Hooray for upstream bugs!
All of the shared libraried in emboss-5.0.0-3 are deficient in their
linkages. They don't link any other libraries, yet they all use
symbols from other libraries. See attached file for output from the
"fink-dyld-link-test" thing in my experimental/ directory on cvs.sf to
see what symbols are unresolved. The makefiles all appear to know the
libs that would be needed, but intentionally avoid dynamically linking
them on darwin (and don't even pass the flags correctly on most other
platforms because they didn't read the automake or libtool manual).
dan
--
Daniel Macks
[EMAIL PROTECTED]
http://www.netspace.org/~dmacks
Preparing...
g++ -all_load -multiply_defined suppress -bind_at_load /tmp/vSdsgacKlN.c -o
/tmp/z82JuI69tD.o
========================================================================
Testing package emboss-ajax5-dev...
------------------------------------------------------------------------
Examining /sw/lib/libajaxg.dylib...
g++ -all_load -multiply_defined suppress -bind_at_load /tmp/vSdsgacKlN.c -o
/tmp/z82JuI69tD.o /sw/lib/libajaxg.a /sw/lib/EMBOSS/libajaxg.5.dylib
/usr/lib/libSystem.B.dylib
ld: Undefined symbols:
_ajAcdGetProgram
_ajAcdInit
_ajAcdInitP
_ajCallRegister
_ajCharMatchC
_ajCharMatchCaseC
_ajCharPrefixCaseS
_ajDebug
_ajDegToRad
_ajErr
_ajFileClose
_ajFileNewOut
_ajFmtPrint
_ajFmtPrintAppS
_ajFmtPrintF
_ajFmtPrintS
_ajFmtStr
_ajFmtString
_ajListstrFree
_ajListstrGetLength
_ajListstrNew
_ajListstrPop
_ajListstrPushAppend
_ajMemAlloc
_ajMemCalloc
_ajMemCalloc0
_ajMemFree
_ajNamInit
_ajSeqGetLen
_ajSeqGetNameS
_ajStrAppendC
_ajStrAssignC
_ajStrAssignEmptyC
_ajStrAssignEmptyS
_ajStrAssignS
_ajStrDel
_ajStrGetCharLast
_ajStrGetLen
_ajStrGetPtr
_ajStrInsertC
_ajStrInsertS
_ajStrKeepRange
_ajStrMatchCaseC
_ajStrNewC
_ajTimeDel
_ajTimeNewToday
_ajTimeNewTodayFmt
_ajUser
_c_pladv
_c_plbox
_c_plcol0
_c_plend
_c_plerrx
_c_plerry
_c_plfill
_c_plgchr
_c_plgpage
_c_plinit
_c_pljoin
_c_plline
_c_pllsty
_c_plmtex
_c_plpoin
_c_plpsty
_c_plptex
_c_plschr
_c_plscol0
_c_plsdev
_c_plsori
_c_plspage
_c_plssub
_c_plvpor
_c_plvsta
_c_plwid
_c_plwind
_c_plxsfnam
_plsc
_plstrl
------------------------------------------------------------------------
Examining /sw/lib/libajax.dylib...
g++ -all_load -multiply_defined suppress -bind_at_load /tmp/vSdsgacKlN.c -o
/tmp/z82JuI69tD.o /sw/lib/libajax.a /sw/lib/EMBOSS/libajax.5.dylib
/usr/lib/libSystem.B.dylib
========================================================================
Testing package emboss-eplplot3-dev...
------------------------------------------------------------------------
Examining /sw/lib/libeplplot.dylib...
g++ -all_load -multiply_defined suppress -bind_at_load /tmp/vSdsgacKlN.c -o
/tmp/z82JuI69tD.o /sw/lib/libeplplot.a /sw/lib/EMBOSS/libeplplot.3.dylib
/usr/lib/libSystem.B.dylib
ld: Undefined symbols:
_XAllocColor
_XAllocColorCells
_XAllocNamedColor
_XCheckWindowEvent
_XClearWindow
_XCloseDisplay
_XCopyArea
_XCreateColormap
_XCreateFontCursor
_XCreateGC
_XCreatePixmap
_XCreateWindow
_XDefineCursor
_XDestroyWindow
_XDrawLine
_XDrawLines
_XFillPolygon
_XFillRectangle
_XFlush
_XFree
_XFreeColors
_XFreeGC
_XFreePixmap
_XGetErrorText
_XGetGeometry
_XGetImage
_XGetVisualInfo
_XLookupString
_XMapRaised
_XOpenDisplay
_XPending
_XPutImage
_XQueryColors
_XQueryPointer
_XSelectInput
_XSetBackground
_XSetErrorHandler
_XSetForeground
_XSetFunction
_XSetLineAttributes
_XSetStandardProperties
_XSetWindowBackground
_XSetWindowColormap
_XStoreColor
_XSync
_XSynchronize
_XUndefineCursor
_XWarpPointer
_XWindowEvent
_gdFree
_gdImageColorAllocate
_gdImageColorDeallocate
_gdImageCreate
_gdImageCreateTrueColor
_gdImageDestroy
_gdImageFilledPolygon
_gdImageFilledRectangle
_gdImageGifPtr
_gdImageLine
_gdImagePngPtrEx
_gdImageSetAntiAliased
_gdImageSetThickness
========================================================================
Testing package emboss-nucleus5-dev...
------------------------------------------------------------------------
Examining /sw/lib/libnucleus.dylib...
g++ -all_load -multiply_defined suppress -bind_at_load /tmp/vSdsgacKlN.c -o
/tmp/z82JuI69tD.o /sw/lib/libnucleus.a /sw/lib/EMBOSS/libnucleus.5.dylib
/usr/lib/libSystem.B.dylib
ld: Undefined symbols:
_ajAZToInt
_ajAlignDefineSS
_ajAlignSetGapR
_ajAlignSetMatrixFloat
_ajAlignSetRange
_ajAlignSetScoreR
_ajDebug
_ajFmtPrintAppS
_ajFmtPrintF
_ajMemAlloc
_ajMemFree
_ajMessCrashFL
_ajMessSetErr
_ajSeqAssignAccS
_ajSeqAssignDescS
_ajSeqAssignNameS
_ajSeqAssignUsaS
_ajSeqDel
_ajSeqGapStandard
_ajSeqGetAccS
_ajSeqGetDescS
_ajSeqGetLen
_ajSeqGetNameS
_ajSeqGetOffend
_ajSeqGetOffset
_ajSeqGetSeqC
_ajSeqGetUsaS
_ajSeqIsReversed
_ajSeqNewNameS
_ajSeqNewRangeC
_ajSeqcvtGetCodeK
_ajSeqstrCountGaps
_ajStrAppendC
_ajStrAppendK
_ajStrAppendS
_ajStrAssignC
_ajStrAssignK
_ajStrAssignS
_ajStrAssignSubC
_ajStrCalcCountK
_ajStrDel
_ajStrDelStatic
_ajStrFmtUpper
_ajStrGetLen
_ajStrGetPtr
_ajStrInsertK
_ajStrNewC
_ajStrReverse
_ajStrSetRes
_ajMemCalloc
_ajMemCalloc0
_ajStrCmpS
_ajStrVcmp
_ajFloatDel
_ajFloatGet
_ajFloatNew
_ajFloatPut
_ajMatrixArray
_ajMatrixCvt
_ajMatrixSize
_ajSeqsetGetseqSeqC
_ajSeqsetGetseqWeight
_ajSeqsetIsNuc
_ajSeqsetIsProt
_ajFileReadLine
_ajFmtError
_ajListFree
_ajListIterDel
_ajListIterDone
_ajListIterGet
_ajListIterNewread
_ajListPushAppend
_ajStrCmpC
_ajStrFindC
_ajStrNew
_ajStrNewRef
_ajStrTokenDel
_ajStrTokenNewC
_ajStrTokenNextParse
_ajTablePut
_ajTablestrFree
_ajTablestrNewCaseLen
_ajAcdGetCmdline
_ajAcdGetInputs
_ajAcdGetProgram
_ajCharDel
_ajCharMatchC
_ajCharMatchWildS
_ajDie
_ajErr
_ajExitAbort
_ajFileClose
_ajFileDirPath
_ajFileGets
_ajFileGetwd
_ajFileLength
_ajFileNewIn
_ajFileNewOut
_ajFileNewOutD
_ajFileSeek
_ajFileTestSkip
_ajFileWrite
_ajFileWriteByte
_ajFileWriteInt2
_ajFileWriteInt4
_ajFileWriteStr
_ajFmtPrintS
_ajListGetLength
_ajListNew
_ajListPop
_ajListPush
_ajListToarray
_ajListstrNew
_ajListstrPushAppend
_ajRegCompC
_ajRegExec
_ajRegFree
_ajRegSubI
_ajStrExchangeCC
_ajStrGetCharLast
_ajStrGetuniquePtr
_ajStrKeepRange
_ajStrMatchCaseC
_ajStrMatchCaseS
_ajStrMatchS
_ajStrNewS
_ajStrToInt
_ajSysArglistBuild
_ajSysArglistFree
_ajTimeDel
_ajTimeNewTodayFmt
_ajWarn
_ajDmxScophitCompPval
_ajDmxScophitDel
_ajDmxScophitNew
_ajDmxScophitTarget
_ajDmxScophitTarget2
_ajFloat2dDel
_ajFloat2dGet
_ajFloat2dNew
_ajFloat2dPut
_ajFmtPrintSplit
_ajFmtScanS
_ajListIterGetBack
_ajListIterInsert
_ajListSort
_ajMatrixfArray
_ajMatrixfCvt
_ajMemResize
_ajRoundF
_ajScopArrFindScopid
_ajStrAssignSubS
_ajStrFindS
_ajStrMatchC
_ajStrParseC
_ajStrParseCountC
_ajStrPrefixC
_ajStrRemoveWhite
_ajStrSetClear
_ajStrTrimWhite
_ajUintDel
_ajUintGet
_ajUintNewL
_ajUintPut
_ajSeqAssignNameC
_ajSeqAssignSeqC
_ajSeqAssignSeqS
_ajSeqFmtLower
_ajSeqGetNameC
_ajSeqGetSeqCopyC
_ajSeqGetSeqCopyS
_ajSeqNew
_ajSeqNewSeq
_ajSeqSetRange
_ajSeqTrim
_ajSysCastItoc
_ajSysCastItouc
_ajUser
_ajExit
_ajExitBad
_ajFileDir
_ajFileDirFix
_ajFileDirUp
_ajFileNameValid
_ajListIterNew
_ajListIterRemove
_ajListstrFreeData
_ajListstrPop
_ajListstrReverse
_ajListstrToarray
_ajNamGetValueC
_ajNamRoot
_ajNamRootInstall
_ajNamRootPack
_ajStrAssignEmptyC
_ajStrAssignResS
_ajStrCmpCaseS
_ajStrCutEnd
_ajStrCutStart
_ajStrExchangeKK
_ajStrExchangeSetCC
_ajStrFmtLower
_ajStrGetCharFirst
_ajStrMatchWordAllS
_ajStrMatchWordOneS
_ajStrPrefixCaseC
_ajStrRemoveWhiteExcess
_ajStrSetValid
_ajStrSuffixC
_ajStrTokenNextParseC
_ajStrTrimC
_ajSysFileWhichEnv
_ajFileDataNewC
_ajSysFuncStrtok
_ajArrCommaList
_ajBtreeCacheDel
_ajBtreeCacheSync
_ajBtreeCreateRootNode
_ajBtreeFreePriArray
_ajBtreeFreeSecArray
_ajBtreeSecCacheNewC
_ajBtreeWriteParams
_ajFileNameTrim
_ajFileScan
_ajNamRsAttrValueC
_ajStrMatchWildS
_ajStrToUint
_ajStrTrimEndC
_ajAcdInit
_ajAcdInitP
_ajNamInit
_ajIntDel
_ajIntGet
_ajIntNew
_ajIntPut
_ajListReverse
_ajStrInsertC
_ajAZToBin
_ajAZToBinC
_ajListMap
_ajListSortTwo
_ajRegComp
_ajRegExecC
_ajRegLenI
_ajRegOffset
_ajSeqGetSeqS
_ajSeqIsProt
_ajSeqstrReverse
_ajStrNewRes
_ajTableFetch
_ajFeatNewII
_ajFeatNewIIRev
_ajFeatSetScore
_ajFeatSetStrand
_ajFeatTagAdd
_ajPatCompDel
_ajPatCompNew
_ajPatlistRegexGetNext
_ajPatlistRegexRemoveCurrent
_ajPatlistRegexRewind
_ajPatlistSeqGetNext
_ajPatlistSeqGetSize
_ajPatlistSeqRemoveCurrent
_ajPatlistSeqRewind
_ajPatternRegexGetCompiled
_ajPatternRegexGetName
_ajPatternSeqGetCompiled
_ajPatternSeqGetMismatch
_ajPatternSeqGetName
_ajPatternSeqGetPattern
_ajPatternSeqGetProtein
_ajPatternSeqSetCompiled
_ajRegPost
_ajSeqGetBegin
_ajSeqGetEnd
_ajSeqReverseForce
_ajArrDoubleLine
_ajPdbChnidToNum
_ajPdbtospArrFindPdbid
_ajFileNew
_ajCharFmtUpper
_ajChararrDel
_ajChararrGet
_ajChararrNew
_ajChararrNewL
_ajChararrPut
_ajFileTell
_ajListPopLast
_ajSeqallNext
_ajSeqcvtGetCodeS
_ajSeqoutDel
_ajSeqoutDumpSwisslike
_ajSeqoutNewFile
_ajStrIsAlpha
_ajUintNew
_ajFeatGetEnd
_ajFeatGetStart
_ajFeatGetType
_ajFeatIsLocal
_ajFeatTagIter
_ajFeatTagval
_ajFeattableCopy
_ajFeattableDel
_ajFmtStr
_ajListNewListref
_ajListstrFree
_ajListstrGetLength
_ajListstrPush
_ajRangeNumber
_ajRangeOverlapSingle
_ajRangeOverlaps
_ajRangeSeqExtract
_ajRangeSeqStuff
_ajRangeText
_ajRangeValues
_ajSeqIsNuc
_ajSeqstrComplement
_ajStrAppendCountK
_ajStrAppendSubS
_ajStrFmtLowerSub
_ajStrGetCharPos
_ajStrInsertS
_ajStrPasteCountK
_ajStrPasteS
_ajStrTruncateLen
_ajTrnSeqOrig
_Assert_Failed
_ajCharCmpCaseLen
_ajCharNewResLenC
_ajExceptRaise
_ajFeatNew
_ajFeatTagSet
_ajFeattableNewSeq
_ajListMapread
_ajListPeekFirst
_ajListPushlist
_ajTableFree
_ajTableGetLength
_ajTableMapDel
_ajTableNewFunctionLen
_ajTableToarray
========================================================================
Results:
$emboss-ajax5-dev = {
'/sw/lib/libajax.dylib' => 'Okay',
'/sw/lib/libajaxg.dylib' => 'Deficient'
};
$emboss-eplplot3-dev = {
'/sw/lib/libeplplot.dylib' => 'Deficient'
};
$emboss-nucleus5-dev = {
'/sw/lib/libnucleus.dylib' => 'Deficient'
};
========================================================================
Summary:
emboss-ajax5-dev Failed
emboss-eplplot3-dev Failed
emboss-nucleus5-dev Failed
-------------------------------------------------------------------------
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