bio-velvet_underground 0.0.1
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- checksums.yaml +7 -0
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- data/ext/src/third-party/zlib-1.2.3/uncompr.c +61 -0
- data/ext/src/third-party/zlib-1.2.3/win32/DLL_FAQ.txt +397 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.bor +107 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.emx +69 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.gcc +141 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.msc +126 -0
- data/ext/src/third-party/zlib-1.2.3/win32/VisualC.txt +3 -0
- data/ext/src/third-party/zlib-1.2.3/win32/zlib.def +60 -0
- data/ext/src/third-party/zlib-1.2.3/win32/zlib1.rc +39 -0
- data/ext/src/third-party/zlib-1.2.3/zconf.h +332 -0
- data/ext/src/third-party/zlib-1.2.3/zconf.in.h +332 -0
- data/ext/src/third-party/zlib-1.2.3/zlib.3 +159 -0
- data/ext/src/third-party/zlib-1.2.3/zlib.h +1357 -0
- data/ext/src/third-party/zlib-1.2.3/zutil.c +318 -0
- data/ext/src/third-party/zlib-1.2.3/zutil.h +269 -0
- data/lib/bio-velvet_underground.rb +12 -0
- data/lib/bio-velvet_underground/external/VERSION +1 -0
- data/lib/bio-velvet_underground/velvet_underground.rb +72 -0
- data/spec/binary_sequence_store_spec.rb +27 -0
- data/spec/data/1/CnyUnifiedSeq +0 -0
- data/spec/spec_helper.rb +31 -0
- metadata +456 -0
@@ -0,0 +1,461 @@
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$! make libz under VMS written by
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$! Martin P.J. Zinser
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$! <zinser@zinser.no-ip.info or zinser@sysdev.deutsche-boerse.com>
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$!
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$ on error then goto err_exit
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$!
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$!
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$! Just some general constants...
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$!
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$ true = 1
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$ false = 0
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$ tmpnam = "temp_" + f$getjpi("","pid")
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$ SAY = "WRITE SYS$OUTPUT"
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$!
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$! Setup variables holding "config" information
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$!
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$ Make = ""
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$ name = "Zlib"
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$ version = "?.?.?"
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$ v_string = "ZLIB_VERSION"
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$ v_file = "zlib.h"
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$ ccopt = ""
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$ lopts = ""
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$ linkonly = false
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$ optfile = name + ".opt"
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$ its_decc = false
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$ its_vaxc = false
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$ its_gnuc = false
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$ axp = f$getsyi("HW_MODEL").ge.1024
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$ s_case = false
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$! Check for MMK/MMS
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$!
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$ If F$Search ("Sys$System:MMS.EXE") .nes. "" Then Make = "MMS"
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$ If F$Type (MMK) .eqs. "STRING" Then Make = "MMK"
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$!
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$!
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$ gosub find_version
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$!
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$ gosub check_opts
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$!
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$! Look for the compiler used
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$!
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$ gosub check_compiler
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$ if its_decc
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$ then
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$ ccopt = "/prefix=all" + ccopt
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$ if f$trnlnm("SYS") .eqs. ""
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$ then
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$ if axp
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$ then
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$ define sys sys$library:
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$ else
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$ ccopt = "/decc" + ccopt
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$ define sys decc$library_include:
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$ endif
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$ endif
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$ endif
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$ if its_vaxc .or. its_gnuc
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$ then
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$ if f$trnlnm("SYS").eqs."" then define sys sys$library:
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$ endif
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$!
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$! Build the thing plain or with mms
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$!
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$ write sys$output "Compiling Zlib sources ..."
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$ if make.eqs.""
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$ then
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$ dele example.obj;*,minigzip.obj;*
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$ CALL MAKE adler32.OBJ "CC ''CCOPT' adler32" -
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adler32.c zlib.h zconf.h
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$ CALL MAKE compress.OBJ "CC ''CCOPT' compress" -
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compress.c zlib.h zconf.h
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$ CALL MAKE crc32.OBJ "CC ''CCOPT' crc32" -
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crc32.c zlib.h zconf.h
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$ CALL MAKE deflate.OBJ "CC ''CCOPT' deflate" -
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deflate.c deflate.h zutil.h zlib.h zconf.h
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$ CALL MAKE gzio.OBJ "CC ''CCOPT' gzio" -
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gzio.c zutil.h zlib.h zconf.h
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$ CALL MAKE infback.OBJ "CC ''CCOPT' infback" -
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infback.c zutil.h inftrees.h inflate.h inffast.h inffixed.h
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$ CALL MAKE inffast.OBJ "CC ''CCOPT' inffast" -
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inffast.c zutil.h zlib.h zconf.h inffast.h
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$ CALL MAKE inflate.OBJ "CC ''CCOPT' inflate" -
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inflate.c zutil.h zlib.h zconf.h infblock.h
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$ CALL MAKE inftrees.OBJ "CC ''CCOPT' inftrees" -
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inftrees.c zutil.h zlib.h zconf.h inftrees.h
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$ CALL MAKE trees.OBJ "CC ''CCOPT' trees" -
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trees.c deflate.h zutil.h zlib.h zconf.h
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$ CALL MAKE uncompr.OBJ "CC ''CCOPT' uncompr" -
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uncompr.c zlib.h zconf.h
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$ CALL MAKE zutil.OBJ "CC ''CCOPT' zutil" -
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zutil.c zutil.h zlib.h zconf.h
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$ write sys$output "Building Zlib ..."
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$ CALL MAKE libz.OLB "lib/crea libz.olb *.obj" *.OBJ
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$ write sys$output "Building example..."
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$ CALL MAKE example.OBJ "CC ''CCOPT' example" -
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example.c zlib.h zconf.h
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$ call make example.exe "LINK example,libz.olb/lib" example.obj libz.olb
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$ if f$search("x11vms:xvmsutils.olb") .nes. ""
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$ then
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$ write sys$output "Building minigzip..."
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$ CALL MAKE minigzip.OBJ "CC ''CCOPT' minigzip" -
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minigzip.c zlib.h zconf.h
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$ call make minigzip.exe -
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"LINK minigzip,libz.olb/lib,x11vms:xvmsutils.olb/lib" -
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minigzip.obj libz.olb
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$ endif
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$ else
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$ gosub crea_mms
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$ SAY "Make ''name' ''version' with ''Make' "
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$ 'make'
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$ endif
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$!
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$! Alpha gets a shareable image
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$!
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$ If axp
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$ Then
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$ gosub crea_olist
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$ write sys$output "Creating libzshr.exe"
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$ call anal_obj_axp modules.opt _link.opt
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$ if s_case
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$ then
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$ open/append optf modules.opt
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$ write optf "case_sensitive=YES"
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$ close optf
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$ endif
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$ LINK_'lopts'/SHARE=libzshr.exe modules.opt/opt,_link.opt/opt
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$ endif
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$ write sys$output "Zlib build completed"
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$ exit
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$CC_ERR:
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$ write sys$output "C compiler required to build ''name'"
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$ goto err_exit
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$ERR_EXIT:
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$ set message/facil/ident/sever/text
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$ write sys$output "Exiting..."
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$ exit 2
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$!
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$!
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$MAKE: SUBROUTINE !SUBROUTINE TO CHECK DEPENDENCIES
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$ V = 'F$Verify(0)
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$! P1 = What we are trying to make
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$! P2 = Command to make it
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$! P3 - P8 What it depends on
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$
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$ If F$Search(P1) .Eqs. "" Then Goto Makeit
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$ Time = F$CvTime(F$File(P1,"RDT"))
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$arg=3
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$Loop:
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$ Argument = P'arg
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$ If Argument .Eqs. "" Then Goto Exit
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$ El=0
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$Loop2:
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$ File = F$Element(El," ",Argument)
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$ If File .Eqs. " " Then Goto Endl
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$ AFile = ""
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$Loop3:
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$ OFile = AFile
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$ AFile = F$Search(File)
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$ If AFile .Eqs. "" .Or. AFile .Eqs. OFile Then Goto NextEl
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$ If F$CvTime(F$File(AFile,"RDT")) .Ges. Time Then Goto Makeit
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$ Goto Loop3
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$NextEL:
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$ El = El + 1
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$ Goto Loop2
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$EndL:
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$ arg=arg+1
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$ If arg .Le. 8 Then Goto Loop
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$ Goto Exit
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$
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$Makeit:
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$ VV=F$VERIFY(0)
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$ write sys$output P2
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$ 'P2
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$ VV='F$Verify(VV)
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$Exit:
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$ If V Then Set Verify
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$ENDSUBROUTINE
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$!------------------------------------------------------------------------------
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$!
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$! Check command line options and set symbols accordingly
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$!
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$ CHECK_OPTS:
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$ i = 1
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$ OPT_LOOP:
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$ if i .lt. 9
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$ then
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$ cparm = f$edit(p'i',"upcase")
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$ if cparm .eqs. "DEBUG"
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$ then
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$ ccopt = ccopt + "/noopt/deb"
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$ lopts = lopts + "/deb"
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$ endif
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$ if f$locate("CCOPT=",cparm) .lt. f$length(cparm)
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$ then
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$ start = f$locate("=",cparm) + 1
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$ len = f$length(cparm) - start
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$ ccopt = ccopt + f$extract(start,len,cparm)
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$ if f$locate("AS_IS",f$edit(ccopt,"UPCASE")) .lt. f$length(ccopt) -
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then s_case = true
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$ endif
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$ if cparm .eqs. "LINK" then linkonly = true
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$ if f$locate("LOPTS=",cparm) .lt. f$length(cparm)
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$ then
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$ start = f$locate("=",cparm) + 1
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$ len = f$length(cparm) - start
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$ lopts = lopts + f$extract(start,len,cparm)
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$ endif
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$ if f$locate("CC=",cparm) .lt. f$length(cparm)
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$ then
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$ start = f$locate("=",cparm) + 1
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$ len = f$length(cparm) - start
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$ cc_com = f$extract(start,len,cparm)
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if (cc_com .nes. "DECC") .and. -
|
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(cc_com .nes. "VAXC") .and. -
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(cc_com .nes. "GNUC")
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$ then
|
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$ write sys$output "Unsupported compiler choice ''cc_com' ignored"
|
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$ write sys$output "Use DECC, VAXC, or GNUC instead"
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$ else
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$ if cc_com .eqs. "DECC" then its_decc = true
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$ if cc_com .eqs. "VAXC" then its_vaxc = true
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$ if cc_com .eqs. "GNUC" then its_gnuc = true
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$ endif
|
225
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$ endif
|
226
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$ if f$locate("MAKE=",cparm) .lt. f$length(cparm)
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227
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$ then
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228
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$ start = f$locate("=",cparm) + 1
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$ len = f$length(cparm) - start
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$ mmks = f$extract(start,len,cparm)
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$ if (mmks .eqs. "MMK") .or. (mmks .eqs. "MMS")
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$ then
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233
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$ make = mmks
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$ else
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235
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$ write sys$output "Unsupported make choice ''mmks' ignored"
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236
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$ write sys$output "Use MMK or MMS instead"
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$ endif
|
238
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$ endif
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239
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$ i = i + 1
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240
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$ goto opt_loop
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241
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$ endif
|
242
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$ return
|
243
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$!------------------------------------------------------------------------------
|
244
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$!
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245
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$! Look for the compiler used
|
246
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$!
|
247
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$CHECK_COMPILER:
|
248
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$ if (.not. (its_decc .or. its_vaxc .or. its_gnuc))
|
249
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$ then
|
250
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$ its_decc = (f$search("SYS$SYSTEM:DECC$COMPILER.EXE") .nes. "")
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251
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$ its_vaxc = .not. its_decc .and. (F$Search("SYS$System:VAXC.Exe") .nes. "")
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252
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$ its_gnuc = .not. (its_decc .or. its_vaxc) .and. (f$trnlnm("gnu_cc") .nes. "")
|
253
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$ endif
|
254
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$!
|
255
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$! Exit if no compiler available
|
256
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$!
|
257
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$ if (.not. (its_decc .or. its_vaxc .or. its_gnuc))
|
258
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$ then goto CC_ERR
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259
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$ else
|
260
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$ if its_decc then write sys$output "CC compiler check ... Compaq C"
|
261
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$ if its_vaxc then write sys$output "CC compiler check ... VAX C"
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262
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$ if its_gnuc then write sys$output "CC compiler check ... GNU C"
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$ endif
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264
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$ return
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265
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$!------------------------------------------------------------------------------
|
266
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$!
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267
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$! If MMS/MMK are available dump out the descrip.mms if required
|
268
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$!
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269
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$CREA_MMS:
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270
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$ write sys$output "Creating descrip.mms..."
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271
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$ create descrip.mms
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272
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$ open/append out descrip.mms
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273
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$ copy sys$input: out
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274
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$ deck
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275
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# descrip.mms: MMS description file for building zlib on VMS
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276
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# written by Martin P.J. Zinser
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277
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# <zinser@zinser.no-ip.info or zinser@sysdev.deutsche-boerse.com>
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278
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|
279
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OBJS = adler32.obj, compress.obj, crc32.obj, gzio.obj, uncompr.obj, infback.obj\
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280
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deflate.obj, trees.obj, zutil.obj, inflate.obj, \
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281
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inftrees.obj, inffast.obj
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282
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283
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$ eod
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284
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$ write out "CFLAGS=", ccopt
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285
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$ write out "LOPTS=", lopts
|
286
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$ copy sys$input: out
|
287
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$ deck
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288
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|
289
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all : example.exe minigzip.exe libz.olb
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290
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@ write sys$output " Example applications available"
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291
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|
292
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libz.olb : libz.olb($(OBJS))
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293
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@ write sys$output " libz available"
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294
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|
295
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example.exe : example.obj libz.olb
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296
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link $(LOPTS) example,libz.olb/lib
|
297
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|
298
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minigzip.exe : minigzip.obj libz.olb
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299
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link $(LOPTS) minigzip,libz.olb/lib,x11vms:xvmsutils.olb/lib
|
300
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|
301
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clean :
|
302
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delete *.obj;*,libz.olb;*,*.opt;*,*.exe;*
|
303
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+
|
304
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+
|
305
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# Other dependencies.
|
306
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adler32.obj : adler32.c zutil.h zlib.h zconf.h
|
307
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compress.obj : compress.c zlib.h zconf.h
|
308
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crc32.obj : crc32.c zutil.h zlib.h zconf.h
|
309
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deflate.obj : deflate.c deflate.h zutil.h zlib.h zconf.h
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310
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example.obj : example.c zlib.h zconf.h
|
311
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gzio.obj : gzio.c zutil.h zlib.h zconf.h
|
312
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inffast.obj : inffast.c zutil.h zlib.h zconf.h inftrees.h inffast.h
|
313
|
+
inflate.obj : inflate.c zutil.h zlib.h zconf.h
|
314
|
+
inftrees.obj : inftrees.c zutil.h zlib.h zconf.h inftrees.h
|
315
|
+
minigzip.obj : minigzip.c zlib.h zconf.h
|
316
|
+
trees.obj : trees.c deflate.h zutil.h zlib.h zconf.h
|
317
|
+
uncompr.obj : uncompr.c zlib.h zconf.h
|
318
|
+
zutil.obj : zutil.c zutil.h zlib.h zconf.h
|
319
|
+
infback.obj : infback.c zutil.h inftrees.h inflate.h inffast.h inffixed.h
|
320
|
+
$ eod
|
321
|
+
$ close out
|
322
|
+
$ return
|
323
|
+
$!------------------------------------------------------------------------------
|
324
|
+
$!
|
325
|
+
$! Read list of core library sources from makefile.in and create options
|
326
|
+
$! needed to build shareable image
|
327
|
+
$!
|
328
|
+
$CREA_OLIST:
|
329
|
+
$ open/read min makefile.in
|
330
|
+
$ open/write mod modules.opt
|
331
|
+
$ src_check = "OBJS ="
|
332
|
+
$MRLOOP:
|
333
|
+
$ read/end=mrdone min rec
|
334
|
+
$ if (f$extract(0,6,rec) .nes. src_check) then goto mrloop
|
335
|
+
$ rec = rec - src_check
|
336
|
+
$ gosub extra_filnam
|
337
|
+
$ if (f$element(1,"\",rec) .eqs. "\") then goto mrdone
|
338
|
+
$MRSLOOP:
|
339
|
+
$ read/end=mrdone min rec
|
340
|
+
$ gosub extra_filnam
|
341
|
+
$ if (f$element(1,"\",rec) .nes. "\") then goto mrsloop
|
342
|
+
$MRDONE:
|
343
|
+
$ close min
|
344
|
+
$ close mod
|
345
|
+
$ return
|
346
|
+
$!------------------------------------------------------------------------------
|
347
|
+
$!
|
348
|
+
$! Take record extracted in crea_olist and split it into single filenames
|
349
|
+
$!
|
350
|
+
$EXTRA_FILNAM:
|
351
|
+
$ myrec = f$edit(rec - "\", "trim,compress")
|
352
|
+
$ i = 0
|
353
|
+
$FELOOP:
|
354
|
+
$ srcfil = f$element(i," ", myrec)
|
355
|
+
$ if (srcfil .nes. " ")
|
356
|
+
$ then
|
357
|
+
$ write mod f$parse(srcfil,,,"NAME"), ".obj"
|
358
|
+
$ i = i + 1
|
359
|
+
$ goto feloop
|
360
|
+
$ endif
|
361
|
+
$ return
|
362
|
+
$!------------------------------------------------------------------------------
|
363
|
+
$!
|
364
|
+
$! Find current Zlib version number
|
365
|
+
$!
|
366
|
+
$FIND_VERSION:
|
367
|
+
$ open/read h_in 'v_file'
|
368
|
+
$hloop:
|
369
|
+
$ read/end=hdone h_in rec
|
370
|
+
$ rec = f$edit(rec,"TRIM")
|
371
|
+
$ if (f$extract(0,1,rec) .nes. "#") then goto hloop
|
372
|
+
$ rec = f$edit(rec - "#", "TRIM")
|
373
|
+
$ if f$element(0," ",rec) .nes. "define" then goto hloop
|
374
|
+
$ if f$element(1," ",rec) .eqs. v_string
|
375
|
+
$ then
|
376
|
+
$ version = 'f$element(2," ",rec)'
|
377
|
+
$ goto hdone
|
378
|
+
$ endif
|
379
|
+
$ goto hloop
|
380
|
+
$hdone:
|
381
|
+
$ close h_in
|
382
|
+
$ return
|
383
|
+
$!------------------------------------------------------------------------------
|
384
|
+
$!
|
385
|
+
$! Analyze Object files for OpenVMS AXP to extract Procedure and Data
|
386
|
+
$! information to build a symbol vector for a shareable image
|
387
|
+
$! All the "brains" of this logic was suggested by Hartmut Becker
|
388
|
+
$! (Hartmut.Becker@compaq.com). All the bugs were introduced by me
|
389
|
+
$! (zinser@decus.de), so if you do have problem reports please do not
|
390
|
+
$! bother Hartmut/HP, but get in touch with me
|
391
|
+
$!
|
392
|
+
$ ANAL_OBJ_AXP: Subroutine
|
393
|
+
$ V = 'F$Verify(0)
|
394
|
+
$ SAY := "WRITE_ SYS$OUTPUT"
|
395
|
+
$
|
396
|
+
$ IF F$SEARCH("''P1'") .EQS. ""
|
397
|
+
$ THEN
|
398
|
+
$ SAY "ANAL_OBJ_AXP-E-NOSUCHFILE: Error, inputfile ''p1' not available"
|
399
|
+
$ goto exit_aa
|
400
|
+
$ ENDIF
|
401
|
+
$ IF "''P2'" .EQS. ""
|
402
|
+
$ THEN
|
403
|
+
$ SAY "ANAL_OBJ_AXP: Error, no output file provided"
|
404
|
+
$ goto exit_aa
|
405
|
+
$ ENDIF
|
406
|
+
$
|
407
|
+
$ open/read in 'p1
|
408
|
+
$ create a.tmp
|
409
|
+
$ open/append atmp a.tmp
|
410
|
+
$ loop:
|
411
|
+
$ read/end=end_loop in line
|
412
|
+
$ f= f$search(line)
|
413
|
+
$ if f .eqs. ""
|
414
|
+
$ then
|
415
|
+
$ write sys$output "ANAL_OBJ_AXP-w-nosuchfile, ''line'"
|
416
|
+
$ goto loop
|
417
|
+
$ endif
|
418
|
+
$ define/user sys$output nl:
|
419
|
+
$ define/user sys$error nl:
|
420
|
+
$ anal/obj/gsd 'f /out=x.tmp
|
421
|
+
$ open/read xtmp x.tmp
|
422
|
+
$ XLOOP:
|
423
|
+
$ read/end=end_xloop xtmp xline
|
424
|
+
$ xline = f$edit(xline,"compress")
|
425
|
+
$ write atmp xline
|
426
|
+
$ goto xloop
|
427
|
+
$ END_XLOOP:
|
428
|
+
$ close xtmp
|
429
|
+
$ goto loop
|
430
|
+
$ end_loop:
|
431
|
+
$ close in
|
432
|
+
$ close atmp
|
433
|
+
$ if f$search("a.tmp") .eqs. "" -
|
434
|
+
then $ exit
|
435
|
+
$ ! all global definitions
|
436
|
+
$ search a.tmp "symbol:","EGSY$V_DEF 1","EGSY$V_NORM 1"/out=b.tmp
|
437
|
+
$ ! all procedures
|
438
|
+
$ search b.tmp "EGSY$V_NORM 1"/wind=(0,1) /out=c.tmp
|
439
|
+
$ search c.tmp "symbol:"/out=d.tmp
|
440
|
+
$ define/user sys$output nl:
|
441
|
+
$ edito/edt/command=sys$input d.tmp
|
442
|
+
sub/symbol: "/symbol_vector=(/whole
|
443
|
+
sub/"/=PROCEDURE)/whole
|
444
|
+
exit
|
445
|
+
$ ! all data
|
446
|
+
$ search b.tmp "EGSY$V_DEF 1"/wind=(0,1) /out=e.tmp
|
447
|
+
$ search e.tmp "symbol:"/out=f.tmp
|
448
|
+
$ define/user sys$output nl:
|
449
|
+
$ edito/edt/command=sys$input f.tmp
|
450
|
+
sub/symbol: "/symbol_vector=(/whole
|
451
|
+
sub/"/=DATA)/whole
|
452
|
+
exit
|
453
|
+
$ sort/nodupl d.tmp,f.tmp 'p2'
|
454
|
+
$ delete a.tmp;*,b.tmp;*,c.tmp;*,d.tmp;*,e.tmp;*,f.tmp;*
|
455
|
+
$ if f$search("x.tmp") .nes. "" -
|
456
|
+
then $ delete x.tmp;*
|
457
|
+
$!
|
458
|
+
$ EXIT_AA:
|
459
|
+
$ if V then set verify
|
460
|
+
$ endsubroutine
|
461
|
+
$!------------------------------------------------------------------------------
|