDERR: read_pgf.c:901:7: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: int i; BUILDSTDERR: ^ BUILDSTDERR: read_pgf.c: In function 'insert_level0': BUILDSTDERR: read_pgf.c:1167:23: warning: unused variable 'temp_ptr' [-Wunused-variable] BUILDSTDERR: probeset_list_node *temp_ptr; BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: read_pgf.c: In function 'pgf_count_probeset_types': BUILDSTDERR: read_pgf.c:1265:28: warning: assignment to 'probeset_list_node *' {aka 'struct *'} from incompatible pointer type 'struct probeset_list_node *' [-Wincompatible-pointer-types] BUILDSTDERR: my_pgf->probesets->current= my_pgf->probesets->current->next; BUILDSTDERR: ^ BUILDSTDERR: At top level: BUILDSTDERR: read_pgf.c:363:12: warning: 'token_ends_with' defined but not used [-Wunused-function] BUILDSTDERR: static int token_ends_with(char *token, char *ends_in){ BUILDSTDERR: ^~~~~~~~~~~~~~~ g++ -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o affyio.so 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 -lpthread -lz -lpthread -L/usr/lib64/R/lib -lR BUILDSTDERR: installing to /builddir/build/BUILDROOT/R-affyio-1.46.0-3.fc29.riscv64/usr/lib64/R/library/affyio/libs BUILDSTDERR: ** R BUILDSTDERR: ** preparing package for lazy loading BUILDSTDERR: ** help BUILDSTDERR: *** installing help indices converting help for package 'affyio' BUILDSTDERR: finding HTML links ... done 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 BUILDSTDERR: ** building package indices BUILDSTDERR: ** testing if installed package can be loaded BUILDSTDERR: * DONE (affyio) + test -d affyio/src + cd affyio/src + rm -f 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 affyio.so + rm -rf /builddir/build/BUILDROOT/R-affyio-1.46.0-3.fc29.riscv64/usr/lib64/R/library/R.css + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig BUILDSTDERR: /sbin/ldconfig: Warning: ignoring configuration file that cannot be opened: /etc/ld.so.conf: No such file or directory + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip /usr/bin/strip + /usr/lib/rpm/brp-strip-comment-note /usr/bin/strip /usr/bin/objdump + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-mangle-shebangs Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.fszJOf Processing files: R-affyio-1.46.0-3.fc29.riscv64 Provides: R-affyio = 1.46.0-3.fc29 R-affyio(riscv-64) = 1.46.0-3.fc29 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libR.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libgcc_s.so.1()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.27)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.27)(64bit) libstdc++.so.6()(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-affyio-1.46.0-3.fc29.riscv64 Wrote: /builddir/build/RPMS/R-affyio-1.46.0-3.fc29.riscv64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.uqYmri + umask 022 + cd /builddir/build/BUILD + cd affyio + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-affyio-1.46.0-3.fc29.riscv64 + exit 0 Child return code was: 0