third party code

weizhouUMICH · Feb 4, 2020 · 53fc9ce · 53fc9ce
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commit 53fc9ce
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Showing 11 changed files with 19 additions and 19 deletions.
diff --git a/src/SAIGE.so b/src/SAIGE.so
diff --git a/src/SAIGE_GENE_readDosageMatrix_vcf.o b/src/SAIGE_GENE_readDosageMatrix_vcf.o
diff --git a/src/SAIGE_fitGLMM_fast.o b/src/SAIGE_fitGLMM_fast.o
diff --git a/src/SAIGE_readDosage_bgen.o b/src/SAIGE_readDosage_bgen.o
diff --git a/src/SAIGE_readDosage_vcf.o b/src/SAIGE_readDosage_vcf.o
diff --git a/src/matrixMultiEigen.o b/src/matrixMultiEigen.o
diff --git a/src/test.o b/src/test.o
diff --git a/thirdParty/bgen/.lock-waf_linux2_build b/thirdParty/bgen/.lock-waf_linux2_build
@@ -1,6 +1,6 @@
 argv = ['./waf', 'configure']
 config_cmd = 'configure'
-environ = {'R_PLATFORM': 'x86_64-pc-linux-gnu', 'LC_TERMINAL_VERSION': '3.3.6', 'R_VERSION': '3.6.1', 'R_SHARE_DIR': '/usr/local/lib/R/share', 'LD_LIBRARY_PATH': '/usr/local/lib/R/lib:/usr/local/lib:/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server:/usr/local/lib/R/lib:/usr/local/lib:/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server', 'LANG': 'en_US.UTF-8', 'R_RD4PDF': 'times,inconsolata,hyper', 'SHELL': '/bin/bash', 'TEXINPUTS': '.:/usr/local/lib/R/share/texmf/tex/latex:', 'TAR': '/bin/tar', 'XDG_DATA_DIRS': '/usr/local/share:/usr/share:/var/lib/snapd/desktop', 'SED': '/bin/sed', '_R_SHLIB_BUILD_OBJECTS_SYMBOL_TABLES_': 'false', 'R_LIBS_USER': '~/R/x86_64-pc-linux-gnu-library/3.6', 'XDG_RUNTIME_DIR': '/run/user/1003', 'R_LIBS': '/home/wei/install_dir', 'R_SESSION_TMPDIR': '/tmp/RtmpP6ygzt', 'R_LIBS_SITE': '', 'XDG_SESSION_ID': '10', 'R_TEXI2DVICMD': 'texi2dvi', 'R_INCLUDE_DIR': '/usr/local/lib/R/include', 'R_BZIPCMD': '/bin/bzip2', 'R_PAPERSIZE': 'a4', 'LESSCLOSE': '/usr/bin/lesspipe %s %s', 'BIBINPUTS': '.:/usr/local/lib/R/share/texmf/bibtex/bib:', 'LC_COLLATE': 'C', 'R_PRINTCMD': '', 'BSTINPUTS': '.:/usr/local/lib/R/share/texmf/bibtex/bst:', 'R_CMD': '/usr/local/lib/R/bin/Rcmd', 'R_GZIPCMD': '/bin/gzip', 'SSH_TTY': '/dev/pts/1', 'MAIL': '/var/mail/wei', 'LS_COLORS': 'rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:', 'OLDPWD': '/home/wei/SAIGE', 'R_PACKAGE_DIR': '/home/wei/install_dir/SAIGE', 'R_STRIP_STATIC_LIB': 'strip --strip-debug', 'R_ARCH': '', 'R_SYSTEM_ABI': 'linux,gcc,gxx,gfortran,gfortran', 'LESSOPEN': '| /usr/bin/lesspipe %s', 'SSH_CLIENT': '209.6.147.149 63409 22', 'LOGNAME': 'wei', 'USER': 'wei', 'R_DEFAULT_PACKAGES': '', 'HOME': '/home/wei', 'PATH': '/home/wei/bin:/home/wei/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin', 'R_PACKAGE_NAME': 'SAIGE', 'R_OSTYPE': 'unix', 'TERM': 'vt100', 'R_DOC_DIR': '/usr/local/lib/R/doc', 'SHLVL': '2', 'R_BROWSER': '/bin/open', 'EDITOR': 'vi', 'R_UNZIPCMD': '/usr/bin/unzip', 'R_PAPERSIZE_USER': 'a4', 'LC_TERMINAL': 'iTerm2', 'R_ZIPCMD': '', 'R_STRIP_SHARED_LIB': 'strip --strip-unneeded', 'R_PDFVIEWER': '/bin/open', '_': './waf', 'SSH_CONNECTION': '209.6.147.149 63409 10.128.0.12 22', 'R_INSTALL_PKG': 'SAIGE', 'MAKE': 'make', 'R_LIBRARY_DIR': '/home/wei/install_dir', 'R_HOME': '/usr/local/lib/R', 'PWD': '/home/wei/SAIGE/thirdParty/bgen', 'LN_S': 'ln -s', 'PAGER': '/usr/bin/less'}
+environ = {'R_PLATFORM': 'x86_64-pc-linux-gnu', 'LC_TERMINAL_VERSION': '3.3.7', 'R_VERSION': '3.6.1', 'R_SHARE_DIR': '/usr/local/lib/R/share', 'LD_LIBRARY_PATH': '/usr/local/lib/R/lib:/usr/local/lib:/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server:/usr/local/lib/R/lib:/usr/local/lib:/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server', 'LANG': 'en_US.UTF-8', 'R_RD4PDF': 'times,inconsolata,hyper', 'SHELL': '/bin/bash', 'TEXINPUTS': '.:/usr/local/lib/R/share/texmf/tex/latex:', 'TAR': '/bin/tar', 'XDG_DATA_DIRS': '/usr/local/share:/usr/share:/var/lib/snapd/desktop', 'SED': '/bin/sed', '_R_SHLIB_BUILD_OBJECTS_SYMBOL_TABLES_': 'false', 'R_LIBS_USER': '~/R/x86_64-pc-linux-gnu-library/3.6', 'XDG_RUNTIME_DIR': '/run/user/1003', 'R_LIBS': '/home/wei/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-SAIGE/00new', 'R_SESSION_TMPDIR': '/tmp/RtmpHepFDa', 'R_LIBS_SITE': '', 'XDG_SESSION_ID': '1', 'R_TEXI2DVICMD': 'texi2dvi', 'R_INCLUDE_DIR': '/usr/local/lib/R/include', 'R_BZIPCMD': '/bin/bzip2', 'R_PAPERSIZE': 'a4', 'LESSCLOSE': '/usr/bin/lesspipe %s %s', 'BIBINPUTS': '.:/usr/local/lib/R/share/texmf/bibtex/bib:', 'LC_COLLATE': 'C', 'R_PRINTCMD': '', 'BSTINPUTS': '.:/usr/local/lib/R/share/texmf/bibtex/bst:', 'R_CMD': '/usr/local/lib/R/bin/Rcmd', 'R_GZIPCMD': '/bin/gzip', 'SSH_TTY': '/dev/pts/0', 'MAIL': '/var/mail/wei', 'LS_COLORS': 'rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:', 'OLDPWD': '/home/wei/SAIGE', 'R_PACKAGE_DIR': '/home/wei/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-SAIGE/00new/SAIGE', 'R_STRIP_STATIC_LIB': 'strip --strip-debug', 'R_ARCH': '', 'R_SYSTEM_ABI': 'linux,gcc,gxx,gfortran,gfortran', 'LESSOPEN': '| /usr/bin/lesspipe %s', 'SSH_CLIENT': '132.183.56.7 16563 22', 'LOGNAME': 'wei', 'USER': 'wei', 'R_DEFAULT_PACKAGES': '', 'HOME': '/home/wei', 'PATH': '/home/wei/bin:/home/wei/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin', 'R_PACKAGE_NAME': 'SAIGE', 'R_OSTYPE': 'unix', 'TERM': 'vt100', 'R_DOC_DIR': '/usr/local/lib/R/doc', 'SHLVL': '2', 'R_BROWSER': '/bin/open', 'EDITOR': 'vi', 'R_UNZIPCMD': '/usr/bin/unzip', 'R_PAPERSIZE_USER': 'a4', 'LC_TERMINAL': 'iTerm2', 'R_ZIPCMD': '', 'R_STRIP_SHARED_LIB': 'strip --strip-unneeded', 'R_PDFVIEWER': '/bin/open', '_': './waf', 'SSH_CONNECTION': '132.183.56.7 16563 10.128.0.12 22', 'R_INSTALL_PKG': 'SAIGE', 'MAKE': 'make', 'R_LIBRARY_DIR': '/home/wei/R/x86_64-pc-linux-gnu-library/3.6', 'R_HOME': '/usr/local/lib/R', 'PWD': '/home/wei/SAIGE/thirdParty/bgen', 'LN_S': 'ln -s', 'PAGER': '/usr/bin/less'}
 files = ['/home/wei/SAIGE/thirdParty/bgen/wscript']
 hash = '\xa24\x8e)j~2\x8f\x8e\xe0\xba\xf6\xd1L\xc9L'
 options = {'profile': 0, 'files': '', 'force': False, 'verbose': 0, 'no_lock_in_run': '', 'no_lock_in_out': '', 'whelp': 0, 'destdir': '', 'zones': '', 'colors': 'auto', 'pdb': 0, 'jobs': 2, 'targets': '', 'out': '', 'progress_bar': 0, 'top': '', 'libdir': None, 'prefix': '/usr/local', 'keep': 0, 'mode': 'release', 'check_c_compiler': None, 'check_cxx_compiler': None, 'distcheck_args': None, 'bindir': None, 'no_lock_in_top': ''}

diff --git a/thirdParty/bgen/build/.lock-waf_linux2_build b/thirdParty/bgen/build/.lock-waf_linux2_build
@@ -1,6 +1,6 @@
 argv = ['./waf', 'configure']
 config_cmd = 'configure'
-environ = {'R_PLATFORM': 'x86_64-pc-linux-gnu', 'LC_TERMINAL_VERSION': '3.3.6', 'R_VERSION': '3.6.1', 'R_SHARE_DIR': '/usr/local/lib/R/share', 'LD_LIBRARY_PATH': '/usr/local/lib/R/lib:/usr/local/lib:/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server:/usr/local/lib/R/lib:/usr/local/lib:/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server', 'LANG': 'en_US.UTF-8', 'R_RD4PDF': 'times,inconsolata,hyper', 'SHELL': '/bin/bash', 'TEXINPUTS': '.:/usr/local/lib/R/share/texmf/tex/latex:', 'TAR': '/bin/tar', 'XDG_DATA_DIRS': '/usr/local/share:/usr/share:/var/lib/snapd/desktop', 'SED': '/bin/sed', '_R_SHLIB_BUILD_OBJECTS_SYMBOL_TABLES_': 'false', 'R_LIBS_USER': '~/R/x86_64-pc-linux-gnu-library/3.6', 'XDG_RUNTIME_DIR': '/run/user/1003', 'R_LIBS': '/home/wei/install_dir', 'R_SESSION_TMPDIR': '/tmp/RtmpP6ygzt', 'R_LIBS_SITE': '', 'XDG_SESSION_ID': '10', 'R_TEXI2DVICMD': 'texi2dvi', 'R_INCLUDE_DIR': '/usr/local/lib/R/include', 'R_BZIPCMD': '/bin/bzip2', 'R_PAPERSIZE': 'a4', 'LESSCLOSE': '/usr/bin/lesspipe %s %s', 'BIBINPUTS': '.:/usr/local/lib/R/share/texmf/bibtex/bib:', 'LC_COLLATE': 'C', 'R_PRINTCMD': '', 'BSTINPUTS': '.:/usr/local/lib/R/share/texmf/bibtex/bst:', 'R_CMD': '/usr/local/lib/R/bin/Rcmd', 'R_GZIPCMD': '/bin/gzip', 'SSH_TTY': '/dev/pts/1', 'MAIL': '/var/mail/wei', 'LS_COLORS': 'rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:', 'OLDPWD': '/home/wei/SAIGE', 'R_PACKAGE_DIR': '/home/wei/install_dir/SAIGE', 'R_STRIP_STATIC_LIB': 'strip --strip-debug', 'R_ARCH': '', 'R_SYSTEM_ABI': 'linux,gcc,gxx,gfortran,gfortran', 'LESSOPEN': '| /usr/bin/lesspipe %s', 'SSH_CLIENT': '209.6.147.149 63409 22', 'LOGNAME': 'wei', 'USER': 'wei', 'R_DEFAULT_PACKAGES': '', 'HOME': '/home/wei', 'PATH': '/home/wei/bin:/home/wei/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin', 'R_PACKAGE_NAME': 'SAIGE', 'R_OSTYPE': 'unix', 'TERM': 'vt100', 'R_DOC_DIR': '/usr/local/lib/R/doc', 'SHLVL': '2', 'R_BROWSER': '/bin/open', 'EDITOR': 'vi', 'R_UNZIPCMD': '/usr/bin/unzip', 'R_PAPERSIZE_USER': 'a4', 'LC_TERMINAL': 'iTerm2', 'R_ZIPCMD': '', 'R_STRIP_SHARED_LIB': 'strip --strip-unneeded', 'R_PDFVIEWER': '/bin/open', '_': './waf', 'SSH_CONNECTION': '209.6.147.149 63409 10.128.0.12 22', 'R_INSTALL_PKG': 'SAIGE', 'MAKE': 'make', 'R_LIBRARY_DIR': '/home/wei/install_dir', 'R_HOME': '/usr/local/lib/R', 'PWD': '/home/wei/SAIGE/thirdParty/bgen', 'LN_S': 'ln -s', 'PAGER': '/usr/bin/less'}
+environ = {'R_PLATFORM': 'x86_64-pc-linux-gnu', 'LC_TERMINAL_VERSION': '3.3.7', 'R_VERSION': '3.6.1', 'R_SHARE_DIR': '/usr/local/lib/R/share', 'LD_LIBRARY_PATH': '/usr/local/lib/R/lib:/usr/local/lib:/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server:/usr/local/lib/R/lib:/usr/local/lib:/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server', 'LANG': 'en_US.UTF-8', 'R_RD4PDF': 'times,inconsolata,hyper', 'SHELL': '/bin/bash', 'TEXINPUTS': '.:/usr/local/lib/R/share/texmf/tex/latex:', 'TAR': '/bin/tar', 'XDG_DATA_DIRS': '/usr/local/share:/usr/share:/var/lib/snapd/desktop', 'SED': '/bin/sed', '_R_SHLIB_BUILD_OBJECTS_SYMBOL_TABLES_': 'false', 'R_LIBS_USER': '~/R/x86_64-pc-linux-gnu-library/3.6', 'XDG_RUNTIME_DIR': '/run/user/1003', 'R_LIBS': '/home/wei/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-SAIGE/00new', 'R_SESSION_TMPDIR': '/tmp/RtmpHepFDa', 'R_LIBS_SITE': '', 'XDG_SESSION_ID': '1', 'R_TEXI2DVICMD': 'texi2dvi', 'R_INCLUDE_DIR': '/usr/local/lib/R/include', 'R_BZIPCMD': '/bin/bzip2', 'R_PAPERSIZE': 'a4', 'LESSCLOSE': '/usr/bin/lesspipe %s %s', 'BIBINPUTS': '.:/usr/local/lib/R/share/texmf/bibtex/bib:', 'LC_COLLATE': 'C', 'R_PRINTCMD': '', 'BSTINPUTS': '.:/usr/local/lib/R/share/texmf/bibtex/bst:', 'R_CMD': '/usr/local/lib/R/bin/Rcmd', 'R_GZIPCMD': '/bin/gzip', 'SSH_TTY': '/dev/pts/0', 'MAIL': '/var/mail/wei', 'LS_COLORS': 'rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:', 'OLDPWD': '/home/wei/SAIGE', 'R_PACKAGE_DIR': '/home/wei/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-SAIGE/00new/SAIGE', 'R_STRIP_STATIC_LIB': 'strip --strip-debug', 'R_ARCH': '', 'R_SYSTEM_ABI': 'linux,gcc,gxx,gfortran,gfortran', 'LESSOPEN': '| /usr/bin/lesspipe %s', 'SSH_CLIENT': '132.183.56.7 16563 22', 'LOGNAME': 'wei', 'USER': 'wei', 'R_DEFAULT_PACKAGES': '', 'HOME': '/home/wei', 'PATH': '/home/wei/bin:/home/wei/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin', 'R_PACKAGE_NAME': 'SAIGE', 'R_OSTYPE': 'unix', 'TERM': 'vt100', 'R_DOC_DIR': '/usr/local/lib/R/doc', 'SHLVL': '2', 'R_BROWSER': '/bin/open', 'EDITOR': 'vi', 'R_UNZIPCMD': '/usr/bin/unzip', 'R_PAPERSIZE_USER': 'a4', 'LC_TERMINAL': 'iTerm2', 'R_ZIPCMD': '', 'R_STRIP_SHARED_LIB': 'strip --strip-unneeded', 'R_PDFVIEWER': '/bin/open', '_': './waf', 'SSH_CONNECTION': '132.183.56.7 16563 10.128.0.12 22', 'R_INSTALL_PKG': 'SAIGE', 'MAKE': 'make', 'R_LIBRARY_DIR': '/home/wei/R/x86_64-pc-linux-gnu-library/3.6', 'R_HOME': '/usr/local/lib/R', 'PWD': '/home/wei/SAIGE/thirdParty/bgen', 'LN_S': 'ln -s', 'PAGER': '/usr/bin/less'}
 files = ['/home/wei/SAIGE/thirdParty/bgen/wscript']
 hash = '\xa24\x8e)j~2\x8f\x8e\xe0\xba\xf6\xd1L\xc9L'
 options = {'profile': 0, 'files': '', 'force': False, 'verbose': 0, 'no_lock_in_run': '', 'no_lock_in_out': '', 'whelp': 0, 'destdir': '', 'zones': '', 'colors': 'auto', 'pdb': 0, 'jobs': 2, 'targets': '', 'out': '', 'progress_bar': 0, 'top': '', 'libdir': None, 'prefix': '/usr/local', 'keep': 0, 'mode': 'release', 'check_c_compiler': None, 'check_cxx_compiler': None, 'distcheck_args': None, 'bindir': None, 'no_lock_in_top': ''}