sys/cdefs.h not found when compiling on kubuntu linux 14.04
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Kaiyin Zhong
Jun 4, 2014, 12:53:48 PM6/4/14
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Here is the output from ./plink_first_compile:
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 74 557k 74 417k 0 0 322k 0 0:00:01 0:00:01 --:--:-- 322k 100 557k 100 557k 0 0 366k 0 0:00:01 0:00:01 --:--:-- 365k
zlib-1.2.8/
zlib-1.2.8/adler32.c
zlib-1.2.8/amiga/
zlib-1.2.8/amiga/Makefile.pup
zlib-1.2.8/amiga/Makefile.sas
zlib-1.2.8/as400/
zlib-1.2.8/as400/bndsrc
zlib-1.2.8/as400/compile.clp
zlib-1.2.8/as400/readme.txt
zlib-1.2.8/as400/zlib.inc
zlib-1.2.8/ChangeLog
zlib-1.2.8/CMakeLists.txt
zlib-1.2.8/compress.c
zlib-1.2.8/configure
zlib-1.2.8/contrib/
zlib-1.2.8/contrib/ada/
zlib-1.2.8/contrib/ada/buffer_demo.adb
zlib-1.2.8/contrib/ada/mtest.adb
zlib-1.2.8/contrib/ada/read.adb
zlib-1.2.8/contrib/ada/readme.txt
zlib-1.2.8/contrib/ada/test.adb
zlib-1.2.8/contrib/ada/zlib-streams.adb
zlib-1.2.8/contrib/ada/zlib-streams.ads
zlib-1.2.8/contrib/ada/zlib-thin.adb
zlib-1.2.8/contrib/ada/zlib-thin.ads
zlib-1.2.8/contrib/ada/zlib.adb
zlib-1.2.8/contrib/ada/zlib.ads
zlib-1.2.8/contrib/ada/zlib.gpr
zlib-1.2.8/contrib/amd64/
zlib-1.2.8/contrib/amd64/amd64-match.S
zlib-1.2.8/contrib/asm686/
zlib-1.2.8/contrib/asm686/match.S
zlib-1.2.8/contrib/asm686/README.686
zlib-1.2.8/contrib/blast/
zlib-1.2.8/contrib/blast/blast.c
zlib-1.2.8/contrib/blast/blast.h
zlib-1.2.8/contrib/blast/Makefile
zlib-1.2.8/contrib/blast/README
zlib-1.2.8/contrib/blast/test.pk
zlib-1.2.8/contrib/blast/test.txt
zlib-1.2.8/contrib/delphi/
zlib-1.2.8/contrib/delphi/readme.txt
zlib-1.2.8/contrib/delphi/ZLib.pas
zlib-1.2.8/contrib/delphi/ZLibConst.pas
zlib-1.2.8/contrib/delphi/zlibd32.mak
zlib-1.2.8/contrib/dotzlib/
zlib-1.2.8/contrib/dotzlib/DotZLib/
zlib-1.2.8/contrib/dotzlib/DotZLib/AssemblyInfo.cs
zlib-1.2.8/contrib/dotzlib/DotZLib/ChecksumImpl.cs
zlib-1.2.8/contrib/dotzlib/DotZLib/CircularBuffer.cs
zlib-1.2.8/contrib/dotzlib/DotZLib/CodecBase.cs
zlib-1.2.8/contrib/dotzlib/DotZLib/Deflater.cs
zlib-1.2.8/contrib/dotzlib/DotZLib/DotZLib.cs
zlib-1.2.8/contrib/dotzlib/DotZLib/DotZLib.csproj
zlib-1.2.8/contrib/dotzlib/DotZLib/GZipStream.cs
zlib-1.2.8/contrib/dotzlib/DotZLib/Inflater.cs
zlib-1.2.8/contrib/dotzlib/DotZLib/UnitTests.cs
zlib-1.2.8/contrib/dotzlib/DotZLib.build
zlib-1.2.8/contrib/dotzlib/DotZLib.chm
zlib-1.2.8/contrib/dotzlib/DotZLib.sln
zlib-1.2.8/contrib/dotzlib/LICENSE_1_0.txt
zlib-1.2.8/contrib/dotzlib/readme.txt
zlib-1.2.8/contrib/gcc_gvmat64/
zlib-1.2.8/contrib/gcc_gvmat64/gvmat64.S
zlib-1.2.8/contrib/infback9/
zlib-1.2.8/contrib/infback9/infback9.c
zlib-1.2.8/contrib/infback9/infback9.h
zlib-1.2.8/contrib/infback9/inffix9.h
zlib-1.2.8/contrib/infback9/inflate9.h
zlib-1.2.8/contrib/infback9/inftree9.c
zlib-1.2.8/contrib/infback9/inftree9.h
zlib-1.2.8/contrib/infback9/README
zlib-1.2.8/contrib/inflate86/
zlib-1.2.8/contrib/inflate86/inffas86.c
zlib-1.2.8/contrib/inflate86/inffast.S
zlib-1.2.8/contrib/iostream/
zlib-1.2.8/contrib/iostream/test.cpp
zlib-1.2.8/contrib/iostream/zfstream.cpp
zlib-1.2.8/contrib/iostream/zfstream.h
zlib-1.2.8/contrib/iostream2/
zlib-1.2.8/contrib/iostream2/zstream.h
zlib-1.2.8/contrib/iostream2/zstream_test.cpp
zlib-1.2.8/contrib/iostream3/
zlib-1.2.8/contrib/iostream3/README
zlib-1.2.8/contrib/iostream3/test.cc
zlib-1.2.8/contrib/iostream3/TODO
zlib-1.2.8/contrib/iostream3/zfstream.cc
zlib-1.2.8/contrib/iostream3/zfstream.h
zlib-1.2.8/contrib/masmx64/
zlib-1.2.8/contrib/masmx64/bld_ml64.bat
zlib-1.2.8/contrib/masmx64/gvmat64.asm
zlib-1.2.8/contrib/masmx64/inffas8664.c
zlib-1.2.8/contrib/masmx64/inffasx64.asm
zlib-1.2.8/contrib/masmx64/readme.txt
zlib-1.2.8/contrib/masmx86/
zlib-1.2.8/contrib/masmx86/bld_ml32.bat
zlib-1.2.8/contrib/masmx86/inffas32.asm
zlib-1.2.8/contrib/masmx86/match686.asm
zlib-1.2.8/contrib/masmx86/readme.txt
zlib-1.2.8/contrib/minizip/
zlib-1.2.8/contrib/minizip/configure.ac
zlib-1.2.8/contrib/minizip/crypt.h
zlib-1.2.8/contrib/minizip/ioapi.c
zlib-1.2.8/contrib/minizip/ioapi.h
zlib-1.2.8/contrib/minizip/iowin32.c
zlib-1.2.8/contrib/minizip/iowin32.h
zlib-1.2.8/contrib/minizip/make_vms.com
zlib-1.2.8/contrib/minizip/Makefile
zlib-1.2.8/contrib/minizip/Makefile.am
zlib-1.2.8/contrib/minizip/miniunz.c
zlib-1.2.8/contrib/minizip/miniunzip.1
zlib-1.2.8/contrib/minizip/minizip.1
zlib-1.2.8/contrib/minizip/minizip.c
zlib-1.2.8/contrib/minizip/minizip.pc.in
zlib-1.2.8/contrib/minizip/MiniZip64_Changes.txt
zlib-1.2.8/contrib/minizip/MiniZip64_info.txt
zlib-1.2.8/contrib/minizip/mztools.c
zlib-1.2.8/contrib/minizip/mztools.h
zlib-1.2.8/contrib/minizip/unzip.c
zlib-1.2.8/contrib/minizip/unzip.h
zlib-1.2.8/contrib/minizip/zip.c
zlib-1.2.8/contrib/minizip/zip.h
zlib-1.2.8/contrib/pascal/
zlib-1.2.8/contrib/pascal/example.pas
zlib-1.2.8/contrib/pascal/readme.txt
zlib-1.2.8/contrib/pascal/zlibd32.mak
zlib-1.2.8/contrib/pascal/zlibpas.pas
zlib-1.2.8/contrib/puff/
zlib-1.2.8/contrib/puff/Makefile
zlib-1.2.8/contrib/puff/puff.c
zlib-1.2.8/contrib/puff/puff.h
zlib-1.2.8/contrib/puff/pufftest.c
zlib-1.2.8/contrib/puff/README
zlib-1.2.8/contrib/puff/zeros.raw
zlib-1.2.8/contrib/README.contrib
zlib-1.2.8/contrib/testzlib/
zlib-1.2.8/contrib/testzlib/testzlib.c
zlib-1.2.8/contrib/testzlib/testzlib.txt
zlib-1.2.8/contrib/untgz/
zlib-1.2.8/contrib/untgz/Makefile
zlib-1.2.8/contrib/untgz/Makefile.msc
zlib-1.2.8/contrib/untgz/untgz.c
zlib-1.2.8/contrib/vstudio/
zlib-1.2.8/contrib/vstudio/readme.txt
zlib-1.2.8/contrib/vstudio/vc10/
zlib-1.2.8/contrib/vstudio/vc10/miniunz.vcxproj
zlib-1.2.8/contrib/vstudio/vc10/miniunz.vcxproj.filters
zlib-1.2.8/contrib/vstudio/vc10/minizip.vcxproj
zlib-1.2.8/contrib/vstudio/vc10/minizip.vcxproj.filters
zlib-1.2.8/contrib/vstudio/vc10/testzlib.vcxproj
zlib-1.2.8/contrib/vstudio/vc10/testzlib.vcxproj.filters
zlib-1.2.8/contrib/vstudio/vc10/testzlibdll.vcxproj
zlib-1.2.8/contrib/vstudio/vc10/testzlibdll.vcxproj.filters
zlib-1.2.8/contrib/vstudio/vc10/zlib.rc
zlib-1.2.8/contrib/vstudio/vc10/zlibstat.vcxproj
zlib-1.2.8/contrib/vstudio/vc10/zlibstat.vcxproj.filters
zlib-1.2.8/contrib/vstudio/vc10/zlibvc.def
zlib-1.2.8/contrib/vstudio/vc10/zlibvc.sln
zlib-1.2.8/contrib/vstudio/vc10/zlibvc.vcxproj
zlib-1.2.8/contrib/vstudio/vc10/zlibvc.vcxproj.filters
zlib-1.2.8/contrib/vstudio/vc11/
zlib-1.2.8/contrib/vstudio/vc11/miniunz.vcxproj
zlib-1.2.8/contrib/vstudio/vc11/minizip.vcxproj
zlib-1.2.8/contrib/vstudio/vc11/testzlib.vcxproj
zlib-1.2.8/contrib/vstudio/vc11/testzlibdll.vcxproj
zlib-1.2.8/contrib/vstudio/vc11/zlib.rc
zlib-1.2.8/contrib/vstudio/vc11/zlibstat.vcxproj
zlib-1.2.8/contrib/vstudio/vc11/zlibvc.def
zlib-1.2.8/contrib/vstudio/vc11/zlibvc.sln
zlib-1.2.8/contrib/vstudio/vc11/zlibvc.vcxproj
zlib-1.2.8/contrib/vstudio/vc9/
zlib-1.2.8/contrib/vstudio/vc9/miniunz.vcproj
zlib-1.2.8/contrib/vstudio/vc9/minizip.vcproj
zlib-1.2.8/contrib/vstudio/vc9/testzlib.vcproj
zlib-1.2.8/contrib/vstudio/vc9/testzlibdll.vcproj
zlib-1.2.8/contrib/vstudio/vc9/zlib.rc
zlib-1.2.8/contrib/vstudio/vc9/zlibstat.vcproj
zlib-1.2.8/contrib/vstudio/vc9/zlibvc.def
zlib-1.2.8/contrib/vstudio/vc9/zlibvc.sln
zlib-1.2.8/contrib/vstudio/vc9/zlibvc.vcproj
zlib-1.2.8/crc32.c
zlib-1.2.8/crc32.h
zlib-1.2.8/deflate.c
zlib-1.2.8/deflate.h
zlib-1.2.8/doc/
zlib-1.2.8/doc/algorithm.txt
zlib-1.2.8/doc/rfc1950.txt
zlib-1.2.8/doc/rfc1951.txt
zlib-1.2.8/doc/rfc1952.txt
zlib-1.2.8/doc/txtvsbin.txt
zlib-1.2.8/examples/
zlib-1.2.8/examples/enough.c
zlib-1.2.8/examples/fitblk.c
zlib-1.2.8/examples/gun.c
zlib-1.2.8/examples/gzappend.c
zlib-1.2.8/examples/gzjoin.c
zlib-1.2.8/examples/gzlog.c
zlib-1.2.8/examples/gzlog.h
zlib-1.2.8/examples/README.examples
zlib-1.2.8/examples/zlib_how.html
zlib-1.2.8/examples/zpipe.c
zlib-1.2.8/examples/zran.c
zlib-1.2.8/FAQ
zlib-1.2.8/gzclose.c
zlib-1.2.8/gzguts.h
zlib-1.2.8/gzlib.c
zlib-1.2.8/gzread.c
zlib-1.2.8/gzwrite.c
zlib-1.2.8/INDEX
zlib-1.2.8/infback.c
zlib-1.2.8/inffast.c
zlib-1.2.8/inffast.h
zlib-1.2.8/inffixed.h
zlib-1.2.8/inflate.c
zlib-1.2.8/inflate.h
zlib-1.2.8/inftrees.c
zlib-1.2.8/inftrees.h
zlib-1.2.8/make_vms.com
zlib-1.2.8/Makefile
zlib-1.2.8/Makefile.in
zlib-1.2.8/msdos/
zlib-1.2.8/msdos/Makefile.bor
zlib-1.2.8/msdos/Makefile.dj2
zlib-1.2.8/msdos/Makefile.emx
zlib-1.2.8/msdos/Makefile.msc
zlib-1.2.8/msdos/Makefile.tc
zlib-1.2.8/nintendods/
zlib-1.2.8/nintendods/Makefile
zlib-1.2.8/nintendods/README
zlib-1.2.8/old/
zlib-1.2.8/old/descrip.mms
zlib-1.2.8/old/Makefile.emx
zlib-1.2.8/old/Makefile.riscos
zlib-1.2.8/old/os2/
zlib-1.2.8/old/os2/Makefile.os2
zlib-1.2.8/old/os2/zlib.def
zlib-1.2.8/old/README
zlib-1.2.8/old/visual-basic.txt
zlib-1.2.8/qnx/
zlib-1.2.8/qnx/package.qpg
zlib-1.2.8/README
zlib-1.2.8/test/
zlib-1.2.8/test/example.c
zlib-1.2.8/test/infcover.c
zlib-1.2.8/test/minigzip.c
zlib-1.2.8/treebuild.xml
zlib-1.2.8/trees.c
zlib-1.2.8/trees.h
zlib-1.2.8/uncompr.c
zlib-1.2.8/watcom/
zlib-1.2.8/watcom/watcom_f.mak
zlib-1.2.8/watcom/watcom_l.mak
zlib-1.2.8/win32/
zlib-1.2.8/win32/DLL_FAQ.txt
zlib-1.2.8/win32/Makefile.bor
zlib-1.2.8/win32/Makefile.gcc
zlib-1.2.8/win32/Makefile.msc
zlib-1.2.8/win32/README-WIN32.txt
zlib-1.2.8/win32/VisualC.txt
zlib-1.2.8/win32/zlib.def
zlib-1.2.8/win32/zlib1.rc
zlib-1.2.8/zconf.h
zlib-1.2.8/zconf.h.cmakein
zlib-1.2.8/zconf.h.in
zlib-1.2.8/zlib.3
zlib-1.2.8/zlib.3.pdf
zlib-1.2.8/zlib.h
zlib-1.2.8/zlib.map
zlib-1.2.8/zlib.pc.cmakein
zlib-1.2.8/zlib.pc.in
zlib-1.2.8/zlib2ansi
zlib-1.2.8/zutil.c
zlib-1.2.8/zutil.h
Checking for gcc...
Checking for shared library support...
Building shared library libz.so.1.2.8 with gcc.
Checking for off64_t... Yes.
Checking for fseeko... Yes.
Checking for strerror... Yes.
Checking for unistd.h... Yes.
Checking for stdarg.h... Yes.
Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf().
Checking for vsnprintf() in stdio.h... Yes.
Checking for return value of vsnprintf()... Yes.
Checking for attribute(visibility) support... Yes.
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -c -o example.o test/example.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o adler32.o adler32.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o crc32.o crc32.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o deflate.o deflate.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o infback.o infback.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inffast.o inffast.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inflate.o inflate.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inftrees.o inftrees.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o trees.o trees.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o zutil.o zutil.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o compress.o compress.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o uncompr.o uncompr.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzclose.o gzclose.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzlib.o gzlib.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzread.o gzread.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzwrite.o gzwrite.c
ar rc libz.a adler32.o crc32.o deflate.o infback.o inffast.o inflate.o inftrees.o trees.o zutil.o compress.o uncompr.o gzclose.o gzlib.o gzread.o gzwrite.o
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o example example.o -L. libz.a
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -c -o minigzip.o test/minigzip.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzip minigzip.o -L. libz.a
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/adler32.o adler32.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/crc32.o crc32.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/deflate.o deflate.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/infback.o infback.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inffast.o inffast.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inflate.o inflate.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inftrees.o inftrees.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/trees.o trees.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/zutil.o zutil.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/compress.o compress.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/uncompr.o uncompr.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzclose.o gzclose.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzlib.o gzlib.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzread.o gzread.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzwrite.o gzwrite.c
gcc -shared -Wl,-soname,libz.so.1,--version-script,zlib.map -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o libz.so.1.2.8 adler32.lo crc32.lo deflate.lo infback.lo inffast.lo inflate.lo inftrees.lo trees.lo zutil.lo compress.lo uncompr.lo gzclose.lo gzlib.lo gzread.lo gzwrite.lo -lc
rm -f libz.so libz.so.1
ln -s libz.so.1.2.8 libz.so
ln -s libz.so.1.2.8 libz.so.1
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o examplesh example.o -L. libz.so.1.2.8
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzipsh minigzip.o -L. libz.so.1.2.8
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o example64.o test/example.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o example64 example64.o -L. libz.a
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o minigzip64.o test/minigzip.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzip64 minigzip64.o -L. libz.a
g++ -Wall -O2 plink.c plink_assoc.c plink_calc.c plink_cluster.c plink_cnv.c plink_common.c plink_data.c plink_dosage.c plink_family.c plink_filter.c plink_glm.c plink_help.c plink_homozyg.c plink_lasso.c plink_ld.c plink_matrix.c plink_misc.c plink_set.c plink_stats.c SFMT.c dcdflib.c pigz.c yarn.c -m32 -o plink -L/usr/lib64/atlas -llapack -lcblas -latlas -lm -lpthread -L. zlib-1.2.8/libz.so.1.2.8
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink.c:19:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_assoc.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_calc.c:73:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_cluster.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_cnv.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_common.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_data.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_dosage.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_family.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_filter.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_glm.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_help.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_homozyg.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_lasso.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_ld.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_matrix.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_misc.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_set.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_stats.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/string.h:25:0,
from SFMT.c:47:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from dcdflib.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdint.h:25:0,
from /usr/lib/gcc/x86_64-linux-gnu/4.8/include/stdint.h:9,
from pigz.c:294:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from yarn.c:33:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
make: *** [plink] Error 1
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 74 557k 74 417k 0 0 322k 0 0:00:01 0:00:01 --:--:-- 322k 100 557k 100 557k 0 0 366k 0 0:00:01 0:00:01 --:--:-- 365k
zlib-1.2.8/
zlib-1.2.8/adler32.c
zlib-1.2.8/amiga/
zlib-1.2.8/amiga/Makefile.pup
zlib-1.2.8/amiga/Makefile.sas
zlib-1.2.8/as400/
zlib-1.2.8/as400/bndsrc
zlib-1.2.8/as400/compile.clp
zlib-1.2.8/as400/readme.txt
zlib-1.2.8/as400/zlib.inc
zlib-1.2.8/ChangeLog
zlib-1.2.8/CMakeLists.txt
zlib-1.2.8/compress.c
zlib-1.2.8/configure
zlib-1.2.8/contrib/
zlib-1.2.8/contrib/ada/
zlib-1.2.8/contrib/ada/buffer_demo.adb
zlib-1.2.8/contrib/ada/mtest.adb
zlib-1.2.8/contrib/ada/read.adb
zlib-1.2.8/contrib/ada/readme.txt
zlib-1.2.8/contrib/ada/test.adb
zlib-1.2.8/contrib/ada/zlib-streams.adb
zlib-1.2.8/contrib/ada/zlib-streams.ads
zlib-1.2.8/contrib/ada/zlib-thin.adb
zlib-1.2.8/contrib/ada/zlib-thin.ads
zlib-1.2.8/contrib/ada/zlib.adb
zlib-1.2.8/contrib/ada/zlib.ads
zlib-1.2.8/contrib/ada/zlib.gpr
zlib-1.2.8/contrib/amd64/
zlib-1.2.8/contrib/amd64/amd64-match.S
zlib-1.2.8/contrib/asm686/
zlib-1.2.8/contrib/asm686/match.S
zlib-1.2.8/contrib/asm686/README.686
zlib-1.2.8/contrib/blast/
zlib-1.2.8/contrib/blast/blast.c
zlib-1.2.8/contrib/blast/blast.h
zlib-1.2.8/contrib/blast/Makefile
zlib-1.2.8/contrib/blast/README
zlib-1.2.8/contrib/blast/test.pk
zlib-1.2.8/contrib/blast/test.txt
zlib-1.2.8/contrib/delphi/
zlib-1.2.8/contrib/delphi/readme.txt
zlib-1.2.8/contrib/delphi/ZLib.pas
zlib-1.2.8/contrib/delphi/ZLibConst.pas
zlib-1.2.8/contrib/delphi/zlibd32.mak
zlib-1.2.8/contrib/dotzlib/
zlib-1.2.8/contrib/dotzlib/DotZLib/
zlib-1.2.8/contrib/dotzlib/DotZLib/AssemblyInfo.cs
zlib-1.2.8/contrib/dotzlib/DotZLib/ChecksumImpl.cs
zlib-1.2.8/contrib/dotzlib/DotZLib/CircularBuffer.cs
zlib-1.2.8/contrib/dotzlib/DotZLib/CodecBase.cs
zlib-1.2.8/contrib/dotzlib/DotZLib/Deflater.cs
zlib-1.2.8/contrib/dotzlib/DotZLib/DotZLib.cs
zlib-1.2.8/contrib/dotzlib/DotZLib/DotZLib.csproj
zlib-1.2.8/contrib/dotzlib/DotZLib/GZipStream.cs
zlib-1.2.8/contrib/dotzlib/DotZLib/Inflater.cs
zlib-1.2.8/contrib/dotzlib/DotZLib/UnitTests.cs
zlib-1.2.8/contrib/dotzlib/DotZLib.build
zlib-1.2.8/contrib/dotzlib/DotZLib.chm
zlib-1.2.8/contrib/dotzlib/DotZLib.sln
zlib-1.2.8/contrib/dotzlib/LICENSE_1_0.txt
zlib-1.2.8/contrib/dotzlib/readme.txt
zlib-1.2.8/contrib/gcc_gvmat64/
zlib-1.2.8/contrib/gcc_gvmat64/gvmat64.S
zlib-1.2.8/contrib/infback9/
zlib-1.2.8/contrib/infback9/infback9.c
zlib-1.2.8/contrib/infback9/infback9.h
zlib-1.2.8/contrib/infback9/inffix9.h
zlib-1.2.8/contrib/infback9/inflate9.h
zlib-1.2.8/contrib/infback9/inftree9.c
zlib-1.2.8/contrib/infback9/inftree9.h
zlib-1.2.8/contrib/infback9/README
zlib-1.2.8/contrib/inflate86/
zlib-1.2.8/contrib/inflate86/inffas86.c
zlib-1.2.8/contrib/inflate86/inffast.S
zlib-1.2.8/contrib/iostream/
zlib-1.2.8/contrib/iostream/test.cpp
zlib-1.2.8/contrib/iostream/zfstream.cpp
zlib-1.2.8/contrib/iostream/zfstream.h
zlib-1.2.8/contrib/iostream2/
zlib-1.2.8/contrib/iostream2/zstream.h
zlib-1.2.8/contrib/iostream2/zstream_test.cpp
zlib-1.2.8/contrib/iostream3/
zlib-1.2.8/contrib/iostream3/README
zlib-1.2.8/contrib/iostream3/test.cc
zlib-1.2.8/contrib/iostream3/TODO
zlib-1.2.8/contrib/iostream3/zfstream.cc
zlib-1.2.8/contrib/iostream3/zfstream.h
zlib-1.2.8/contrib/masmx64/
zlib-1.2.8/contrib/masmx64/bld_ml64.bat
zlib-1.2.8/contrib/masmx64/gvmat64.asm
zlib-1.2.8/contrib/masmx64/inffas8664.c
zlib-1.2.8/contrib/masmx64/inffasx64.asm
zlib-1.2.8/contrib/masmx64/readme.txt
zlib-1.2.8/contrib/masmx86/
zlib-1.2.8/contrib/masmx86/bld_ml32.bat
zlib-1.2.8/contrib/masmx86/inffas32.asm
zlib-1.2.8/contrib/masmx86/match686.asm
zlib-1.2.8/contrib/masmx86/readme.txt
zlib-1.2.8/contrib/minizip/
zlib-1.2.8/contrib/minizip/configure.ac
zlib-1.2.8/contrib/minizip/crypt.h
zlib-1.2.8/contrib/minizip/ioapi.c
zlib-1.2.8/contrib/minizip/ioapi.h
zlib-1.2.8/contrib/minizip/iowin32.c
zlib-1.2.8/contrib/minizip/iowin32.h
zlib-1.2.8/contrib/minizip/make_vms.com
zlib-1.2.8/contrib/minizip/Makefile
zlib-1.2.8/contrib/minizip/Makefile.am
zlib-1.2.8/contrib/minizip/miniunz.c
zlib-1.2.8/contrib/minizip/miniunzip.1
zlib-1.2.8/contrib/minizip/minizip.1
zlib-1.2.8/contrib/minizip/minizip.c
zlib-1.2.8/contrib/minizip/minizip.pc.in
zlib-1.2.8/contrib/minizip/MiniZip64_Changes.txt
zlib-1.2.8/contrib/minizip/MiniZip64_info.txt
zlib-1.2.8/contrib/minizip/mztools.c
zlib-1.2.8/contrib/minizip/mztools.h
zlib-1.2.8/contrib/minizip/unzip.c
zlib-1.2.8/contrib/minizip/unzip.h
zlib-1.2.8/contrib/minizip/zip.c
zlib-1.2.8/contrib/minizip/zip.h
zlib-1.2.8/contrib/pascal/
zlib-1.2.8/contrib/pascal/example.pas
zlib-1.2.8/contrib/pascal/readme.txt
zlib-1.2.8/contrib/pascal/zlibd32.mak
zlib-1.2.8/contrib/pascal/zlibpas.pas
zlib-1.2.8/contrib/puff/
zlib-1.2.8/contrib/puff/Makefile
zlib-1.2.8/contrib/puff/puff.c
zlib-1.2.8/contrib/puff/puff.h
zlib-1.2.8/contrib/puff/pufftest.c
zlib-1.2.8/contrib/puff/README
zlib-1.2.8/contrib/puff/zeros.raw
zlib-1.2.8/contrib/README.contrib
zlib-1.2.8/contrib/testzlib/
zlib-1.2.8/contrib/testzlib/testzlib.c
zlib-1.2.8/contrib/testzlib/testzlib.txt
zlib-1.2.8/contrib/untgz/
zlib-1.2.8/contrib/untgz/Makefile
zlib-1.2.8/contrib/untgz/Makefile.msc
zlib-1.2.8/contrib/untgz/untgz.c
zlib-1.2.8/contrib/vstudio/
zlib-1.2.8/contrib/vstudio/readme.txt
zlib-1.2.8/contrib/vstudio/vc10/
zlib-1.2.8/contrib/vstudio/vc10/miniunz.vcxproj
zlib-1.2.8/contrib/vstudio/vc10/miniunz.vcxproj.filters
zlib-1.2.8/contrib/vstudio/vc10/minizip.vcxproj
zlib-1.2.8/contrib/vstudio/vc10/minizip.vcxproj.filters
zlib-1.2.8/contrib/vstudio/vc10/testzlib.vcxproj
zlib-1.2.8/contrib/vstudio/vc10/testzlib.vcxproj.filters
zlib-1.2.8/contrib/vstudio/vc10/testzlibdll.vcxproj
zlib-1.2.8/contrib/vstudio/vc10/testzlibdll.vcxproj.filters
zlib-1.2.8/contrib/vstudio/vc10/zlib.rc
zlib-1.2.8/contrib/vstudio/vc10/zlibstat.vcxproj
zlib-1.2.8/contrib/vstudio/vc10/zlibstat.vcxproj.filters
zlib-1.2.8/contrib/vstudio/vc10/zlibvc.def
zlib-1.2.8/contrib/vstudio/vc10/zlibvc.sln
zlib-1.2.8/contrib/vstudio/vc10/zlibvc.vcxproj
zlib-1.2.8/contrib/vstudio/vc10/zlibvc.vcxproj.filters
zlib-1.2.8/contrib/vstudio/vc11/
zlib-1.2.8/contrib/vstudio/vc11/miniunz.vcxproj
zlib-1.2.8/contrib/vstudio/vc11/minizip.vcxproj
zlib-1.2.8/contrib/vstudio/vc11/testzlib.vcxproj
zlib-1.2.8/contrib/vstudio/vc11/testzlibdll.vcxproj
zlib-1.2.8/contrib/vstudio/vc11/zlib.rc
zlib-1.2.8/contrib/vstudio/vc11/zlibstat.vcxproj
zlib-1.2.8/contrib/vstudio/vc11/zlibvc.def
zlib-1.2.8/contrib/vstudio/vc11/zlibvc.sln
zlib-1.2.8/contrib/vstudio/vc11/zlibvc.vcxproj
zlib-1.2.8/contrib/vstudio/vc9/
zlib-1.2.8/contrib/vstudio/vc9/miniunz.vcproj
zlib-1.2.8/contrib/vstudio/vc9/minizip.vcproj
zlib-1.2.8/contrib/vstudio/vc9/testzlib.vcproj
zlib-1.2.8/contrib/vstudio/vc9/testzlibdll.vcproj
zlib-1.2.8/contrib/vstudio/vc9/zlib.rc
zlib-1.2.8/contrib/vstudio/vc9/zlibstat.vcproj
zlib-1.2.8/contrib/vstudio/vc9/zlibvc.def
zlib-1.2.8/contrib/vstudio/vc9/zlibvc.sln
zlib-1.2.8/contrib/vstudio/vc9/zlibvc.vcproj
zlib-1.2.8/crc32.c
zlib-1.2.8/crc32.h
zlib-1.2.8/deflate.c
zlib-1.2.8/deflate.h
zlib-1.2.8/doc/
zlib-1.2.8/doc/algorithm.txt
zlib-1.2.8/doc/rfc1950.txt
zlib-1.2.8/doc/rfc1951.txt
zlib-1.2.8/doc/rfc1952.txt
zlib-1.2.8/doc/txtvsbin.txt
zlib-1.2.8/examples/
zlib-1.2.8/examples/enough.c
zlib-1.2.8/examples/fitblk.c
zlib-1.2.8/examples/gun.c
zlib-1.2.8/examples/gzappend.c
zlib-1.2.8/examples/gzjoin.c
zlib-1.2.8/examples/gzlog.c
zlib-1.2.8/examples/gzlog.h
zlib-1.2.8/examples/README.examples
zlib-1.2.8/examples/zlib_how.html
zlib-1.2.8/examples/zpipe.c
zlib-1.2.8/examples/zran.c
zlib-1.2.8/FAQ
zlib-1.2.8/gzclose.c
zlib-1.2.8/gzguts.h
zlib-1.2.8/gzlib.c
zlib-1.2.8/gzread.c
zlib-1.2.8/gzwrite.c
zlib-1.2.8/INDEX
zlib-1.2.8/infback.c
zlib-1.2.8/inffast.c
zlib-1.2.8/inffast.h
zlib-1.2.8/inffixed.h
zlib-1.2.8/inflate.c
zlib-1.2.8/inflate.h
zlib-1.2.8/inftrees.c
zlib-1.2.8/inftrees.h
zlib-1.2.8/make_vms.com
zlib-1.2.8/Makefile
zlib-1.2.8/Makefile.in
zlib-1.2.8/msdos/
zlib-1.2.8/msdos/Makefile.bor
zlib-1.2.8/msdos/Makefile.dj2
zlib-1.2.8/msdos/Makefile.emx
zlib-1.2.8/msdos/Makefile.msc
zlib-1.2.8/msdos/Makefile.tc
zlib-1.2.8/nintendods/
zlib-1.2.8/nintendods/Makefile
zlib-1.2.8/nintendods/README
zlib-1.2.8/old/
zlib-1.2.8/old/descrip.mms
zlib-1.2.8/old/Makefile.emx
zlib-1.2.8/old/Makefile.riscos
zlib-1.2.8/old/os2/
zlib-1.2.8/old/os2/Makefile.os2
zlib-1.2.8/old/os2/zlib.def
zlib-1.2.8/old/README
zlib-1.2.8/old/visual-basic.txt
zlib-1.2.8/qnx/
zlib-1.2.8/qnx/package.qpg
zlib-1.2.8/README
zlib-1.2.8/test/
zlib-1.2.8/test/example.c
zlib-1.2.8/test/infcover.c
zlib-1.2.8/test/minigzip.c
zlib-1.2.8/treebuild.xml
zlib-1.2.8/trees.c
zlib-1.2.8/trees.h
zlib-1.2.8/uncompr.c
zlib-1.2.8/watcom/
zlib-1.2.8/watcom/watcom_f.mak
zlib-1.2.8/watcom/watcom_l.mak
zlib-1.2.8/win32/
zlib-1.2.8/win32/DLL_FAQ.txt
zlib-1.2.8/win32/Makefile.bor
zlib-1.2.8/win32/Makefile.gcc
zlib-1.2.8/win32/Makefile.msc
zlib-1.2.8/win32/README-WIN32.txt
zlib-1.2.8/win32/VisualC.txt
zlib-1.2.8/win32/zlib.def
zlib-1.2.8/win32/zlib1.rc
zlib-1.2.8/zconf.h
zlib-1.2.8/zconf.h.cmakein
zlib-1.2.8/zconf.h.in
zlib-1.2.8/zlib.3
zlib-1.2.8/zlib.3.pdf
zlib-1.2.8/zlib.h
zlib-1.2.8/zlib.map
zlib-1.2.8/zlib.pc.cmakein
zlib-1.2.8/zlib.pc.in
zlib-1.2.8/zlib2ansi
zlib-1.2.8/zutil.c
zlib-1.2.8/zutil.h
Checking for gcc...
Checking for shared library support...
Building shared library libz.so.1.2.8 with gcc.
Checking for off64_t... Yes.
Checking for fseeko... Yes.
Checking for strerror... Yes.
Checking for unistd.h... Yes.
Checking for stdarg.h... Yes.
Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf().
Checking for vsnprintf() in stdio.h... Yes.
Checking for return value of vsnprintf()... Yes.
Checking for attribute(visibility) support... Yes.
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -c -o example.o test/example.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o adler32.o adler32.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o crc32.o crc32.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o deflate.o deflate.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o infback.o infback.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inffast.o inffast.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inflate.o inflate.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inftrees.o inftrees.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o trees.o trees.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o zutil.o zutil.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o compress.o compress.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o uncompr.o uncompr.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzclose.o gzclose.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzlib.o gzlib.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzread.o gzread.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzwrite.o gzwrite.c
ar rc libz.a adler32.o crc32.o deflate.o infback.o inffast.o inflate.o inftrees.o trees.o zutil.o compress.o uncompr.o gzclose.o gzlib.o gzread.o gzwrite.o
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o example example.o -L. libz.a
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -c -o minigzip.o test/minigzip.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzip minigzip.o -L. libz.a
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/adler32.o adler32.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/crc32.o crc32.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/deflate.o deflate.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/infback.o infback.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inffast.o inffast.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inflate.o inflate.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inftrees.o inftrees.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/trees.o trees.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/zutil.o zutil.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/compress.o compress.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/uncompr.o uncompr.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzclose.o gzclose.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzlib.o gzlib.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzread.o gzread.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzwrite.o gzwrite.c
gcc -shared -Wl,-soname,libz.so.1,--version-script,zlib.map -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o libz.so.1.2.8 adler32.lo crc32.lo deflate.lo infback.lo inffast.lo inflate.lo inftrees.lo trees.lo zutil.lo compress.lo uncompr.lo gzclose.lo gzlib.lo gzread.lo gzwrite.lo -lc
rm -f libz.so libz.so.1
ln -s libz.so.1.2.8 libz.so
ln -s libz.so.1.2.8 libz.so.1
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o examplesh example.o -L. libz.so.1.2.8
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzipsh minigzip.o -L. libz.so.1.2.8
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o example64.o test/example.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o example64 example64.o -L. libz.a
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o minigzip64.o test/minigzip.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzip64 minigzip64.o -L. libz.a
g++ -Wall -O2 plink.c plink_assoc.c plink_calc.c plink_cluster.c plink_cnv.c plink_common.c plink_data.c plink_dosage.c plink_family.c plink_filter.c plink_glm.c plink_help.c plink_homozyg.c plink_lasso.c plink_ld.c plink_matrix.c plink_misc.c plink_set.c plink_stats.c SFMT.c dcdflib.c pigz.c yarn.c -m32 -o plink -L/usr/lib64/atlas -llapack -lcblas -latlas -lm -lpthread -L. zlib-1.2.8/libz.so.1.2.8
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink.c:19:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_assoc.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_calc.c:73:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_cluster.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_cnv.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_common.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_data.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_dosage.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_family.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_filter.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_glm.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_help.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_homozyg.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_lasso.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_ld.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_matrix.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_misc.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_set.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from plink_common.h:6,
from plink_stats.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/string.h:25:0,
from SFMT.c:47:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from dcdflib.c:1:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdint.h:25:0,
from /usr/lib/gcc/x86_64-linux-gnu/4.8/include/stdint.h:9,
from pigz.c:294:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
In file included from /usr/include/stdio.h:27:0,
from yarn.c:33:
/usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>
^
compilation terminated.
make: *** [plink] Error 1
Christopher Chang
Jun 5, 2014, 6:07:27 AM6/5/14
to plink2...@googlegroups.com
This appears to be related to http://stackoverflow.com/questions/9303037/cannot-compile-simple-c-program-in-ubuntu . See if there's a problem with your PATH, and maybe try editing the plink Makefile to use gcc instead of g++ as the compiler.
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